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The Darwinism contradiction of repair systems

When a thing is false, is false from all points of view. In fact it cannot exist a point of view from which the thing becomes true, given it is false, rather each view point manifests a particular aspect of the falsity of the thing. As a consequence, when a thing is false, whether we suppose it is true we get contradictions, one for every point of view we consider the thing from. All that is simple logic.

When the above principles are applied to Darwinism (which according to ID theory is false) they make us conclude that Darwinism is false from all viewpoints and has internal contradictions. Of course the falsity of Darwinism is its fundamental axiom of unguided macroevolution: all biological complexity arose from a unique simple common ancestor only thank to random mutations and natural selection. RM and NS, individually taken, per se are not false, insofar they really happen. No one denies that and all appreciate Darwin who studied natural selection. The problem is in the infinitely stronger claim about the creative power of RM + NS contained in the fundamental axiom.

Here I will consider, among the Darwinism contradictions, that concerning the control-repair systems, which is particularly clear and easy to understand.

Molecular biology shows that many complex control-repair mechanisms work inside the cell to recover genetic errors. For example there are at least three major DNA repair mechanisms. Without such mechanisms life would be impossible because the internal entropy of the cell would be too high and destructive. Each of them involves the complex and coordinated action of several enzymes/proteins. See here.

In general, in its simplest form, a control-repair system B on a controlled system A is composed of two main parts: a control unit and a repair unit. See the following diagram:

rm

The control unit is able somehow to get an input scenario X from a specific point of the structure or the events-space of A. X is compared to a predefined correct scenario Y and the result is a Boolean value yes/no. This Y scenario is not a trivial thing because it implies that the control/repair system must know what should be the correct scenario in that particular point of A. If the result of the question “X match Y?” is “no” it is inputted into the repair unit. In turn the repair unit takes an action Z on A to recover partially or entirely the X situation. And here again the repair unit must have a (rich enough) correspondence table between the possible couples X,Y and the Z actions to be taken to fix the failure X. In a sense a feedback or loop must be created between the controlled system and the repair system. In another sense we could even say that in some cases between the controlled system and the control system must exist cCSI (see my previous post about “coupled complex specified information”). Repair systems of all sorts have to be designed frequently in engineering, but, despite the simplicity of the above diagram, they are often hard to implement.

At this point, before the presence of repair systems in the cells, one might asks why Darwinian processes create such systems, as evolutionary biology claims. After all what are random mutations but errors? If Darwinian processes are not based on errors are not Darwinian at all. Darwinism says us that random mutations and natural selection are a process that needs errors and in the same time this process creates mechanisms to eliminate them? Non sense, it should create mechanisms to produce errors instead, to accelerate macroevolution. Either Darwinian processes are based on DNA errors and then don’t create DNA-repair mechanisms deleting errors or Darwinian processes do create DNA and its repair systems and then Darwinian processes cannot be based on errors. You cannot have it both ways.

The bottom line is that repair mechanisms are incompatible with Darwinism in principle. Since sophisticated repair mechanisms do exist in the cell after all, then the thing to discard in the dilemma to avoid the contradiction necessarily is the Darwinist dogma.

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64 Responses to The Darwinism contradiction of repair systems

  1. Either Darwinian processes are based on DNA errors and then don’t create DNA-repair mechanisms deleting errors or Darwinian processes do create DNA and its repair systems and then Darwinian processes cannot be based on errors. You cannot have it both ways.

    You can have it both ways because the two ways are not mutually exclusive. Take a toy example of a simple replicator that generates variable copies of its self. It, on average, generates copies where fifty percent of the copies are not functional enough to make copies themselves. If one of the functional copies (one that can replicate) has a better replication system, one that produces seventy five percent success by avoiding some copying errors that are always catastrophic, then it is a more successful replicator and will be more likely to dominate, and pass on this better error correcting replication system to its offspring.

    This drive for generating good copies is balanced by differences and changes in the environment, which drives the need for variation by providing different niches for organisms to exploit, and changing resources that require different behaviours to exploit. There is no contradiction there, it is a balancing act between two different pressures.

    Variation is good, but too much variation is bad, so there are selection pressures to generate functional but different copies, but to not generate non functional copies. Repair mechanisms are entirely compatible with evolution, an organism that can produce functional copies of its self most of the time is fitter than one that produces bad copies of its self most of the time. You don’t need to start with a very good replicator either, as long as it produces good copies more than zero percent of the time then there is scope for some of those copies to do better.

