Intelligent Design research published in Nature
| March 20, 2008 | Posted by idnet.com.au under Intelligent Design |
The following is an edited extract from a Nature paper. It is an example of real ID research. Notice that the designers only used evolutionary techniques to very slightly tweak the enzymes scaffold structure that had been designed with “borrowed components” from existing enzymes tacked together. The novel active site was completely intelligently designed. doi:10.1038/nature06879
Kemp elimination catalysts by computational enzyme design
“We designed eight enzymes with computationally designed active sites. In vitro evolution enhanced the computational designs, demonstrating the power of combining computational protein design with directed evolution for creating new enzymes.
Natural enzymes bind their substrates in a well-defined active site with precisely aligned catalytic residues to form highly active and selective catalysts for a wide range of chemical reactions. The design of stable enzymes with new catalytic activities is of great practical interest, with potential applications in biotechnology, biomedicine and industrial processes.
We recently developed our computational enzyme design to create new enzymes for a reaction for which no naturally occurring enzyme exists.
Our in silico design process seems to be drawn towards the same structural features as naturally occurring enzyme evolution.
Following the active site design, a total of 59 designs in 17 different scaffolds were selected for experimental characterization. Eight of the designs showed initial measurable activity.
Directed evolution
We reasoned that in vitro evolution would be an excellent complement to our computational design efforts.
Directed evolution can be valuable both in improving the designed catalysts and in stimulating improvements in the computational design methodology by shedding light on what is missing from the designs.
Seven rounds of random mutagenesis and shuffling followed by screens yielded variants that had 4–8 mutations and an improvement of 200-fold in activity.
The key aspects of the computational design, including the identities of the catalytic side chains, were not altered by the evolutionary process.
The mutations provide subtle fine-tuning of the designed enzyme.
Conclusions
We anticipate the successful use of the combination of computational design and molecular evolution that we have described here, for a wide range of important reactions in the years to come, including design catalysts for more complex multistep reactions.”
84 Responses to Intelligent Design research published in Nature
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I am not aware of convincing evidence about the nylonase issue, though I have searched the internet for it some time ago. All the issue seemed to me rather unconvincing and hypothetical.
But I will be glad to deepen my understanding of the subject, if someone can point the most convincing references.
Up to now, I am convinced that nylonase is one of a very restricted repertoire of very dubious examples that darwinists, when really embarassed, resort to in the attempt to show that there are at least one or two examples of how the most revered biological theory of our times should work.
idnet.com.au (wrote #45): “Other than ID, no other experimentally verified method of de novo enzyme design is known…”
hrun0815 (wrote #56): “…Nylonase has about 400 amino acids and random assembly of such an enzyme is surely beyond the UPB. In addition, Nylonase is easily specified as: enzyme that hydrolases Nylon. So, the Nylonase does fulfill the requirements for specified complexity”
Patrick (wrote #54): “Serious ID proponents have never claimed that they cannot produced lower levels of functional complexity. Those single protein enzymes are very simple ones which simply hydrolyze precursors to nylon.”
Even if it was conceded that a de novo enzyme was produced by natural law(s) or chance, and Patrick was wrong, the irreducible core of the system still tells us that a code is there functioning as an instruction set as part of greater machine. It is incredible how it can co-opt nylon as a metabolic resource and survive another day. The funny thing is, intelligent causes are always required in every instance when it comes to the origin of any machine or code, precisely because only our intelligence can produce these constructs, so we know it takes intelligent causes. This particular type of intelligence (machines and codes) should be regarded as a subset of Intelligent Design for which humans are unique in abililty, INNATE if you will, much like the bird making a birds nest. Natural law(s) and chance causes have never to this day been empirically shown to produce a machine or code. When it comes to these constructs, not even the chimpanzee or any other animal for that matter can produce them, only human intelligence can (That we can empirically detect right now). A chimp with funny tools means nothing when you come to understand that the chimp will never add concept onto matter to make a machine or code. If humans and other biological organisms are the only machines possessing a code to build our bodies, then it seems very logical that an intelligent cause (although greater than we can produce in complexity and specificity currently) was responsible as to the origin of such structures, simply because it has not been shown otherwise. So, intelligent causes must be involved in the origin of any machine or code.
Please come up with any code or machine that can be empirically tested and demonstrated to originate from purely natural law(s) and chance together or separate. If you come up with one, I will concede that ID has lost. CSI, explanatory filter, IC, all of these are excellent tools when truly seeking the correct delineation between intelligent causes and all the other causal forces of the universe. I commend everyone in the ID community for wanting to know the truth in those regards.
