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Design Principles in Protein Science


The Protein Society’s upcoming big annual meeting (July 30 to August 3, 2005) has a session that should give proponents of unintelligent evolution pause and proponents of intelligent design courage:

Session 1, July 31, 2005, 8:00AM to 12Noon
Systems Biology:
Understanding Design Principles of Protein Networks

Chair: Andrew Murray, Harvard University
Speakers: Howard Berg, Harvard University
Andrew Murray, Harvard University (Sponsored by Chroma Technology Corp)
Roy Kishony, Harvard University
James Collins, Boston University
Adam Arkin, Lawrence Berkeley National Laboratory

Ask yourself how design principles from human engineering contexts can be so usefully employed in studying biological systems if those systems themselves are not, as proponents of unintelligent evolution assure us, the product of intelligent design. By the way, Howard Berg, the first speaker listed, is the same person who said that the bacterial flagellum is “the most efficient machine in the universe.”

Hi Qualiatative, It seems that we weren't really communicating past one another. Because comment #6 was missing at the time, your comment #7 looked to be a direct response to #5. It all makes sense now that #6 is where it belongs. Sorry for partaking in the confusion. Charlie Charlie
i wonder what you guys would think of the following comments i got when i posted half of this blog on a site i frequent: .................................................................................. Well, where to begin? In reply to: To appreciate the problem here, consider the following analogy. That's not the problem here. In reply to: The only well-documented examples that we have of successful co-option come from human engineering. It's this kind of bullshit straw man rhetoric that makes it so no scientists take IDCers seriously. No examples of co-option? Gee, ever notice how bat wings are really similar to arms? Or whale flippers to arms/legs? This is the kind of argument a conman makes. He's not really trying to convince anybody, he's making money telling some people what they want to hear. Examples including more complicated co-option In reply to: In biological terms, each step requires an increase in fitness as measured in terms of survival and reproduction. Also false. Genetic Drift is one of the most important evolutionary mechanisms. Why bother to understand evolutionary theory when you can make a comfortable living frothing at the mouth about it? In reply to: Consequently, it is not enough merely to presuppose that a fitness-increasing sequence of baby steps connects two biological systems—it must be demonstrated...Only then do we have a mechanistic explanation (acceptable to evolutionary theory) of how one system arose from another. Only then can we legitimately say that unintelligent evolution is confirmed. Gosh, we only have to do this for every biological structure on Earth? That sure could take a while, considering some of this stuff happened billions of years ago. But hey, let's be fair. IDC has been around a couple hundred years. Pick any biological structure around, and explain how the designer designed it. Baby step by baby step. Or, if in two hundred years not one design process has been determined, just explain how you are going to determine design processes. In reply to: Unintelligent evolution remains an unsupported, speculative hypothesis. ^(infinity) Credibility --> 0. Statements like this confirm that this is not in any way a serious discussion of scientific issues. It is preaching to the choir, if you will. The snide dismissive tone, the blatant falsehoods... it makes one wonder if Dembski sells used cars on the side... I guess if you say this over and over again, some people who don't know better might think it's true. Did you know that gullible is not an actual word? Try looking it up in the dictionary if you don't believe me. In reply to: Thus I’ve seen evolutionists compare their theory favorably to Einsteinian physics, claiming that it is just as well established as general relativity. Yet how many physicists, to argue for the truth of Einsteinian physics, will claim that general relativity is as well established as evolutionary theory? Zero. This is solely because the Bible does not offer a competing 'explanation'. If the Bible had talked about how we stick to Earth because of God's love, then physicists would be forced to defend the 'theory' of unintelligently directed gravity and it would be against the law to teach it in Kansas. ................................................................................... mark777
I think Charlie hit the nail on the head. One suspects that this paper has little or nothing to do with controversies over Darwin. Rather, the design language is there because the subject matter calls forth language that maps on closely with the language we use for disciplines involving human design (engineering, architecture, etc.) I think Dr. Dembski made mention of the article here because of what it portends in terms of a growing openness for using design analogies by those who study things like protein networks, and not because this is an "ID" paper simpliciter. jayman