  2. Mr BillB,

    I think you have to take the last part part of your argument and be a little more explicit about the reasoning, otherwise it looks like a teleologic argument “evolution knows it will need variation”.

    If a replicator gets too good at copying, say 99.9999… percent correct, it will continue to churn out copies. But another less perfect replicator will produce copies that contain a low level of error, not usually fatal, simply neutral variation. One of these variants will be better adapted to a change in the environment.
    So a perfect replicator is only expected to evolve in a completely static environment.

    Another approach is that perfect replication would be something that is difficult to evolve by natural processes in the first place. We know about ideas such as checksums and error correcting codes that are not used in DNA replication, but could be used to lower error rates further.
    So I doubt that the actual history of the worl saw a perfect replicator that was outcompeted by one that allowed errors at a low rate. I think the current systems are the best evolution could find before getting locked in by too much infra structure being built on top of them.

  3. BillB #1

    Your objection based on a balancing act between two different modalities, variation and stability, doesn’t avoid the contradiction. Repair mechanisms are not compatible with unguided evolution however because unguided implies blindness and non teleology. As you can see in my drawing of a repair system model, a repair mechanism must know (for definition) the correct Y scenario, both in the control and repair unit. This is a necessary (and not sufficient) condition for system repairing. You can fix an error only if you know the correct item, otherwise you not even detect the error (less than never you will repair it). Unguided evolution cannot know the correct items because is non teleological. As such repair systems are entirely out of its range of possibilities in principle. The selection pressures cannot act on nothingness.

  4. Nakashima,

    Fair point. I agree that perfect replication would never appear unless you had a static environment. I believe some people are investigation what is termed ‘the evolution of evolvability’ which roughly speaking investigates the ways in which selection pressures have shaped the reproductive mechanisms – reducing the likelihood of catastrophic errors whilst allowing for near neutral variation. Not really my area though.

  5. Mr Nirwad,

    I think you should check with the site admins, the images in your posts are not displaying.

    As Mr BillB showed, your logic is flawed by assuming that more is always better, or less is always better. There are many physical systems that work best in a zone inbetween extremes, a “Goldilocks” zone if you know that fairy tale.
    There are many systems that balance two separate forces to maintain a position for long periods, for example gravity vs light pressure in stars. The value of fidelity is balanced against the value of variation, in evolution of repair mechanisms.

  6. niwrad:

    The selection pressure acts on offspring. Error detection, without an error detection mechanism in the organism, occurs by selection. If the error reduces its ability to replicate then it won’t produce many or any copies.

    If, on the other hand, a copy is produced that then produces copies that are less prone to the error because of a change in the copying mechanism then you have, in effect, an error mitigation mechanism. No teleology is required, just a feedback loop via selection imposed from the environment on new generations.

  7. I look on the error mechanism of the cell as fantastic design. It is like Goldilocks’ porridge, not too hot and not too cold. It is just right. But it is just right for micro evolution and nothing else.

    If it could produce macro evolution, we would never hear the end of it from some very prominent irritants in our environment. And a good reason is because it may have been designed that way. Organisms need to adjust a little as environments change and variation is better then complete conformity. But too much variation creates chaos and probably quick extinction through the entropy you mention.

    But just enough error creates the necessary variants we see in our ecologies. It doesn’t go any further or else we would have seen it. The error system is a gradual but it is also a very limited one as we have seen in nature. It can not explain the more complicated differences between many species.

    But you are right, the Goldilocks system we have does not make sense in terms of Darwinian processes. It would not know when to stop.

    A related book on this topic is Ray Bohlin’s The Natural Limits to Biological Change which goes into just what the title says. There seems to be a biological limit on change built into organisms. Why don’t certain organisms take over an ecology and in the end destroy themselves. There is nothing Darwinian in limiting their change because it is their own reproduction rate that is at stake and in the short run they do not know the long run that will cause them to go extinct as they get faster, smarter, bigger etc and destroy their neighbors and the ecology essential for their existence.

  8. the Goldilocks system we have does not make sense in terms of Darwinian processes. It would not know when to stop.

    There is a feedback loop via selection that imposes limits and prevents the systems running away to an extreme.

    Why don’t certain organisms take over an ecology and in the end destroy themselves.

    I think they do sometimes, but more often than not an organism that takes over will also present opportunities for other organisms to exploit new niches, counterbalancing the organism that is taking over.

