A Biologic Institute challenge to Darwinism: two protein chains, combined length over 1,400 amino acid residues

_{Denyse O'Leary

May 1, 2012

Cell biology, Intelligent Design, News}

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In “Intricate Co-ordination”(Biologic Perspectives,, April 30, 3012), Biologic Institute senior scientist Ann Gauger explains,

Meet carbamoyl phosphate synthetase (CPS), a remarkably complex enzyme. This enzyme uses bicarbonate, glutamine, ATP, and water to make carbamoyl phosphate via a multi-step reaction at three separate active sites, involving several unstable intermediates. [details linked]

CPS is made of two protein chains with a combined length of over 1,400 amino acid residues. We now know from extensive biochemical data that a fully coupled CPS requires the hydrolysis of one glutamine and two molecules of MgATP for every molecule of carbamoyl phosphate formed. …

…

How does a neo-Darwinian process evolve an enzyme like this? Even if enzymes that carried out the various partial reactions could have evolved separately, the coordination and combining of those domains into one huge enzyme is a feat of engineering beyond anything we can do. More.

Note: Biologic Institute is not to be confused with Biologos. The former is a research group that agrees that there is design in nature, and publishes journal papers on relevant issues. The latter was founded by NIH head Francis Collins to help theologians and scientists promote Darwinism to Christians.

