Intelligent Design

Intelligent design in practice

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Although Nature titled this piece “Tackling Unintelligent Design” they betray their own bias and fail to appreciate the irony in their claims.

According to R. John Ellis from the University of Warwick “Rubisco, the key enzyme in photosynthesis, is a relic of a bygone age.”

Researchers now plan to genetically manipulate the enzyme to make a designer enzyme fit for the modern world.

Although Rubisco is the most important enyzme on the planet, it is also one of the most inefficient. It evolved when the atmosphere was different and failed to adapt to the modern atmosphere. Attempts to improve the properties of this key enzyme of plants and cyanobacteria have failed because it proved impossible to reconstitute Rubisco in vitro. Liu et al. (Nature 463, 197–202 (2010) Vol 463 14 January 2010 doi:10.1038/nature08651) have overcome this problem with a cyanobacterial Rubisco by using two different chaperone proteins, which guide the folding and assembly of the enzyme.

Ribulose 1,5- bisphosphate carboxylase/oxygenase, reacts with either CO2 or oxygen. The reaction with oxygen competes with the carboxylation reaction in which CO2 is fixed, and feeds a pathway called photorespiration that is peculiar to plants. Photo respiration causes the loss of up to 25% of the carbon that is fixed by the carboxylation reaction.

Rubisco is near the bottom of the league table of enzyme efficiency, with a catalytic rate of only three to ten molecules of CO2 fixed per second per molecule of enzyme. This inefficiency explains why Rubisco is the most abundant protein in the world. To cap it all, the enzyme is not saturated at current levels of CO2 in the atmosphere, which is why some growers elevate this concentration inside their greenhouses. None of these deficiencies mattered when Rubisco first evolved, as there was no oxygen in the atmosphere and the level of CO2 was much higher than it is today.

Rubisco is a large oligomer, consisting of eight catalytic large subunits bound to eight structural small subunits. This is why plant Rubisco is one of the few proteins that has never been successfully reconstituted in vitro into an active enzyme from its unfolded subunits.

Molecular chaperones work by combating protein aggregation by binding to transiently exposed, interactive surfaces on individual protein chains at the stage of folding and/or assembly.

The protein that mediates Rubisco folding is called a chaperonin. They function by enclosing each individual folding chain inside a closed cavity, where the chain completes its folding into a monomer in the absence of other folding chains. The closing and opening of the cavity requires ATP — the molecular source of energy used by cells.

Liu et al. defined the conditions necessary for the formation of active enzyme in vitro from purified, unfolded large subunits and folded small subunits of a cyanobacterial Rubisco. First incubate unfolded large subunits with GroEL/ES, RbcX and ATP, to allow the large subunit to fold and bind to RbcX, then add folded small subunits to displace the RbcX and so bind the folded large subunits. RbcX chaperone acts as a ‘molecular staple’ that binds to partly folded large-subunit chains in such a way that they interact correctly with small subunits, rather than aggregating with one another.

The authors set up an in vitro system from which they obtained active Rubisco in yields up to 40% and can be used to screen the effects of mutations in the large-subunit chains in the hope of obtaining an improved enzyme.

Just how successful they will be in manipulating this brillianty molecule remains to be seen.

19 Replies to “Intelligent design in practice

  1. 1
    EvilSnack says:

    So while everything else that has been alive for the past 2.7 gigayears has been evolving at an amazing clip, Rubisco is still the same? And nothing came along to take its place?

    An intelligent designer might have a reason for deliberately making this enzyme so inefficient–I can think of a couple–but natural selection should have produced a better result by now.

  2. 2

    The whole story of C3-photosynthesis proving to be inferior to C4-photosythesis, intermediate forms between different forms of photosynthesis, photorespiration as inefficient and wastful process and rubisco constituting a relic from the past is not new. See http://members.liwest.at/rammerstorfer/C3C4.htm and http://www.wort-und-wissen.de/.....ij151.html.

    Rubisco has a difficult job to do. Researchers begin to realize that it might represent a good design after all:

    TCHERKEZ et al.:„Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized“, PNAS vol.103/no.19/7246-7251, May 2006 wrote:

    „…despite appearing sluggish and confused, most Rubiscos may be near-optimally adapted to their different gaseous and thermal environments. If so, genetic manipulation can be expected to achieve only modest improvements in the efficiency of Rubisco and plant growth.“ (p7250)

    Gutteridge and Pierce commented in the same issue:

    „Tcherkez et al. caution that the amount of improvement that could be introduced by design is unlikely to exceed the superior variants that have evolved naturally. Implicit in this view is whether we have sampled the natural orders extensively enough to know the true bounds of these two parameters.“

    and despite some unanswerd questions they conclude:

    „One might argue about the definition of perfection, but from a biological perspective, perhaps nature most often finds the „best“ solution for any particular catalytic need. Sometimes perfection may not immediately obvious.“

    „Indeed, the detailed analysis of Techerkez et al. is required to see any signs at all of perfection in the slow, nonspecific, discordant activities of Rubisco.“

  3. 3
    REC says:

    Might Rubisco be “on the edge of evolution,” so to speak? So constrained by its complex chaperone system, and hexadecameric state that it has little room to change?