  9. BillB:

    Take a toy example of a simple replicator that generates variable copies of its self.

    And where do you get that from- a magic shop?

    Ya see BB, your scenario can’t even get started.

  10. Nakashima #5

    Thanks for your warning about the missing picture. WordPress has a bug in inserting images into a post (clearly a Darwinian mutation not yet corrected by the evolutionary repairing system … ) Now it should be ok.

  11. Joseph,

    I borrowed one from Von Neumann.

  12. The most obvious thing, that Darwinists are never able to see, is that there is no such thing as an error detection/correction system without knowledge of what the correct system state should be.

    So, as per the OP, these mechanisms intrinsically imply intelligence.

    You cannot detect error without knowledge of correct state and a means of measuring current state. You cannot repair it unless you can detect it.

    All of this clearly argues for teleology in the origin of the cell.

    Programmers all know this.

    We find the same kind of exception trapping logic and mechanisms in DNA that they build into their applications to preempt errors from crashing the system.

    Amazing that Darwinists believe this is just pure luck.

    Amazing that they can think the very mechanisms which prevent the cell from ‘wandering’ too far off its correct system state, are also the very things that make it do so!!

  13. Borne,

    Darwinism explains everything. Even counter-intuitiveness. How you ask? Because that’s how it evolved.

  14. By the way, I think it’s pivotal to note that we aren’t merely talking about an organism’s natural tendency toward stasis. We’re talking about its capacity to take corrective action when said stasis is interrupted by error.

    First there must be a known correct state as Borne mentioned. Then there must be a method in place to make specific changes to return to this correct state when error is introduced. It’s also worth noting that this system must cater to each and every specific error within its capacity to repair, each of which may need to be handled differently. The sophistication of the error detection within repair mechanisms and the method in which each one carries out repair must not be taken for granted.

    This goes quite a large leap beyond the “because that’s how it evolved” stories I’ve seen so far in this thread.

  15. By the way, it’s good to see you’ve returned Nakashima-san.

  16. What a great entry niwrad. The repair mechanism itself must be updated as the organism (supposedly) mutates. The same random mutations that are “advancing” the creature must be updating the repair mechanism to recognize the new state! All unguided without previous knowledge of where the design is going. Not…

    Excellent post to expose how quickly Darwinism breaks down in the details. Look at the details and see the vast gap between what changes random mutations actually impart and what Darwinism needs them to be able to accomplish.

  17. …of course niwrad you speak to the amazing complexity behind the notion of actually monitoring a mechanism and encoding and storing the correct state for comparison.

    But once change occurs…how does the undirected mutation know that this is a good change and should now be a part of the stored correction information used for comparisons?

    Another dilemma that invalidates Darwinism since by definition there is no way to know if the change wrought by the mutation is good and should be kept around until it is selected….

    …and even if somehow some part of the process knows its a good change, the complexity of updating the repair information is way beyond the ability of “undirected” processes.

  18. “There is a feedback loop via selection that imposes limits and prevents the systems running away to an extreme.”

    Nonsense. If such a thing happened it would be happening all the time and there is no documentation for this. It would have to have foresight to know it is heading on a deadly course and that is verboten.

  19. It would have to have foresight to know it is heading on a deadly course . . .

    Does the organism need foresight to reproduce?

    If you produce offspring and some of them fail to reproduce then the traits they inherited, or acquired by variation, that caused them to fail do not get passed on any further.

    If some of your offspring succeed in reproducing then they pass on some of the traits that lead to successful reproduction, including any improvements in self repair and replication mechanisms.

    No foresight is required, just descent with modification filtered through selection.

  20. We’re not talking about “improvements” here. We’re are talking origins.

  21. jerry,

    It would have to have foresight to know it is heading on a deadly course . . .

    density dependent selection is one way what BillB is talking about occurs. e.g. when a population gets too big, selection starts to favor different life history traits that may slow down population growth. an experimental example can be found here:

    http://www.sciencemag.org/cgi/.....3/5018/433

  22. tragic mishap:

    So in order to explain how error correcting mechanisms might arise in pre-existing self replicating systems, we need to first explain how non-error correcting self replicating systems originate?

  23. “Does the organism need foresight to reproduce?

    If you produce offspring and some of them fail to reproduce then the traits they inherited, or acquired by variation, that caused them to fail do not get passed on any further.

    If some of your offspring succeed in reproducing then they pass on some of the traits that lead to successful reproduction, including any improvements in self repair and replication mechanisms.