Interesting side note, nylon happens to be one of the few things man-made, which is purely made out of organic elements. Hydrogen, Carbon, Nitrogen, and Oxygen. Biological organisms need these.
Patrick
Thanks for clarifying this.
JPCollado @ 55 – is anyone claiming any more that BDD wasn’t peer reviewed?
Bob, do you mean BBB? Some posters here are under the impression that it was not reviewed by Behe’s peers.
Daniel King @ 60 re: Japanese monopoly on the nylonase issue -
“Is the whole story a scam? Are the Japanese less trustworthy than other scientists? This could be a scandal.”
Mr. King, anything is possible these days. Humans by nature are certainly capable of a lot of deception, and scientists are not immune to this. The Hwang Woo-suk scandal is still fresh in my mind, which took a slew of South Korean scientists for a ride. Are we so naïve as to believe that this is an isolated case, never to be repeated again? It is such an attitude that leaves the door open for more of these hoaxes and abuses to abound.
Of course, woe to me if I were to suggest that a scandal is taking place with the Japanese scientists, without any proof; but, it just seems odd that a significant finding like this has not been pursued further or replicated in other labs. You would think Darwinists will pounce on this and milk it for all its worth. I have as of yet to see an American or European scientist confirming these observed results in scientific journal. It’s not as if we don’t have plenty of plastic and bacteria on our side.
Your reaction to my comments is well deserved and very natural. In my field of work (audits and investigations), deception and fraud are some of the things I have to always look out for. One way for fraud to creep into a financial system, for example, is through the absence of controls, like the guy writing checks also reconciling the bank statements. It seems like we have the same observation going on here. You need someone else outside your constituency to keep you honest.
I have been thinking about the comments by some that this is not ID research.
ID maintains that some features of the natural world are BEST explained by intelligence, RATHER THAN by processes like natural selection.
If enzymes have been designed by intelligent agents, as shown in this post, and no very impressive new enzyme has ever resulted from observed Darwinian processes, then does this paper not support the hypothesis, that enzymes are more likely to be the result of intelligence than of natural selection?
“and no very impressive new enzyme has ever resulted from observed Darwinian processes.”
That’s the rub, isn’t it. Nylonase was offered and it was apparently not “impressive” enough. This despite nylonase evolving in response to nylon, a substance which is entirely manmade. In other words, Darwinian processes created a an enzyme that eats up a completely new substance. There’s no way that was front-loaded, and there’s no way that the information required for the evolution of nylonase is old — because the situation is absolutely novel. What’s more, nylonase emerged in a remarkably short time.
Yet this is not “impressive” enough.
Here’s the point: no matter what examples are provided, the evidence is never enough. The same refusal accompanies transitional forms (“not transitional enough”), speciation (“not different enough”), etc.
Give it up, evolutionists.
larrynormanfan,
I believe the problem with nylonase was that (as Patrick mentioned) it only took a single frameshift mutation to create it from another enzyme gene. This is not a lot of information that random variation has to produce. It started with a pre-existing enzyme gene (if I remember correctly) changed a small part of it, and got another enzyme gene. Isn’t this what Patrick means by transfer of pre-existing CSI?
One thing I will give credit for is that a new function (digesting nylon) was created from the old function. It didn’t take much to create it, but it is nice that two functions were so close to each other in the search space. If all functions are near each other in this way, then Darwinism can be true. If I were you, I’d focus on showing each function can be reached from another nearby function. If it can, you will make the best case for Darwinism anyone has seen. You will actually provide evidence for it.
So I’d hold onto the nylonase example as it is the first step in actually providing evidence that Darwinism is capable of producing biological function. You just need to show that this isn’t an isolated lucky case of one function being near another function.
What is the latest findings or cutting edge research on this Nylonase phenomenon? Can anyone give me the name of an American scientist who has come up with aditional supplemental work?
I am lost. Don’t you define the search space for a given protein over its entire length? From what I’ve read here the likelyhood of evolving nylonase should be so small that it could not happen since the origin of life.
JPCollado:
Well, the freshest scandal is the paper by Warda and Han published in Proteomics:
The paper was actually refering to a supernatural designer.
JPCollado,
You are definitely on to something. I did a PubMed search and couldn’t find anything but oriental authors. As I remarked earlier, JP, the exclusively Asian provenance of this “discovery” that you have so astutely questioned, naturally makes one suspicious that this is a case of scientific fraud.
Or gullibility.
Or both.
I am not saying that Nylonase is a fraud. It is no new kid on the block. I looked into it some time ago and was not very impressed. It may be useful to have bacteria that can burn Nylon.
