Evolution Intelligent Design Science

Design and engineering of an O2 transport protein

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Here is another way to use ID:

Nature 458, 305-309 (19 March 2009)

Ronald L. Koder1,2,3, J. L. Ross Anderson1,2, Lee A. Solomon1, Konda S. Reddy1, Christopher C. Moser1 & P. Leslie Dutton1

The principles of natural protein engineering are obscured by overlapping functions and complexity accumulated through natural selection and evolution. Completely artificial proteins offer a clean slate on which to define and test these protein engineering principles, while recreating and extending natural functions. Here we introduce this method with the design of an oxygen transport protein, akin to human neuroglobin. Beginning with a simple and unnatural helix-forming sequence with just three different amino acids, we assembled a four-helix bundle, positioned histidines to bis-histidine ligate haems, and exploited helical rotation and glutamate burial on haem binding to introduce distal histidine strain and facilitate O2 binding. For stable oxygen binding without haem oxidation, water is excluded by simple packing of the protein interior and loops that reduce helical-interface mobility. O2 affinities and exchange timescales match natural globins with distal histidines, with the remarkable exception that O2 binds tighter than CO.

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15 Replies to “Design and engineering of an O2 transport protein

  1. 1
    David Kellogg says:

    If that’s ID, then all laboratory science is ID, because all laboratory science involves the creation of artificial (laboratory) conditions. What, pray tell, makes this ID beyond Mr. Lopez’s fervent wish that it be so?

  2. 2

    Thank you, David.

    I only wish for science to recognize actual design when it is present. Designing proteins is not emulating the effects of RM+NS, it is simply good engineering. The challenge for those who embrace the idea that “biology is the study of complicated things that give the ‘appearance’ of having been designed for a purpose” is to demonstrate exactly how that is. ID is frequently in practice, like with the scientists that engineered the O2 transport protein. The question is not whether intelligent agents can produce them; the question is whether the much hailed process of RM+NS can pull it off.

    Make that your research project. 🙂

  3. 3
    David Kellogg says:

    Mario,

    ID is frequently in practice, like with the scientists that engineered the O2 transport protein.

    Not to be the Screech to your Slater, but I don’t see it. These researchers did not use design detection (ID): they used biological engineering.

    Creating a prosthetic limb does not detect ID in the limbs that remain. Making a levee does not detect design in natural riverbanks. Buying a duck call at a hunting supply store does not enable you to detect design in the birds that respond.

  4. 4

    David,

    ID is a pretty broad concept and it encompasses much more than design detection. In order to make ID heuristically fruitful in science, there must be an “applied” component to ID research.

    J. Wells has a good example of an applied ID concept. His work is not looking to detect design, as it were, but to buttress the concept of ID beyond detection and into ID research foresight.

    Do centrioles exhibit a mechanism designed to function as a turbine?

    That is a good question and it is one that requires one to look at centrioles as though they were designed, not as thought they were produced by a random or blind process.

    Blessings,
    –Mario

  5. 5
    Pendulum says:

    I think I got it. Intelligent design in biology is apparent (and detectible) when proteins lack common descent and lack overlapping functions. Under these circumstances the inference of design is unambiguous.

  6. 6

    Hello Pendulum,

    Thank you for joining.

    I think you are misunderstanding the concept. In order to distinguish design from non design, it is adequate to ask whether a natural process can account for it. If something has been shown to arise by natural means, then ID has nothing going for it, except perhaps as philosophical embellishment. However, demonstrating that proteins did not arise by a naturalistic process does not prove design. It is the positive markers that do that.

  7. 7
    idnet.com.au says:

    Hey Mario,

    I am with you on this one. This research shows that it is possible for intelligent beings to purposefully manipulate biochemicals to produce functions. These functions are detectable and this process is Intelligent Design.

    I posted something similar to this some time back and some people responded in the same way.

    I think all who support ID will get your point. Those who don’t will fail to acknowledge it. That is OK.

    This is an interesting part of the paper.

    “However common it may be in nature, we maintain that complexity is not an essential feature of protein as a material, nor is it an essential feature of catalysis, as shown by synthetic chemical systems.

    By understanding the origins of complexity and making purposeful efforts to separate multiple utilities and minimize complexity during the design and testing of artificial proteins that are completely independent of natural selection, we show how to progressively build in sophisticated biochemical features that reproduce and exceed natural protein function.

    Our approach follows that long used by artists and architects who develop maquettes–simple models that are progressively altered to test and determine the ultimate characteristics of their constructions.”

    His idea of “complexity” is not the same as ID theorists think of complexity. Multiple functions served by single proteins increases the necessary complexity.

    Haemoglobins are particularly complicated molecules and must take up and let go of the O2 molecules under very specific conditions.

    Before these people boast that they have improved on natural haemoglobin, they should first produce red cells containing their new protein, then transfuse rats with these cells, and see how their design behaves under different physiological conditions.

    The Hb used in foetal red cells is different from that used when babies are delivered. This is because a different set of exchange conditions are needed in the foetus than in the air breather.

    Like vestibular organs that have one by one showed their value, I think ID predicts that these claims of improving O2 transport proteins will prove exagerated.

  8. 8
    idnet.com.au says:

    Sorry that last sentance should read vestigial organs.

  9. 9

    Thank you, idnet.

    Good point.

  10. 10
    Borne says:

    Any form of bio engineering implies some ID principles.

    The fact that there are companies specializing in design detection within the genome explicity says that ID is science. Companies that detect modifications as per genetically modified organisms prove the science of ID.

    If we can engineer proteins or ‘sign’ anything in the genome (Venter) then, inversely, we can also detect design.

    If we can engineer in biological cellular systems we can also reverse engineer.

    So, in the end, both designing and design detection are useful and will become incredibly more useful as time passes.

    In the 19th century, simply washing ones hands was laughed at by supposedly intelligent doctors. It was even vehemently opposed by many. It took quite a few years before virtually all medical doctors accepted the facts involved.

    Today washing hands is now obligatory in hospitals.

    ID will go the same route. In spite of all the codswallop being uttered against it, it will prevail through empirical evidence and sheer usefullness.

    Later,it will come to be considered, as it was before, obvious.

    The way research is going, this is inevitable.

  11. 11
    sparc says:

    If that is ID who is the greatest ID scientist then and why is he not posting here?

  12. 12
    sparc says:

    Or is it me?

  13. 13
    Freelurker says:

    Mario,

    I assume that you are an engineer and that you have heard of Murphy’s Law.

    1) In your experience, do engineers find it useful to act as if “Anything that can go wrong will go wrong.”?

    2) In your experience, do engineers believe that the universe actually seeks out the weak spots in our plans and designs?

  14. 14

    Hello Freelurker,

    Please don’t assume anything.

    I am not sure where you are going with your questions, but if you can elaborate I’d be glad to respond. 🙂

  15. 15
    Freelurker says:

    Mario,
    If you don’t have experience as an engineer then you can’t address my questions (no offense.) They have to do with the use of heuristics in engineering design. This relates to comment #4 where you refer to the use of heuristics in science.

    I’m not going to comment further on this thread. Somehow I didn’t notice how old it was. What makes it worse is that my comments are delayed in moderation, a situation that started under the old regime despite the fact that I have always been polite and on-topic. I thought that this might get better under the “new” moderation policy, but this blog’s treatment of Reciprocating_Bill shows that this blog still moderates people to avoid difficult questions.

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