    No foresight is required, just descent with modification filtered through selection.”

    I am sorry but this is a non sequitur. All you have stated is a truism that has nothing to do with the issue. Why would a mechanism for a lower correction rate succeed better when there is no need for it. We know that a higher correction rate produces more offspring since they are already viable but a lower correction rate by definition is problematic yet this one that can foresee the possibilities of the future are somehow allowed to flourish.

    A perfect correction rate produces variation if it already exists so the need for variation in the offspring to face a new environment is not a normal issue. There is no need for a lower correction rate that would leave more offspring. But it could be designed that way.

  24. Mr PaulN,

    Thank you for your good wishes. I was in Europe for a few weeks with limited access to a computer. But I did get to visit the Mendel Museum in Brno, which I found a very powerful experience.

  25. jerry,

    A perfect correction rate produces variation if it already exists so the need for variation in the offspring to face a new environment is not a normal issue. There is no need for a lower correction rate that would leave more offspring. But it could be designed that way.

    you are confusing individual- and population-level variation. a perfect correction rate (in asexual organisms), at an individual level, would produce clones that would all be wiped out if the environment changes. if one of the offspring has a slight variation created by a less-than-perfect replication, it might allow that individual offspring to survive. 1>0, so imperfect correction evolves.

  26. 26

    niwrad:

    What a wonderful arguument. The Darwinists are left asserting that a sophisticated error-checking system “just can” come into existence via random mutation and then “just happen” to get perfectly set for macroevolution by failing to correct itself when errors appear in its coding; and then just happens to fail to correct some mutations and then just happens to itself become mutated in synthesis to the other mutations so that it doesn’t error correct that mutation …

    ROFLMAO!!!!

  27. BillB,

    If you produce offspring and some of them fail to reproduce then the traits they inherited, or acquired by variation, that caused them to fail do not get passed on any further.

    Not necessarily. Just because a finch has a short beak does not mean it doesn’t have the genetic information for a long beak as well. When talking about inherited traits, then dormant and active traits must be accounted for. If a parent passes on a bad gene to its 4 children, and only one of those children expresses the failed trait and consequently fails to reproduce, then that leaves the other 3 to continue to pass it on. Errors can still grow exponentially while circumventing selection altogether. Again, simple Mendelian genetics. It seems the only thing preventing such tendencies from total catastrophe is in fact said repair systems, which Darwinian explanations fail to well… explain. You can say that an error-driven system produces error-checking repair systems. You can also say that record low temperature trends = catastrophic global warming.

    Nakashima-san,

    Wow, sounds like a great trip! I’ve always been a fan of Mendel. If you don’t mind me asking, what was it like?

  28. I am very certain that error correction can not evolved. (de Visser j.A., R. E. 2002. Long-term experimental evolution in Escherichia coli. XI Rejection of non-transitive interactions as cause of declining rate of adaptation.) In this experiment DNA repair mechanisms broke got pass natural selection. Error repair does give the cells that have it ,get it very very little advantage over those who don’t. Plus with out error correcting mechanisms the mutation rate goes up and what natural selection can see goes down. I very sure that in that cause natural selection will not see Error repair.

  29. I’ve been thinking this for a while and it needs to be fleshed out.

    How does a system based on errors create an error-control system? It would undermine itself. At the very least, it is going against the flow.

    Darwinism is unfalsifiable so I’m not sure that this will be a deathblow, but it should at the very least give food for thought.

    And I would hazard a guess that error control systems are irreducibly complex themselves, but that’s another story.

  30. thanks Murray – to me its like someone needed to inject some sanity into this – some “perspective” some common sense. Isn’t it fascinating just how much humans can create such imaginative scenarios simply because they want to and to them their story actually makes sense. To me it the choice (to want that story) that makes credulous such stories. How many falsifying points of view are needed to change such a desire? Thanks niward for this (from so many) one point of view.

  31. p.s. ROFLMAO = ?

  32. I’m personally very glad to see this thread. I’ve been arguing for design based on biological error detection/correction mechanisms for years and most of the time the Darwinist elements (and even some IDists) just don’t seem to “get it”.

    I never could understand how anyone could miss it!

    Its just so obvious that detecting errors and ‘knowing’ how to correct them, intrinsically implies knowledge of correct system state.

    I mean, take the teacher watching the student writing a sentence. When the student writes say, ‘inteligents’ instead of ‘intelligence’ – the teacher spots the error ONLY because she *knows* what the word is (by subconscious pattern recognition) and how it is supposed to be alphabetically sequenced!

