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Finnish peer-reviewed article that’s pro-ID

Here’s a pro-ID article without the usual disclaimers (e.g., a ritualistic suck-up to Darwin, an obligatory sneer at ID). Perhaps this is a sign of things to come.

Protein engineering: opportunities and challenges
Matti Leisola1 and Ossi Turunen1

Journal Applied Microbiology and Biotechnology
Publisher Springer Berlin / Heidelberg
SpringerLink Date Tuesday, April 03, 2007
SOURCE: http://www.springerlink.com/content/d514772515583767/

Received: 28 February 2007 Revised: 20 March 2007 Accepted: 21 March 2007 Published online: 3 April 2007

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.

Keywords: Protein engineering – Directed evolution – Enzymes

(1) Laboratory of Bioprocess Engineering, Helsinki University of Technology, P.O. Box 6100, 02015 HUT Espoo, Finland

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13 Responses to Finnish peer-reviewed article that’s pro-ID

  1. 1

    “For the near future, however, in enzyme development, we need to rely on a combination of both.”

    Using Darwinian processes makes sense. Since we do not yet know how to write a BP sequence to produce a structure, use the empirical method to determine what sequence tends to make what form.

    After we’ve got a little bit of that ironed out, the expectation would be that our own intelligent design through theory would outshine the use of the empirical method.

  2. Hi to all. I have a big favor to ask of the ID community- Two days ago, I posted a comment on a paper which Dr. Dembski had so kindly shared with us ( Carlos Gershenson’s paper on Viewing the world as information). In that comment, I mentioned that I had a debate going with several atheists in the comments section of an essay I had written on intelligent design versus evolution at my own blog. I invited folks to weigh-in and got deluged by about 400 hits. My intention was to try to bring some balance to the discussion by getting an ID and/or creationist perspective on the matter. Somehow or another, I managed to accomplish the exact opposite. I put my fist in a hornet’s nest, and I am now single-handedly trying to defend myself against a total atheist/evolutionist onslaught. A small sampling of a few words that have been applied to my sincere and polite advocacy of ID are as follows- ” go educate yourself”, I “argue from ignorance”, I am an “intellectual coward”, I speak ” despicable lies”, I “pretend”, I “know nothing”, my arguments are “ludicrous”, I display ” agressive ignorance”, I am “ignorant”, “dishonest”, and “intellectually dishonest”. All this because I politely, and reasonably ( or so I thought), expessed some conscerns that I had about the probabilistic liklihood of human DNA evolving from random particles. I am absolutely getting hammered guys. If there is ANYBODY out there with a reasonable, rational, and polite argument in FAVOR of creationism, could you please stop by and add a comment? I feel like a one-legged man in a butt-kicking contest. Dr. Dembski, all I can say is that you must have a very, very thick skin. Because I have tasted but a thimbleful from the cup of scorn that you drink deeply from every day, ( despite the fact that all you do is offer fair alternatives to an established orthodoxy in the marketplace of ideas ), and I havent’ enjoyed the taste very much. Again, thanks for your efforts to enlighten and inform. By the way, have you ever considered just how much the advent of the internet has changed the terms of the debate? When you consider how much hate and resistance there is out there in academia directed at ID even having a chance to be CONSIDERED, arent we all blessed beyond our wildest dreams by the ability to take the message straight to the people? There is really no stopping the free exchange of ideas now. ID advocates have such an opportunity to be heard now, that we never could have dreamed possible 10 years ago. Anyways, if there are any thick-skinned ID advocates or creationists out there, who are ready for an intellectual rumble, please feel free to stop by and enter the comments-war-zone at;
    http://tyharris.wordpress.com

  3. tyharris,

    All I have to say is that you either need to get really, really thick-skinned or implement a better moderation/filtering system if possible. It’s amazing how nasty these people can be…and how much free time they seem to have.

  4. tyharris,

    I agree with Patrick. Moderate your blog. There is no need for you to accept abuse. There are plenty of places where the rabid can go to bully people.

    If what you are asking for is reasonable discussion of a topic, then enforce that through moderation, and steadily build a community of folks who do not immediately resort to name calling when they’re presented with a topic that makes them uncomfortable.