Nylonase was already known about when ID was born, when DBB and The Design Inference were written. If Nylonase is so impressive, that it can with a single stroke defeat ID, then how could ID be born, and why is Nylonase not repeated always as the single example needed to instantly falsify ID?
“Here’s the point: no matter what examples are provided, the evidence is never enough.” That goes both ways. I think the bulk of the evidence is on the ID side though. I have no a priori committment to ID. There are plenty of religious believers who think ID is bad science and bad religion. That is the most respectable intellectual position. I happen to think the evidence increasingly supports ID.
sparc @ #72, something’s fishy about that paper….I don’t know, but it’s giving me a bad feeling…hmmmmm…..
….this looks like a parody setup as a valid project only to be deflated later and used as a ruse against Sternberg. It wouldn’t surprise me to find out PZ Myers and company using this to their advantage.
Why on earth would a scientific journal allow the use of the words “mighty creator” as part of their verbiage and explanation? This is a tell-tale sign that Mohammad Warda and Jin Han, whoever they are, were in it for the parodical effect and nothing more.
Ah, my suspicions have been confirmed. At least the following blog is making a connection with creationism.
Regarding post # 75, see
http://lippard.blogspot.com/20.....paper.html
Google false flag. It seems like the same tactics used by international intelligence agencies are being executed here.
nylB (acc. no. X02864) encodes a 392 aa peptide (acc. no. P07062). Wouldn’t make a search space of 20^392?
sparc:
“Wouldn’t make a search space of 20^392?”
Yes, that’s correct. The problem is that in my opinion there is no clear evidence of how nylonase arised. The assumptions that it didn’t exist before, and that it arose by a frameshift mutation, and was selected therefore, are indeed assumptions: they may be interesting as a starting point, but they are being pumped up as if they were absolute evidence only because that is conveniente for darwinists as the only known example of a new enzyme arising by mere luck (as darwinists really need tons and tons of mere luck, the simple idea of that is very reassuring for them).
I find the data about nylonase very confused, and, as usual, forced by ideological presuppositions. Notwithstanding that, it is certainly an interesting issue, and further research about it is certainly warranted. The problem is, maybe darwinists are not so motivated to do further research about that, as they think that they already have their explanation, and that is just what they need.
http://www.answersingenesis.or.....cteria.asp
Please, explain more. Particularly the Sternberg connection.
crow thrall:
thank you indeed for the link to that very interesting article. I was not aware of it. It very well summarizes many of my perplexities about the issue, and tries to suggest some very reasonable, and deeply interesting, lines of answer.
That’s exactly a good example of why darwinism ia a real science stopper. We have here a really perplexing example of molecular events, which warrant further investigation and intelligent debate. But has that happened?
No, official science has provided a highly hypothetical, and in my opinion absolutely unbelievable, explanation for the origin of those molecules (random frameshift mutation), so that they could become an useful tool in their fight against ID. That’s the end of it. A very unlikely model has suddenly become the undisputable truth, and no further analysis, least of all research, has taken place to investigate the many unsoloved problems involved.
Don Batten’s analysis is especially interesting because it takes into account two extremely important variables of the bacterial scenario, whose potential relevance cannot be overestimated: plasmidia and transposones. It has often been debated here how possible answers to presently unsolvable mysteries are probably to be found in non coding DNA. It has always been my personal conviction that transposable elements must have a fundamental, and yet completely non understood role. It is equally likely that the first clues to understanding that role may more easily be found in simpler organisms, like bacteria. Bacteria have still many things to teach us, as Shapiro has recently debated.
But, as long as the fog of reductionism goes on blinding scientific thought, researchers will be comfortable only with potential answers which are well inscribed in their current understanding and ideological frame, and will be extremely reluctant to look elsewhere.
crow thrall, thanks for the reference in 79.
Daniel King @ # 60:
“Are the Japanese less trustworthy than other scientists?”
Mr.King, you are committing a faulty generalization here. Please correct and re-phrase, or else, people might think that you are in the habit of making such careless logical errors with frequency.
Tremendous research opportunities we have here for IDT.
Imagine the breakthroughs if we could combine the scientific results of what we have been discussing here so far
(1) the Nature paper id.net brought that started this thread;
(2) Behe’s lab work with regard to the evolution of certain viruses and the limits and efficacy of mutations/NS;
(3) the alleged results on work done with Nylonase;
(4) Axe’s ongoing research wrt protein folding, and other forthcoming projects at the Biologic Institute;
And to add to the list, new findings on molecular evolutionary measurements.
The same could not have been said twenty years ago. Imagine the opportunities twenty years from now!