    There is no other possibility, So why hasn’t this specific argument not showed up in any of the many books I’ve read on arguments for ID? It’s not something hard!

    I’ve never understood why this aspect of cellular machinery has not been more efficiently exploited by the ID community.

    Anyone have any ideas on that?

    Thanks again niwrad!

  33. ROFLMAO = Rolling On the Floor Laughing My A** Off.
    Check here from now on – its getting to be vital on the web!

  34. Bill, you claimed that Darwinian process could explain any “improvements in self repair and replication mechanisms.”

    If you meant that Darwinian processes could explain the “origin” of self-repair mechanisms, than perhaps you should restate your assertion. You kind of tied the issue of self-replication and self-repair together, when they are separate. You also talked about “improvements” when we are talking about origins. If that’s what you meant, than ok, but it’s a bit off-topic. If it’s not what you meant please clear it up for me.

    Thanks.

  35. Dar-win is a misnomer, Dar-lose is more accurate.

  36. Mr PaulN,

    The Mendel Museum is located in the Augustinian Abbey in Brno. Mendel entered as a monk and eventually became Abbot. The museum covers all aspects of his life, and how the Abbey supported basic science in the 19th century. Mendel’s experiments are given context in his life and society. Basic genetic principles of heredity are reviewed to explain Mendel’s data gathering. The exhibits are very modern. You can view the garden where Mendel’s experiments were carried out.

    The exhibits make clear that Mendel was aware of Darwin’s work. He read several of Darwin’s books in German translations. Mendel’s copy of OoS with his pencilled marks is still in the Abbey Library. He was just finishing his experiments when he read OoS and marked several passages where his results were at odds with Darwin’s ideas about heredity.

    I also visited Olomouc to see the university where Mendel went to school.

  37. Tragic:

    The issue of self replication and self repair are tied together by niwrad:

    Molecular biology shows that many complex control-repair mechanisms work inside the cell to recover genetic errors.

    This is referring to internal self repair mechanisms in an organism.

    before the presence of repair systems in the cells, one might asks why Darwinian processes create such systems, as evolutionary biology claims. After all what are random mutations but errors? If Darwinian processes are not based on errors are not Darwinian at all.

    And this is referring to reproductive errors.

    Niwrad also states:

    RM and NS, individually taken, per se are not false, insofar they really happen.

    The two different issues here, that of internal repair mechanisms and of errors in copying, are both related in that they both affect reproductive success, and are therefore regulated by selection.

    Niwrad makes this claim as well:

    For example there are at least three major DNA repair mechanisms. Without such mechanisms life would be impossible because the internal entropy of the cell would be too high and destructive.

    This may be true when looking at a modern single celled organism but is it true of a much simpler self replicating system? How can we establish if any of the simplest possible self replicators actually require error correcting mechanisms to function? Bear in mind that ‘function’ in this context simply means the ability to produce at least one copy that is also capable of producing a copy, so the error rate in reproduction and the likelihood of the entity falling apart can be very high.

    When you have an entity like this, one that can just about manage to copy its self successfully, and one that introduces some variety into those copies, then you are generating variety in both the internal stability of the organism and in its ability to generate functional copies, so the two issues are tied together via reproduction, variation and selection.

    I happen to agree that there are plenty of interesting and difficult questions surrounding the ways in which simple self replicators can function, and the way they can vary. This impacts on the possible ways in which self repairing mechanisms can arise, but I think the lines between internal stability and active repair are blurred. Can slight modifications to an organisms molecular structure increase its resilience and stop it falling apart as fast, and if so where do you draw the lines between these structural improvements and what we would observe to be a self repair mechanism?

    On the issue of foresight, I just don’t see why it is needed provided you have variety and selection. These provide a mechanism for rejecting errors already, it just happens at the generational level rather than within an individuals life cycle. The process of descent with modification coupled with the filtering effect of selection can generate variety, and will select for variations that reproduce better, both by regulating errors in copying, and by improving the stability of the entities during their lives.

    In terms of the idea of structural stability and error correction, try this very simplified example. You have an entity and part of that entity has an aperture that allows molecules to pass through, the aperture is large and admits many types of molecule, some of which will damage or destroy the entities ability to function. The entity can reproduce, and during reproduction the copies have apertures of varying shapes and sizes – structural differences. The entities from the parent generation might have low reproductive success rates because there is a high probability that some will suffer damage, but those that do manage to reproduce may produce copies with an aperture that admits fewer harmful molecules, and increases their reproductive success. This structural change in the aperture functions as an error checking mechanism and to an observer we could look at it in terms of niwrads diagram and say that it is checking molecules to see if they are ‘correct’. No foresight is required, just variation in structure.