    Take the arguments one at a time, and insist on proper conduct and generally on-topic posts. It’s your blog, don’t feel like you can’t make the rules, and create a safe place for those interested in design arguments to have a reasonable discussion. Being intelectually honest does not mean that you have to make a defence of every ad hominem attack. Reject the trouble makers and they will make their way back to the hive.

    There are plenty of cases for design that are problems for evolution. There are plenty of books written that can help. Here is a list of essential reading from Discovery Institute:

    Discovery CSC’s Essential Reading List

    For a good introduction I recommend Lee Strobel’s book, Case For A Creator. Also check out the DVDs, Unlocking the Mysteries of Life, and The Privileged Planet. There’s actually a lot of stuff on ARN.org. Their video list is at:

    ARN Video List

    And just so that you know you’re not the only one:

    Jonathan Wells responds to P. Z. Myer’s tantrum

  5. Dr Dembski:

    Thanks for keeping us up to date on peer-reviewed publications that support ID. I note the article is behind one of those US$ 32.00 walls — h’mm price is going up, a few weeks back it was only $30.00.

    So much for the idea of the Web as an information commons!

    And, speaking of the tragedy of the commons:

    Ty Harris:

    I put my fist in a hornet’s nest, and I am now single-handedly trying to defend myself against a total atheist/evolutionist onslaught . . .

    My sympathies, I — and many others — have had very similar experiences. [BTW, Dr Wells, you probably have grounds for a slander suit against those who propagated lies on your qualifications; Pharyngula, if it does not take down and apologise for hosting those lies, probably is also liable.] I think several levels of response are appropriate here:

    1] Those who abuse a privilege should only blame themselves if they lose it, so I join with Patrick and Apollos in saying: MODERATE.

    2] Since you have WordPress, put up a prominent page on your comments policy and why you have taken it up, telling abusers they can go open up their own blog to rant away to their heart’s content. Point out that abuse will if necessary be traced and handled as the offence that it is, which can lead to loss of ISP privileges — cf your contract to get net access.

    3] More broadly, this is a sign of ill-informed arrogance, disrespect and the intellectual and moral bankruptcy of evolutionary materialism as a movement. These people are living out Dawkins’ outrageous village atheist declaration that those who dare to doubt the wisdom of their favourite worldview, “must” be ignorant, stupid insane and/or wicked.

    4] Point out the prejudice and zealous contempt of those who ask questions and beg to differ. Challenge them to justify the moral tinge to their accusations and concern over moral issues, relative to the ethical foundations of their worldview and its manifestations over the past 150 years. Challenge them as Schaeffer did, on the inconsistency between their moral intuitions and how they cannot ground the cogency of such intuitions relative to their worldview — morality boils down to “might makes right” and “nature red in tooth and claw” so while there is cooperative behaviour in nature there is also predator-prey behaviour — on evo mat presuppositions, after all the fancy phil footwork is done. That is, why should the hungry lion heed the bleat of the tasty, vulnerable gazelle? [Read: e.g. Hitler and lebesraum athe expense of the rest of Europe etc.]

    4a] Raise the question as to what the objectivity of morality points to: the Giver of the Core Moral Law written on all our hearts, which we are all guilty before. Cf Rom two five to eleven and fourteen to sixteen if you are a CHristian to see how this works out. [C S Lewis' point on the implications of the fact and way in which we quarrel is a good place to start.]

    5] Add to that, the issue highlighted by Aristotle in his The Rhetoric ever since the unjust death of Socrates was fresh in mind: arguments draw persuasive power from emotions, authority, facts and logic. Hostile emotions often distort judgements and easily deceive. No authority is better than his or her facts and reasoning. So, it is the credibility and materiality of claimed and omitted facts, and the quality of logic that should be the focus of reasonable discussion.

    6] In that context, selective hyperskepticism that begs worldview level questions — “extraordinary [i.e. cuts across the world as I see it] claims require extraordinary [i.e. unrealistically demanding] evidence” — instead of addressing the actually present, adequate evidence, should be exposed for the fallacy it is.