    The article believes that rubisco evolved in a world flush with CO2, and little oxygen as a competitor.

    But, as evil points out, designs don’t have to be optimal, just suitable (not just thinking of designed obsolescence-but my car is not designed for the max. speed of land vehicles!!!!).

  4. 4
    DLH says:

    Which came first – Protein or Chaperones?
    Life requires photosynthesis
    The Rubisco Activase protein is key to photosynthesis.
    Chaperonin is necessary for Rubisco to fold into shape.
    Photosynthesis is needed to convert sunlight to biotic energy (ATP)
    ATP is needed to form Rubisco and Chaperonin etc.
    Which came first?
    How do you get the first to stick around until you form the second or third? Etc.
    Biochemists synthesize carbon-locking molecule for the first time

    . . .The key protein in photosynthesis, Rubisco, is thus one of the most important proteins in nature. It bonds with carbon dioxide and starts its conversion into sugar and oxygen. “But this process is really inefficient”, explains Manajit Hayer-Hartl. “Rubisco not only reacts with carbon dioxide but also quite often with oxygen.” . . .
    The protein Rubisco is a large complex consisting of 16 subunits. Up to now, its complex structure made it impossible to reconstruct Rubisco in the laboratory. To overcome this obstacle, scientists at the MPI of Biochemistry and at the Gene Center of the Ludwig Maximilians University Munich used the help of cellular chaperones. . . .The molecular chaperones within the cell work in a similar way: They ensure that only the correct parts of a newly synthesized protein will come together. As a result of this process, the protein acquires its correct three dimensional structure. “With 16 subunits like those of Rubisco, the risk is very high that the wrong parts of the protein clump together and form useless aggregates,” says the biochemist. Only with its correct structure will Rubisco be able to fulfil its function in plants.
    The MPI researchers showed that two different chaperone systems, called GroEL and RbcX, are necessary to produce a functional Rubisco complex. . . .

      Chaperonin-assisted Protein Folding. Manajit Hayer-Hart
    Chaperones for climate protection

    C. Liu, A. L. Young, A. Starling-Windhof, A. Bracher, S. Saschenbrecker, B. Vasudeva Rao, K. Vasudeva Rao, O. Berninghausen, T. Mielke, F. U. Hartl, R. Beckmann and M. Hayer-Hartl. Coupled chaperone action in folding and assembly of hexadecameric Rubisco. Nature, January 14, 2010

    Scientific studies have shown that atmospheric Carbon Dioxide in past eras reached concentrations that were 20 times higher than the current concentration. If Rubisco and Chaperonin were actually designed, there are likely numerous parameters in its optimization that have yet to be discovered. e.g. the ability to operate across such 20 fold variations in CO2 concentration.

  5. 5
    REC says:

    DLH,

    Interesting point. I guess design-detection needs to be objective. It could become very anthropocentric to guess the function of the design.

    My own proposal suffers from this. I am curious about the design mechanisms that will prevent extinction of humanity due to a uneven mutation vs. birth/selection rate. This presumes such a design exists, but also, that we are not designed for obsolescence.

  6. 6
    idnet.com.au says:

    Suppose they find that they can improve the efficiency of the enzyme. That will be hailed as proving that ID was not involved in its initial creation.

    If they are unable to improve the efficiency, they will say it proves that ID was not involved and that evolution produced the most efficient form of the enzyme by selecting from the early variants.

    IT IS A WIN WIN FOR THEM!

  7. 7
    REC says:

    DLH,

    There are lots of other ways besides photosynthesis to make ATP. Chemoautotrophs would be the extreme example. A ATP-synthesis and chaperone machinery could predate rubisco.

    Idnet,

    I don’t think their primary effort is to defeat ID. It sounds like their primary hypothesis is that Rubisco is an evolutionary contingent, and can be improved. Neither evolution nor design need to be optimal. Do you think this work is pro-id, anti-id, or neutral?

  8. 8
    Jehu says:

    From the article. A spit face inducing quote:

    Rubisco is near the bottom of the league table of enzyme efficiency, …This inefficiency explains why Rubisco is the most abundant protein in the world.

    So Rubisco is the most abundant protein in the world because it is so inefficient? Are you kidding me? Was this article actually peer reviewed? So now inefficiency = reproductive success? I guess Darwinism really can explain everything. /sarc.

  9. 9
    Jehu says:

    REC:

    Do you think this work is pro-id, anti-id, or neutral?

    I think it is unbelievably arrogant.

  10. 10
    idnet.com.au says:

    Some cropped quotes from the editorial.

    Heading.
    “Tackling unintelligent design”

    “Rubisco is a superb example of unintelligent design for the modern world.”

    Pro or Anti?

  11. 11
    hrun0815 says:

    idnet.com.au writes: […] IT IS A WIN WIN FOR THEM!

    Interestingly, the ‘It’s a win for them’ also applies to ID. Many times optimality has been used to suggest design and likewise (see post #1) has suboptimality.