  38. BillB #37

    The process of descent with modification coupled with the filtering effect of selection can generate variety, and will select for variations that reproduce better, both by regulating errors in copying, and by improving the stability of the entities during their lives.

    You cannot have in the same time and in the same mechanism variety and stability, variations (read errors) and errors “regulation” (read deletion), exactly as you cannot have a single figure that in the same time is a circle and a square.

    You have an entity and part of that entity has an aperture that allows molecules to pass through, the aperture is large and admits many types of molecule, some of which will damage or destroy the entities ability to function. The entity can reproduce, and during reproduction the copies have apertures of varying shapes and sizes – structural differences. [...] This structural change in the aperture functions as an error checking mechanism and to an observer we could look at it in terms of niwrads diagram and say that it is checking molecules to see if they are ‘correct’. No foresight is required, just variation in structure.

    Your example is not an implementation of a repair system (as illustrated in my block diagram). DNA error-checking mechanisms, which are real repair systems, work on the basis of what is correct and what is not correct in the DNA string. They don’t work on the terms of global fitness or reproductive capacity or other selection functions. They work for the stability of DNA and to decrease its degeneration. We could say that they work specifically and locally to fix errors based on the knowledge of the relative correct values.

    In your natural selection example there is a fitness function which globally selects individuals, eliminating the unfitted. This selective force can be unintelligent because its job is easy. Natural selection doesn’t work based on knowledge. Natural selection at the very end is simply the survival of the fittest and the death of the unfitted. Selection is the individuals.

    As a consequence, to compare your selection example with a real repair system is like to compare a horizontal bar placed at 2 m that selects who jumps it and who doesn’t with a math prof while correcting a student on a formula.

  39. You cannot have in the same time and in the same mechanism variety and stability, variations (read errors) and errors “regulation” (read deletion)

    Yes you can. Simple control systems admit errors. Take a simple proportional controller for example, perturbing it will introduce an error but it will also try and oppose the error with more effort as it gets larger. If you have a weak proportional control it will admit a wide variety of errors (variation) but still try and limit these errors to maintain a degree of stability.

    The example I used works to reduce errors that occur when the entity is functioning, the refinement of that error reduction system occurs via reproduction with modification and selection for individuals with better error correction. It is not as refined as your diagram but it is a step towards a more refined system.

  40. Mr Nirwad,

    Just to be specific, you are claiming that photolyase could not evolve, correct?

  41. Bill, you simply don’t understand the kind of repair mechanisms we are talking about. Are you really suggesting that membrane-spanning proteins involved in chemical transport evolved into DNA-binding enzymes with active sites that do not reside in membranes but as globular proteins in the nucleus? That is the most ridiculous story I have ever, I repeat, ever heard from an evolutionist. If you have any sort of evidence for this, I would wet my pants and suck them clean.

  42. Tragic,

    I’m making no such claim anywhere, I’m just trying to illustrate how niwrad’s idea that foresight is required to construct regulatory mechanisms doesn’t seem to hold true. If you want a detailed explanation for how the particular cellular mechanism arose then you might want to ask a cell biologist.

    Do you have any evidence, beyond your own personal disbelief, that these mechanisms can ONLY be the result of design? If not then what is wrong with trying to understand how they might be a result of evolution or other natural processes, rather than assuming design and closing the book?

  43. BillB:

    If only the scientific community would show the objectivity and open-mindedness you suggest.

    Do you have any evidence, beyond your own personal disbelief, that these mechanisms can ONLY be the result of design? If not then what is wrong with trying to understand how they might be a result of evolution or other natural processes, rather than assuming design and closing the book?

    Switch design and natural processes in that statement and get everyone to agree that we should keep an open mind and examine the evidence before jumping to conclusions and closing the book. Half of this debate will disappear.

  44. Nakashima #40

    I am claiming that any error-correction mechanism cannot evolve by mean of a process of random errors inside a complex system. A process of random variations is non teleological for definition (randomness has no purpose). A repair system is teleological for definition (has the purpose of fixing errors because “know” how things should be). Here “know” has to be intended in metaphorical sense, in that the real knowledge is in the designer, who necessarily knows the controlled system and its repair mechanisms. A teleological thing cannot arise from a non teleological thing. In other words, purpose or goal cannot come from nothingness.