    7] Finally, link on your blogroll to some good survey presentations on the matter,and make reference to these in your onward responses. If you want a basic survey onthe matter, my own presentation is in my always linked. [Just click the link on my name.]

    God bless all at Easter

    Gordon

  6. In the long run, random methods cannot replace insight in constructing life-like proteins

    No kiding.

  7. 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.

    Well by golly it seems there’s empirical evidence Darwinism doesn’t work so well in the very areas it hopes for vindication. Reminds me of the old “cobalt bomb” lab experiments on plants that were conducted with the belief that accelerated mutation via radiation would accelerate the create process — NOT!

    If novel proteins are highly specific (there are relatively few functional sequences compared to the vast number of possible sequences), then of course Darwinism won’t find them. DUH! It’s like using a genetic algorithm to figure out someone’s password. It doesn’t work because passwords are IC, and complex proteins may be that as well.

    Glad to see Biotic Message playing out in proteins.

    Salvador
    PS
    regards to my brethren on this Good Friday…

  8. tyharris,

    You might be interested in the thread by Jonathan Wells below. He quotes Johnny Cash who indirectly quotes a wise teacher many centuries ago: ” it’s good to be hated by the right people.”

    So I salute you, tyharris. They may be inconvenient folks to deal with, but their response to you suggests you are doing a good job.

    Sal

  9. Ty –

    Your problem is simple — your blog entry is way too long. This allows your opponents to criticize you without reading it (because no one has the time to read it in-depth), and keeps your friends from supporting you because, well, it’s too much to read.

    I would break it up into chunks, and post it a piece at a time, each a self-contained thought. Then you can argue specifics and people won’t get bogged down in the specifics.

  10. tyharris,

    I posted a commentary at UD this morning on the topic of the irrational hatred of ID, before I saw your comments on this thread. Perhaps I’ve provided some insight into the hostility you’ve experienced.

  11. TyHarris: I don’t have a clear recommendation about the hatred you’ve experience, but unless you feel scrappy you should just closely monitor the commentary. You will get no quarter on their terms. However, back to design parameters, you might find this interesting also. Seems a Brand New Mosquito(!) has been developed that when interbred with the “background” population tends to weed out those that can carry the malarial virus. Both sides might claim this is “evolution” of the micro type in action. Or not. Yes, mosquitoes breed, they breed quickly, and yes like Darwin’s finches traits get passed around quickly if allowed to survive. But the main point is that this is an ENGINEERED insect. Supposedly mother nature’s evolutionary answer to malarial infections was for humans to resist by developing sickle-cell anemia. But the lab-induced trick demonstrates that purposeful reshuffling of the genome can alter living things to do our bidding. So perhaps the ID crowd can claim this is a “testable” claim that other bio-features commonly thought to be around due to some “just so” story of purposeless, blind interaction with the environment were actually modified in some OTHER manner more quickly than we imagined? The problem is you have to know exactly what you’re doing.

    Adding to this climate “design parameter” findings, we have yet another Adult Stem Cell success story: I think all here would appreciate yet another success story (or certainly great potential) with Adult stem cells(ASCs), which can be pulled and grown from you and me without the ethical controversy that surrounds the embryonic version (ESCs) (which in the latter case–if extracted new–must be taken from fertilized human ova). ASCs are apparently demonstrating a “multipotency” that has all the potential of the much heralded “pluripotency” of ESCs.

    We can’t fix a broken heart just yet, but we might be able to soon regrow part of one. From the UK Telegraph see here, and also, here!

  12. 12

    Thanks, Sal. In case I forget, happy resurrection day.

  13. tyharris:

    The same thing happened to me. At first I tried to allow all comments, but I finally had to turn on the moderation to stop all the cowardly, anonymous bombs that were being thrown. I figured, “Hey, its my blog. I don’t have to put up with this.”

    Most of these people don’t want to play fair. They make anonymous posts, and they make snide remarks. They must be unhappy people.

    Turn on moderation. You’ll still have to read the stupid remarks, but you’ll have the satisfaction of rejecting them.

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