  12. 12
    REC says:

    IdNet,

    I wasn’t sure what your take on this was. I thought you were indicating the work to be evidence for ID in action. Similar work has been used in pro-ID literature (see Behe regarding the ‘epistatic ratchet).

    Suboptimal design, or evolution of a suboptimal enzyme are both possible. Contingency in evolution has been put forth many times by Darwinists. I think they would argue Rubisco conferred a fitness advantage, so plants and bacteria bearing it prospered. It doesn’t work so well, so they have to make a lot of it. This may or may not be bad for the plant-making protein isn’t that costly, and might be a good store of amino acids. But once using the system, and what evolved around it, the likelyhood of something functionally replacing it could be very small.

    Likewise, the design of Rubisco could appear suboptimal. But this is to todays viewer, who wants to fix lots of carbon. Perhaps it is optimized for different conditions then today. Perhaps the production of protein biomass due to its inefficienct is useful to nature-a ecological design.

    Given this why is it arrogant to try to improve?

    The article is spun very negatively, but I am talking about the work itself. I would say neutral.

  13. 13
    Collin says:

    hrun0815,

    I don’t think that suboptimality has been used to argue for Id, merely that it does not prove that ID is not true. I would like to see an example of suboptimality argued as a case for intelligent design.

  14. 14
    REC says:

    Colin,

    ID certainly must accept suboptimal design, or it has to account for the array of better possibilities that could be. Dr. Dembski’s “Design is not Optimal design” strongly makes this point, and suggests imperfect design may be a hallmark of intellegent design.

    “intelligent design refuses to speculate about the nature of this designing intelligence. Whereas optimal design demands a perfectionistic, anal-retentive designer who has to get everything just right, intelligent design fits our ordinary experience of design, which is always conditioned by the needs of a situation and therefore always falls short of some idealized global optimum. ”
    “No real designer attempts optimality in the sense of attaining perfect design.”

    A quick google search turned up a number of persons advocating suboptimal design as a hallmark and cheering point for ID. I would agree with them on some points.

    http://www.willedinduction.com.....esign.html

    “The fact that one is designed sub-optimally does not deny an intelligent designer. Quite the opposite is true, and I would submit to you that the lesser design points to a very ingenious mind operating perhaps with available materials. Both are marvels of engineering and the obvious product of intelligent design.”

    “The science of intelligent design theory quickly disposes with such moral objections through the simple observation that even things with an evil moral purpose can be intelligently designed. Torture chambers and electric chairs, terrible as they may be, are full complex specified information…. all designers may not intend for all aspects of their designs to perform at the highest possible levels…Every engineer realizes that when designing a machine, one must act within design constraints. Sometimes one aspect of the functionality of a machine must be compromised in order to allow for another more crucial design parameter to be met. The final result is a machine that has overall optimal design, though perhaps functioning at a lower than possible level of performance with regards to some particular aspect of functionality. “

  15. 15
    REC says:

    Sorry….missed a link for the third quote

    http://www.ideacenter.org/cont.....hp/id/1172

  16. 16
    hrun0815 says:

    Thanks REC for doing the footwork in answering Collin. I had just started to start googling for examples when I saw that you posted a bunch of examples already.

  17. 17
    Mung says:

    hrun0805:

    Interestingly, the ‘It’s a win for them’ also applies to ID. Many times optimality has been used to suggest design and likewise (see post #1) has suboptimality.

    The whole concept of optimality (and so therefore also suboptimality) is incoherent in a non-teleological world.

    So why is it that biologists, who are incessant in their rejection of teleology, insist on using these teleological terms? Can’t they get by without them?

    And now, in case you missed it, you know why both these terms are meaningful and relevant to ID, but not available to the non-ID crowd.

  18. 18
    REC says:

    Mung,

    In the original article, I don’t see the word “optimal”.

    Rather, I see “inefficient.” Enzyme efficiencies can be measured as a catalytic constant, or preferably Kcat/Km. The scale would range from a non-catalyst of 0 to a protein like carbonic anhydrase, which catalyzes 10 million reactions per second. Rubisco does 3. So it is pretty inefficient.

    Nature’s decision to talk about design (implying a criticism relying a notion of optimal design) is short-sighted. However, efficiency seems to be a well-grounded scale.

  19. 19
    hrun0815 says:

    Mung writes:

    The whole concept of optimality (and so therefore also suboptimality) is incoherent in a non-teleological world.

    So why is it that biologists, who are incessant in their rejection of teleology, insist on using these teleological terms?

    Well, there are only very few choices:

    1) Biologists actually favor teleology but claim not to.
    2) Biologists are simply blissfully incoherent and all of them are too stupid to notice
    3) Maybe there is a reason for them to use teleological terms to describe non-teleological phenomena.

    Can’t they get by without them?

    Maybe they can’t. Have you any thoughts as to why?

    And now, in case you missed it, you know why both these terms are meaningful and relevant to ID, but not available to the non-ID crowd.

    This sentence, in case you missed it, strikes me as incoherent.

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