    About the photolyase enzymes, since after all they repair damages in DNA, they belong to the group of repair systems. Of course there are many different kinds of repair systems, depending on how the control unit detects the wrong X scenario (see my drawing), on how it compares X to the correct Y scenario, on how it interfaces with the repair unit, and what action Z the repair unit takes. The details of how photolyase works are sure very different from those of the three DNA repair systems I referenced in my post. Nonetheless photolyase repairs, doesn’t destroy the DNA information and this is what matters.

    As a general principle, consider that repairing and correction are things going directly against the thermodynamic trend towards disorder (entropy). The default trend in nature is disorder, not order. The natural evolution of all non intelligent things is towards errors, not towards repairing errors. Also from this viewpoint repair mechanisms cannot be “natural” and have to be designed.

  45. Scott:

    Its the old debate about what constitutes evidence FOR design, as opposed to just a gap in existing knowledge which can be filled by invoking an unknown designer with unquestionable motives. Evolution is a known mechanism, how and if it can account for some cellular mechanisms is an on-going research project.

    niwrad presented, or seemed to present, a lack of knowledge as evidence for design. I suspect that cell biologists who are studying these systems perceive less of a gap than onlookers but, like niwrad, I am not an expert, I just don’t see these gaps as ones that can ONLY be filled by design.

    Contrary to what some on this forum might believe there are plenty of scientists, cell biologists included, who will entertain the idea of an intelligent creator, what they don’t do is conclude that a creator intervened to produce a mechanism before science has come to a thorough understanding of the mechanism in question, and how it relates to other, known natural processes.

  46. BillB:

    there are plenty of scientists, cell biologists included, who will entertain the idea of an intelligent creator, what they don’t do is conclude that a creator intervened to produce a mechanism before science has come to a thorough understanding of the mechanism in question, and how it relates to other, known natural processes.

    And yet, given that same absence of information, many seem to have no problem concluding that an as-of-yet unexplained series of accidents produced the same mechanisms.

    I don’t fault your reasoning. But if we applied it without bias we would have to honestly admit that we don’t know the cause.
    Instead “science” seems to assume a vague cause and rule out any line of inquiry that doesn’t seek to specify and validate it.

  47. If we knew empirically that some features of the cell were the product of design then it might be reasonable to ask if other features might also be the result of design.

    We do know that some features of the cell can be explained by the process of evolution so it is not unreasonable to ask if other mechanisms might also be the result of evolution.

    But if we applied it without bias we would have to honestly admit that we don’t know the cause.

    Not knowing the cause is very different than assuming a cause based on lack of knowledge. We have a known cause that does account for some features, and may be able to account for others.

  48. BillB:

    As a matter of clarification, could you provide a list of those features of the cell that we know empirically were caused by evolutionary processes?

  49. Mr Nirwad,

    So any article titled “Functional evolution of the photolyase/cryptochrome protein family” is a fantasy, correct?

  50. Mr Nirwad,

    An article on enzyme promiscuity may be of interest to you for insight into how DNA repair mechanisms may have evolved. The source “Catalytic promiscuity and the divergent evolution of DNA repair enzymes” seems to be behind a paywall.

    Thank you for helping me to learn more, by posing your challenge.

  51. I’ve been following this site for a while now but have only just now registered. The discussions certainly are interesting to follow!

    Hi Nakashima, I’m interested whether this part of your referred article was observed or implied. If this reference site below is wrong (I googled it), please let me know:

    http://www.ncbi.nlm.nih.gov/pubmed/16478995

    “the acquirement of different (species-specific) C termini during evolution

  52. Mr Nakashima,

    The whole subject of promiscuous proteins is a fascinating one. They may explain how novel protein functions can arise via mutations to that portion of the sequence concerned with promiscuous function, and yet not adversely affect the fitness of the organism, since the core function of the protein is not impacted. Dan Tawfik’s lab has been doing quite a bit of work in that area.

  53. If you want a detailed explanation for how the particular cellular mechanism arose then you might want to ask a cell biologist.

    I think you provided about the most detailed explanation I’d ever get from anybody. Thanks for trying.

  54. Nakashima #49 #50

    thank you for the references to the articles and for your polite way of debating.