Comments

In “Intricate Co-ordination”(Biologic Perspectives,, April 30, 3012), Biologic Institute senior scientist Ann Gauger...
Just thought I'd point out that we're not one thousand years in the future ;)Genomicus_{May 2, 2012
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"...the “tons” of scientific poofs .." Sorry, I meant to write "proofs", even if in the mistake there's an hidden onomatopoeic meaning that...;)Jonin_{May 2, 2012
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One of the most disappointing discovery in my recent insights on the evolutionary thinking, especially about the "hard" and "heavy" science that support it, was that almost the strongest argument in support for it is relied on comparisons. Genetic sequences comparisons, body plans comparisons, bones comparisons, phenotype comparisons. That's really sad... I thought there were lots of scientific "wonders" in the "backstage" of one of the most followed theory of the last two centuries but, reading, for example, in Lodish's "Molecular cell biology" - by the way an excellent book that, at the very least, doesn't mention all the "iconographic" stuff like finches, moths, archaeopterix, etc - all those speculations and conjectures just because "..sequences analysis demonstrate the evolution.." of "this" or "that" made me extremely unsatisfied.. I can really imagine the disappoint of YOU guys when I read comment like the one above by Nick Matzke.. But the thing that truly impressed me in this case is the "tons" of scientific poofs that a guy like him should "use" to criticize Gauger's and Axe's excellent work, instead of pointing out [only] to [the same] mere comparisons pubblications.. http://en.wikipedia.org/wiki/Nick_Matzke "..the former Public Information Project Director at the National Center for Science Education (NCSE).." Ooops, I really didn't know...:(Jonin_{May 2, 2012
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Here is corroborating evidence that 'protein specific' quantum information/entanglement resides in functional proteins:
Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/
Moreover, another fact that is completely contrary to neo-Darwinian thinking, besides 'regulated errors', is the fact that mathematical information is now found to reside along the entirety of a protein chain, constraining the protein chain to a specific function;
Proteins with cruise control provide new perspective: "A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order." http://www.princeton.edu/main/news/archive/S22/60/95O56/
Cruise Control permeating the whole of the protein structure??? This is an absolutely fascinating discovery. The equations of calculus involved in achieving even a simple process control loop, such as a dynamic cruise control loop, are very complex. In fact it seems readily apparent to me that highly advanced mathematical information must reside 'transcendentally' along the entirety of the protein structure, in order to achieve such control of the overall protein structure. This fact gives us clear evidence that there is far more functional information residing in proteins than meets the eye. Moreover this ‘oneness’ of cruise control, within the protein structure, can only be achieved through quantum computation/entanglement principles, and is inexplicable to the reductive materialistic approach of neo-Darwinism! For a sample of the equations that must be dealt with, to 'engineer' even a simple process control loop like cruise control for a single protein, please see this following site:
PID controller A proportional–integral–derivative controller (PID controller) is a generic control loop feedback mechanism (controller) widely used in industrial control systems. A PID controller attempts to correct the error between a measured process variable and a desired setpoint by calculating and then outputting a corrective action that can adjust the process accordingly and rapidly, to keep the error minimal. http://en.wikipedia.org/wiki/PID_controller
It is in realizing the staggering level of engineering that must be dealt with to achieve ‘cruise control’ for each individual protein, along the entirety of the protein structure, that it becomes apparent even Axe’s 1 in 10^77 estimate for rarity of finding specific functional proteins within sequence space is far, far too generous. In fact probabilities over various ‘specific’ configurations of material particles simply do not even apply, at all, since the 'cause' of the non-local quantum information does not even reside within the material particles in the first place (i.e. falsification of local realism; Alain Aspect, Anton Zeilinger). Here is corroborating evidence that 'protein specific' quantum information/entanglement resides in functional proteins and DNA:
Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/ Quantum Information/Entanglement In DNA - short video http://www.metacafe.com/watch/5936605/
In fact since quantum entanglement/information falsified reductive materialism/local realism in the first place (Alain Aspect; Anton Zeilinger) then finding quantum entanglement/information to be ‘protein specific’ is absolutely shattering to any rational hope that materialists had in whatever slim probabilities there were for specific functional protein sequences, since a ‘transcendent', 'non-local’, cause must be supplied which is specific to each unique protein structure. Reductive materialism, which is the basis of neo-Darwinian thought, is simply at a complete loss to supply such a 'non-local' transcendent cause, whereas Theism has always postulated a transcendent 'non-local' cause for life! Though the authors of the 'cruise control' paper tried to put a evolution friendly spin on the 'cruise control' evidence, for finding such a highly advanced 'Process Control Loop' at such a base molecular level, (before natural selection even has a chance to select for any morphological novelty that a protein may have from 'random' mutations), the fact is that this strict limit to the variability of a protein, imposed by the quantum information of a protein to the protein's specific function, is very much to be expected from a Intelligent Design/Genetic Entropy viewpoint, and this finding is in fact a very constraining thing to the amount of variation we should reasonably expect from any specific protein in the first place! As well, needless to say, the overall implications of finding non-local quantum information in life on a massive scale are staggering to put it mildly!!!
