DNA Repair Proteins: Efficiently Finding Genome Errors

_{Cornelius Hunter

March 15, 2010

Intelligent Design}

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The heroics of the cell’s DNA repair system are well known, but new research is adding yet another incredible facet to the story. Experimentalists tagged DNA repair proteins with nanocrystals that light up. They then observed how they interact with DNA molecules. As reported: Read more

Comments

Joseph writes (137):
Blind, undirected (chemical) processes is what is being debated.
That's fine, we'll leave the discussion of the evolution of such processes to other subthreads. Focus is good.
In that case, the fact that we observe a variety of these mechanisms operating in real cells refutes your assertion quite handily.
There isn’t any evidence that what we observe in real cells are blind, undirected (chemical) processes.
You have presented absolutely no evidence that anything else is going on.
DNA does not get repaired outside of a cell. That refutes your position.
Actually, the biochemistry of the repair mechanisms does work outside of a cell. What would make you think otherwise? In any case, you're attempting to move the goalposts. The fact is that you have not provided any evidence whatsoever that anything other than well-understood biochemistry is taking place in the repair process. Your assertion remains unsupported.Pan Narrans_{March 23, 2010
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Pan Narrans:
Some of your supporters in this thread seem to think that your assertion was about the evolvability of repair mechanisms, not their efficacy as observed now.
There isn't any evidence DNA repair mechanisms evolved via an accumulation of genetic accidents from some population that never had a DNA repair mechanism. Blind, undirected (chemical) processes is what is being debated. Pan Narrans:
In that case, the fact that we observe a variety of these mechanisms operating in real cells refutes your assertion quite handily.
There isn't any evidence that what we observe in real cells are blind, undirected (chemical) processes. DNA does not get repaired outside of a cell. That refutes your position. But thanks for continuing to avoid my questions. It is very telling that A) You avoid answering my questions and B) You are unable to make an argument for blind molecules being able to identify and correct errors.Joseph_{March 21, 2010
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Joseph writes (133):
If you want to make the argument that evolution of repair mechanisms is implausible,
I am not making that argument. Again “evolution” has nothing to do with it.
Thank you for that clarification. Some of your supporters in this thread seem to think that your assertion was about the evolvability of repair mechanisms, not their efficacy as observed now.
Blind, undirected (chemical) processes is what is being debated.
In that case, the fact that we observe a variety of these mechanisms operating in real cells refutes your assertion quite handily.Pan Narrans_{March 21, 2010
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hrun0815- Still afraid to answer my question- Do you think that spellchecker is a blind process? hrun0815:
And, as always, I bet that scientists don’t actually qualify as people who understand how science operates, correct?
Why would you say that? Can you find ONE scientist which can demonstrate DNA repair is a blind process? Ya see my point is that when scientists make an observation/ observations- if every time they observe X and it is always due to Y then when they observe X and didin't see Y they infer Y was responsible. Then if someday something other than Y is observed to cause X they amend their initial inference. Do you understand that?Joseph_{March 20, 2010
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But definitely not to those who understand how science operates.
And, as always, I bet that scientists don't actually qualify as people who understand how science operates, correct?hrun0815_{March 19, 2010
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Pan Narrans:
He said “Blind molecules can’t identify anything, let alone correct mistakes.”
And what do you have to counter that claim? Apparently nothing but a bald claim of assertion. My support is observations and experience. Your "support" is to cry assertion. Pan Narrans:
If you want to make the argument that evolution of repair mechanisms is implausible,
I am not making that argument. Again "evolution" has nothing to do with it. Blind, undirected (chemical) processes is what is being debated. Also do you think that by avoiding my posts it helps your case? Your simple arguments from avoidance are unconvincing.Joseph_{March 19, 2010
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Joseph All unicorns are pink. http://www.homestarrunner.com/crystal.htmlCollin_{March 19, 2010
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Clive Hayden writes (128):
Pan,
Do we know exactly how it happened? No, but it is an area of active research. The important point in this discussion is that it is not logically impossible. Joseph’s assertion remains unsupported.
It is not logically impossible like a square circle, but it is logical to claim that it is logically implausible. It doesn’t have to be logically impossible to be implausible.
True, but Joseph didn't claim implausibility. He said "Blind molecules can’t identify anything, let alone correct mistakes." That's an unequivocal assertion that requires support.
It’s not logically impossible that I can, unaided, fly like an eagle, but it is implausible, and so here, the same logic applies.
Actually, the logic is quite different. If you want to make the argument that evolution of repair mechanisms is implausible, you're going to have to get into the details of exactly how those mechanisms work in various organisms, what the shared characteristics tell us about the repair mechanisms in common ancestors, and the biochemistry of possible precursors. Simple arguments from incredulity are unconvincing.Pan Narrans_{March 19, 2010
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Pan Narrans:
If Joseph or someone else wanted to support his assertion that “Blind molecules can’t identify anything, let alone correct mistakes.” by demonstrating that it is logically impossible for a biochemical process to repair a DNA strand, that would of course be valid.
That doesn't make any sense. Pan is saying that in order for my claim to be correct we shouldn't observe DNA repair. SO DNA repair is a blind process because we can observe it happening. And by extension spellchecker is a blind process because we can observe it happening. CSI can arise by blind, undirected processes because we can observe CSI. The words appear on this blog, not because they are directed by something, it is all blind processes and amazing coincidences.
What is really happening is that organisms that have higher fidelity replication are more likely to reproduce than organisms that do not.
And therefor blind, undirecetd (chemical) processes can account for living organisms arising from non-living matter?
Phrased that way, it is easy to see how evolutionary mechanisms could gradually improve the repair capabilities.
So now we have some equivocation. But yes if living organisms can arise from non-living matter via blind, undirected (chemical) processes, then repair can arise from blind, undirected processes. But without that huge bit of supporting data, one has to figure out how a blind molecule can repair something without having any knowledge of a mistake existing and how to correct it. And it appears you are unable to make that argument.Joseph_{March 19, 2010