    As you suggested, I read the article “Functional evolution of the photolyase/cryptochrome protein family: importance of the C terminus of mammalian CRY1 for circadian core oscillator performance”. The article is not fantasy but I must frankly admit that I was unable to find in it a detailed explanation about the arise of the photolyase, as DNA repair system, from a process of random errors.

    I read also the interesting article “Enzyme promiscuity: evolutionary and mechanistic aspects”. Although the article well describes the aspects of plasticity and catalytic promiscuity of enzymes and their microevolution derived by mutations, one cannot properly say that it explains as groups of different enzymes coordinate their actions to obtain a complete error-recovery system, which seems to me at a higher systemic level (beyond what microevolutionary processes can achieve).

    I am always more convinced that the ID/evo debate will reach more clearness and insight when the fundamental difference between microevolution (plasticity of components) and macroevolution (new functional hierarchical architectures using such components) will be more clarified.

  55. Interesting paper Mr. Nakashima. I noticed a lot of words like “targeted”, “directed evolution” and “site-directed mutagenesis”.

  56. I’m glad several people found those articles helpful.

    I agree that neither one makes the direct case for the origin of photolyase kinds of DNA repair in exaptation or the recruitment of other functional elements, though I have the impresion that O’Brien’s article does come closer to that.

    But Mr Nirwad, I wouldn’t want you to start moving the goalposts towards a “complete error recovery system” when you’ve just finished telling me that photolyase itself _is_ an example of unevolvable DNA repair. Also, I do think it is close to the second of your three repair mechanisms that you reference in your OP.

    It sounds as if the concept of “broad specificity” and “enzyme promiscuity” are quite oxymoronic and surprising. How wonderful that the world still can surprise us!

    Mr Mishap, indeed these terms crop up regularly. Scientists don’t have the luxury of waiting a billion years for all of these things to happen at the same rate they do in nature. It is publish or perish after all. Depending on the claim being made, the use of these terms should alert us to greater scrutiny.

  57. Mr Drawingtheline,

    Hello, and welcome to the discussion. To your question, I admit to only having access to the abstract. I don’t know if this article maps out the photolyase/cryptchrome families and aligns them with other trees.

  58. In billions of years of evolution, some enzymes can change their active sites to catalyze different reactions. Sounds about right to me.

  59. Nakashima @86

    But Mr Nirwad

    Mr Nakashima, please, it’s not Mr. Nirwad. That would be Dawrin spelled backwards, and it just doesn’t make sense.

  60. Nakashima #56

    But Mr Nirwad, I wouldn’t want you to start moving the goalposts towards a “complete error recovery system” when you’ve just finished telling me that photolyase itself _is_ an example of unevolvable DNA repair. Also, I do think it is close to the second of your three repair mechanisms that you reference in your OP.

    I think that it doesn’t matter if the thing that repairs is a single enzyme or a group of enzymes. What matters is the function. If the repairing function is carried out by a single enzyme this means that it contains inside itself the potentiality to carry out the two basic roles of a repairing system: control and fixing. Another thing that matters is that the papers you referenced don’t seem to succeed in showing any unguided evolutionary pathway from basic chemical components to a recovery mechanism, be it a single enzyme or a set of them (and you agree on this).

  61. Mr Nirwad,

    In the case of photolyase, I’m not sure what you would say the control function is. It seems to me that the molecule is just taking advantage of a situation opportunistically.

  62. Nakashima #61

    Mr Nirwad,
    In the case of photolyase, I’m not sure what you would say the control function is. It seems to me that the molecule is just taking advantage of a situation opportunistically.

    You continue to write my name incorrectly, despite a warning of a reader. I am an IDer and as such I attribute importance to signs. My name represents symbolically the negation of Darwin. Your will to write it incorrectly might have a Freudian explanation: it represents a sign of your unavowed fear that Darwinism finishes. But you must resign, the end of Darwinism is unavoidable (and likely forthcoming) for only the Truth is eternal and Darwinism has nothing to do with truth.

    About photolyase, it seems clear to me that it fixes damages in DNA. Its action is directed only to the damaged sites and not to other sites. You can, if you like, call it opportunism. I call it control because for me a choice (though Boolean as that between damaged and undamaged sites) necessarily entails detection and detection is synonym of control after all.

  63. Hey somebody should make a shirt:

    “Four billion years of evolution and all I got was this beer belly.”

    lmao

  64. Mr Niwrad,

    My apologies for dyslexicizing your name. I assure you it was unintentional.

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