Sorry, I accidentally "submitted" that while trying to edit it. Mentally remove the words "all of" in the 6th line. dr. dembski, you wouldn't fix that for me, would you? I didn't think so. Oh well. Charlie
Qualiatative: It seems we might be missing on all cylinders here, communication-wise. My wordiness could well be the cause. I didn't mean to imply that the use of the word "design" constitutes a bias but rather that it indicates a growing acceptance of all of design and related terms ("engineered" "machines" etc.). Of course this doesn't mean that these researchers believe in ID in any way, but the use of these design terms does indicate, and might further precipitate, a gradual shift, unspoken and likely unconscious, away from the reigning paradigm. I'm sure you're right that the word "design", in a materialistic sense, is already pervasive, but as more and more (and more) researchers become used to thinking this way I think that design as a CAUSE of complexity, and not just as a result of complexity, will become obvious. Where the bias comes into play, in my opinion, is with the aggressive Darwinist activists who may chastise their fellows for allowing ID its proverbial "foot in the door" - especially if it is siezed upon too aggressively by the ID proponents. Does this mean that ID proponents should not point out such instances? I don't think so. But I think they must be wary of driving unwitting allies back into the shadows. Charlie
I left a comment here about the ubiquity of the word "design" in the mainstream research literature, but it got deleted without a comment. What's the deal? arensb
I don't get it? Is PaV coming out against design. I thought he was critical of darwinian theory. Benjii
PaV, Sorry, I am no wordsmith. Perhaps I should have replaced my "Also" with "Alternatively" or "Yet still". At any rate, I agree with your (and Charlie's) Darwinian skepticism but I do not think the use of the word "design" constitutes a bias towards ID. Qualiatative
Qualitative: is your wording correct? Or did you leave a word out? You sound like someone who wants to defend Darwinism, yet your last sentence seems to be anti-Darwinistic. PaV
The word "design" is already ubiquitous in biology literature. However, it is typically used loosely to mean: "structural pattern/feature" (or something similar). Also, nobody is questioning the apparent design. That is why the burden of proof is on those who subscribe to Darwinism to show that it is not. Qualiatative
Charlie writes:
It is a very brave move to include such words as “design” in your titles if you want to stay among the mainstream.
A quick search at PubMed shows 5109 papers on proteins that have "design" in the title, going back to 1962 (Some observations on the basic principles of design in protein molecules, Comp Biochem Physiol. 1962 Oct;4:229-40) through today (Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates, Proteins. 2005 Jul 18). So perhaps the word "design" isn't as provocative as you seem to think it is. Oh, and PubMed also lists 8 papers with "intelligent design" in the title. arensb
I think we must give credit where it is due. It is a very brave move to include such words as "design" in your titles if you want to stay among the mainstream. Perhaps it is only to be a little provocative and to pique some interest in one's topic but I rather feel it will slowly inure the community to the idea of design. As they get used to the word and to hearing it in the context of biolgical systems the y will slowly come to see design as the cause. Even the most open minds believe, for the most part, only what has been repeatedly imprinted often enough to be accepted as truth. We see what we already believe. The problem is the vocal minority, those who while away their time arguing for pure unintelligent evolution, are always on the lookout for these examples and are eager to demean them to further their own agenda. The double-edged sword of the ID proponents is that in pointing out the examples of mainstream acceptance, which can aid its general appeal, they could easily cause those timid souls to pull their toes out of the water to escape the inevitable onslaught of the neo-Darwinists who fear the breach. I think of Sternberg's plight, as well as the case of the Privileged Planet showing, as examples of the effects of such backlash pressure. I hope that drawing attention to such cases emboldens more to test the water than are driven back by the hostility of the backlash. Charlie
And there's more: 8/1/2005: Session 4: Protein Engineering and Design 8/1/2005: Session 6: Function and Assembly of Molecular Machines eswrite
Great comment, PaV! Benjii
What's intriguing about the Darwinists is that they have the answer to their own questions right in front of their eyes and can't see them. Then when you point it out to them they get indignant and say you don't know what you're talking about. ("Quote mining") Just think about it: design principles. How can something be designed if you don't know where you want to go with something? That is, how can design be undirected? And if protein networks are designed, well...? PaV
Sounds intriguing! Benjii

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