Quantum Entangled Consciousness - Life After Death - Stuart Hameroff - video http://vimeo.com/39982578 Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068
Music and verse
Carrie Underwood - Temporary Home http://www.youtube.com/watch?v=LraOiHUltak Matthew 6:19-21 "Do not store up for yourselves treasures on earth, where moth and rust destroy, and where thieves break in and steal. But store up for yourselves treasures in heaven, where moth and rust do not destroy, and where thieves do not break in and steal. For where your treasure is, there your heart will be also.
bornagain77_{May 2, 2012
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As Nick Matzke repeatedly makes clear on this and other sites, and as Dr. Gauger has briefly pointed out here, there is a profound disconnect between what neo-Darwinists presuppose to be true for the ability of a functional protein to easily change into other proteins of other functions and from what the laboratory work has very strongly indicated. Laboratory work indicating that such changes in functional protein sequences to other functional protein sequences are impossible. The fact of the matter is that the sequence comparisons that Nick, and other neo-Darwinists, repeatedly refer to, (as if the sequence comparisons themselves are the conclusive proof they need for the very thing they are presupposing to be true), is not supported in the least by solid empirical research. Needless to say, without a firm demonstration that proteins, any proteins at all, can actually change from one function to another different function, by a step by step gradual Darwinian process, one is not even in the field of rigorous empirical research with such careless and unsubstantiated rhetoric, but one is left completely adrift in a world of pure speculation and imagination. Clearly, such unsupported dogmatic claims, by neo-Darwinists, of the ability of functional proteins to easily change into other functional proteins, by step by step neo-Darwinian processes, is completely antagonistic to the practice of good science. It is hard to believe that neo-Darwinists can actually get away with such tripe and call it science! Notes:
Nothing In Molecular Biology Is Gradual - Doug Axe PhD. - video http://www.metacafe.com/watch/5347797/ "Charles Darwin said (paraphrase), 'If anyone could find anything that could not be had through a number of slight, successive, modifications, my theory would absolutely break down.' Well that condition has been met time and time again. Basically every gene, every protein fold. There is nothing of significance that we can show that can be had in a gradualist way. It's a mirage. None of it happens that way. - Doug Axe PhD. When Theory and Experiment Collide — April 16th, 2011 by Douglas Axe Excerpt: Based on our experimental observations and on calculations we made using a published population model [3], we estimated that Darwin’s mechanism would need a truly staggering amount of time—a trillion trillion years or more—to accomplish the seemingly subtle change in enzyme function that we studied. http://www.biologicinstitute.org/post/18022460402/when-theory-and-experiment-collide Wheel of Fortune: New Work by Thornton's Group Supports Time-Asymmetric Dollo's Law - Michael Behe - October 5, 2011 Excerpt: Darwinian selection will fit a protein to its current task as tightly as it can. In the process, it makes it extremely difficult to adapt to a new task or revert to an old task by random mutation plus selection. http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html Stability effects of mutations and protein evolvability. October 2009 Excerpt: The accepted paradigm that proteins can tolerate nearly any amino acid substitution has been replaced by the view that the deleterious effects of mutations, and especially their tendency to undermine the thermodynamic and kinetic stability of protein, is a major constraint on protein evolvability,, http://www.ncbi.nlm.nih.gov/pubmed/19765975 Corticosteroid Receptors in Vertebrates: Luck or Design? - Ann Gauger - October 11, 2011 Excerpt: if merely changing binding preferences is hard, even when you start with the right ancestral form, then converting an enzyme to a new function is completely beyond the reach of unguided evolution, no matter where you start. http://www.evolutionnews.org/2011/10/luck_or_design051801.html “Mutations are rare phenomena, and a simultaneous change of even two amino acid residues in one protein is totally unlikely. One could think, for instance, that by constantly changing amino acids one by one, it will eventually be possible to change the entire sequence substantially… These minor changes, however, are bound to eventually result in a situation in which the enzyme has ceased to perform its previous function but has not yet begun its ‘new duties’. It is at this point it will be destroyed” Maxim D. Frank-Kamenetski, Unraveling DNA, 1997, p. 72. (Professor at Brown U. Center for Advanced Biotechnology and Biomedical Engineering) "A problem with the evolution of proteins having new shapes is that proteins are highly constrained, and producing a functional protein from a functional protein having a significantly different shape would typically require many mutations of the gene producing the protein. All the proteins produced during this transition would not be functional, that is, they would not be beneficial to the organism, or possibly they would still have their original function but not confer any advantage to the organism. It turns out that this scenario has severe mathematical problems that call the theory of evolution into question. Unless these problems can be overcome, the theory of evolution is in trouble." Problems in Protein Evolution: http://www.cs.unc.edu/~plaisted/ce/blocked.html Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors - Doug Axe Excerpt: Contrary to the prevalent view, then, enzyme function places severe constraints on residue identities at positions showing evolutionary variability, and at exterior non-active-site positions, in particular. http://nsmserver2.fullerton.edu/departments/chemistry/evolution_creation/web/AxeProteinEvolution.pdf Darwin's God: Post Synaptic Proteins Intolerant of Change - December 2010 Excerpt: Not only is there scant evidence of intermediate designs leading to the known proteins, but the evidence we do have is that these proteins do not tolerate change. http://darwins-god.blogspot.com/2010/12/post-synaptic-proteins-intolerant-of.html
As well, the vast majority of 'errors/mutations' that are found to 'naturally' occur in protein sequences, which are 'suppose' to be the driving force for Darwinian evolution of phenotypes, are actually found to be 'designed errors'. Designed errors of a 'non-random' nature:
Cells Defend Themselves from Viruses, Bacteria With Armor of Protein Errors - Nov. 2009 Excerpt: These "regulated errors" comprise a novel non-genetic mechanism by which cells can rapidly make important proteins more resistant to attack when stressed, http://www.sciencedaily.com/releases/2009/11/091125134701.htm
bornagain77_{May 2, 2012
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Nick, All the evolutionary hypotheses concerning the evolution of CPS that I have seen are based on sequence and structural analysis only. No testing. In fact it would quite interesting to see if the hypothetical fusions and duplications that supposedly formed the first CPS in the first cells can be accomplished by purely undirected processes. A worthy experiment indeed. But until it has been shown that such a process can in fact generate an enzyme capable of channeling unstable intermediates from one active site to the next, these remain hypotheses only. The problem is that similarity of sequence *alone* does not establish the existence of a plausible evolutionary path.gauger_{May 1, 2012
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Re: BioLogic’s challenge about carbomoyl phosphate synthetase evolution. Here, let me google that for you: http://lmgtfy.com/?q=evolution.....synthetase
In keeping with the criteria set forth by Judge Jones in Ktzmiller v Dover SB, which article, Nick, demonstrates that blind and undirected chemical processes prodiced the carbamoyl phosphate synthetase? Or was that just ANOTHER literature bluff?Joe_{May 1, 2012
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Don’t you find it disturbing that dozens of researchers have worked on the exact question that Gauger asks, and that neither Gauger, nor the DI, nor BioLogic, could be bothered to do the elementary literature review Okay, I want to point this out. Nick has a gimmick. He's not really responding to me here, or really, to just about anyone who ever asks questions of him. He's playing to the lurkers. Which is why he says things that I know is ludicrous, and that HE knows is ludicrous - but which he hopes anyone reading won't realize is ludicrous. People who are glancing in, who don't follow these topics very close. It's a common gimmick - accuse someone you dislike of something, and even if it's completely baseless, just hope the charge sticks among the people who encounter it and then never hear about it again. He's saying that Ann Gauger and Douglas Axe - active researchers in this exact field - have "not done elementary literature review". Adorable claim. Just one problem: it's not only false, it's demonstrably false. And in this case, all that's necessary to do is to show the very work Ann cites, in that exact article and not only read it, but look at the references. Here's the thing: Nick knows this. He knows that Ann Gauger and Douglas Axe are actually doing research, and they aren't doing it in a vacuum. Right or wrong, they're consulting the work of their colleagues, they're commenting on it, and they are - as you can see in that link I just gave, and which Ann Gauger herself gave - documenting quite a lot of what they reference in the process. Now, Nick throws around the lazy/dishonest charge. I ask any onlooker here: who's lazy and dishonest? Ann Gauger, for writing up a blog entry which references the work of herself and Douglas Axe, which in turn lists dozens of references to other scientists' work on the relevant field? Or Nick Matzke, for claiming - not only sans evidence, but in direct conflict with the actual evidence on hand - that Axe and Gauger "coudl not be bothered to do the elementary literature review" in this field? I'll be waiting for your apology on this one, Nick. I mean, I know I won't be seeing that - it's not your MO, even when you've been proven dead wrong in a bold accusation. But I'll be waiting all the same. I've got a handy reference that may help you out, however.nullasalus_{May 1, 2012
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Don't you find it disturbing that dozens of researchers have worked on the exact question that Gauger asks, and that neither Gauger, nor the DI, nor BioLogic, could be bothered to do the elementary literature review that any serious scientific endeavor would require, and thus didn't bother to inform readers that a substantial amount of relevant work scientists have done? It's lazy/dishonest to not know this/not cite it. No scientist will ever take you guys seriously with this kind of self-imposed ignorance as your modus operandi. As for "fully address", no scientific explanation is ever complete, but it looks like we have a decent outline of how CPS evolved. It's detailed enough to test, which is all that matters in science. The ID requirement for infinite detail in evolutionary explanations is a ridiculous phantasm they conjure up when they are desperate and have nothing else to say (it's just a matter of time in this thread, I'm sure).NickMatzke_UD_{May 1, 2012
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Re: BioLogic’s challenge about carbomoyl phosphate synthetase evolution. Here, let me google that for you: Do ya find it at all damaging to your case that the links turned up in the search don't fully address the question you know is being posed here? Wait a sec, Nick. I think I know what answer to expect from you. ;)nullasalus_{May 1, 2012
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Re: BioLogic's challenge about carbomoyl phosphate synthetase evolution. Here, let me google that for you: http://lmgtfy.com/?q=evolution+carbamoyl+phosphate+synthetaseNickMatzke_UD_{May 1, 2012
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The latter was founded by NIH head Francis Collins to help theologians and scientists promote Darwinism to Christians. I don't know if this is a new edition, but Biologos' website now says under 'our beliefs':
We reject ideologies such as Deism that claim the universe is self-sustaining, that God is no longer active in the natural world, or that God is not active in human history. We reject ideologies such as Darwinism and Evolutionism that claim that evolution is a purposeless process or that evolution replaces God. We reject ideologies such as Materialism and Scientism that claim science is the sole source of knowledge and truth, that science has debunked God and religion, or that the physical world constitutes the whole of reality.
nullasalus_{May 1, 2012
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