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Thanks Pan! Yeah we observe DNA repair in action therefor it is a blind process! Is that still your position? That is hilarious Pan. I supported my claim with facts- and the facts are that every time we have observed proof-reading and error correction agency has always been involved- always and without exception. That said you refuse to answer my question: Do you think that spellchecker is a blind process? Do you think that continuing to aviod the question helps your position? Pan states:
Joseph’s assertion remains unsupported.
Perhaps to you. But definitely not to those who understand how science operates.Joseph_{March 19, 2010
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Pan,
Do we know exactly how it happened? No, but it is an area of active research. The important point in this discussion is that it is not logically impossible. Joseph’s assertion remains unsupported.
It is not logically impossible like a square circle, but it is logical to claim that it is logically implausible. It doesn't have to be logically impossible to be implausible. It's not logically impossible that I can, unaided, fly like an eagle, but it is implausible, and so here, the same logic applies.Clive Hayden_{March 19, 2010
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Clive Hayden writes (126):
Using logic, which is metaphysical, is just as valid evidence.
Certainly. If Joseph or someone else wanted to support his assertion that "Blind molecules can’t identify anything, let alone correct mistakes." by demonstrating that it is logically impossible for a biochemical process to repair a DNA strand, that would of course be valid. Unfortunately for that argument, we observe exactly such biochemical processes happening. If one wanted to support, solely with logic, the assertion that such processes could not develop without intelligent intervention, one would have to demonstrate the logical impossibility of that happening. This is where a knowledge of biochemistry is essential. While we talk about these processes as "repair mechanisms" and they do, in fact, increase the fidelity of DNA replication, anthropomorphizing the process leads to confusion about what is really happening, as exemplified in your statement that
you can do no correcting unless there is something that is known in some fashion to be corrected and how that correction works.
What is really happening is that organisms that have higher fidelity replication are more likely to reproduce than organisms that do not. Phrased that way, it is easy to see how evolutionary mechanisms could gradually improve the repair capabilities. Even a simple, inefficient repair capability would be better than nothing, and this benefit could be selected for. Do we know exactly how it happened? No, but it is an area of active research. The important point in this discussion is that it is not logically impossible. Joseph's assertion remains unsupported.Pan Narrans_{March 19, 2010
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Pan,
If you or Joseph want to move beyond unfounded assertions, you’ll need to demonstrate clearly, with real physical evidence, that something other than what we’ve observed is required for those mechanisms to operate.
This is exactly your problem, in my humble opinion. You require physical evidence, you probably require physical evidence as to why you trust you mother and why you believe your friends when they tell you things. Using logic, which is metaphysical, is just as valid evidence. And Joseph is right, you can do no correcting unless there is something that is known in some fashion to be corrected and how that correction works. Stereochemical reactions and laws of physics don't cut it logically. Your fixation on physical evidence itself doesn't have any physical evidence, it's a philosophical position, one that you think you have come to as a conclusion of logic. What's good for the goose....Clive Hayden_{March 18, 2010
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I didn't call anyone an "intellectual coward". I made an observation. What is a person that refuses to answer relevant questions all the while badgering people with nonsense?Joseph_{March 18, 2010
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Joseph, I've warned you before, don't call people intellectual cowards. I'm putting you into moderation.Clive Hayden_{March 18, 2010
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hrun0815:
Read the statement by Appolo in #64 and read the approving messages by andrewjg and Upright BiPed. They believe you are wrong.
Wrong again hrun. You are 0 for the whole thread. Sweet....Joseph_{March 18, 2010
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hrun0815:
All unicorns are pink.
Is that based on observation and experience? This is. Not that I would expect you to understand the difference. And thank you for continuing to expose your intellectual cowardice- Do you think that spellchecker is a blind process?Joseph_{March 18, 2010
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Re #114: All unicorns are pink.hrun0815_{March 18, 2010
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Thanks Apollos. Well it looks like the only baseless assertions in this thread have come from hrun0815 and Pan Narrans-> Their "evidence" that DNA repair is carried out by blind molecules? We have observed the process...Joseph_{March 18, 2010
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To clarify the above: only the first sentence was meant to address Joseph's comment. The remainder is just me spouting off in general.Apollos_{March 17, 2010
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Joseph wrote:
"I will politely disagree and offer that the operation of a grandfather clock can only be explained by design."
My qualification would be that the clock's existence also requires an explanation, and that merely describing its operation via the laws of physics is not a justification of the thing itself, regardless of how detailed an account we can give for its physical function. A clock is autonomous -- as long as it's wound -- but nothing about its operation is blind. To argue about whether a clock "tells time" is rather pointless, because the thing has no agency. However an agency has most certainly formed and set it in motion. For the clock, this is unequivocal. Just because the operation of a thing can be explained by physical law doesn't mean it's reducible to the same. As I eluded to in #64, a detailed account of the operation of a clock can be given and understood, even in terms of precise physical laws, but the arrangement of the parts and their contingent specification also requires accounting for. In this case design is the reasonable explanation. I would agree with hrun's sentiment @105 that this may turn on how one defines 'blind.' I had suggested previously that the thread appears to be a semantic disagreement, although I believe it actually boils down to competing world views. I suppose 'blind' in this context can either mean: a) having no agency of its own; or b) having no agency and never having required it in order to function. Each has a different connotation. The first definition simply suggests autonomous behavior; and the second suggests a strictly material explanation. I want to reiterate that just because we can understand how a thing operates by physical law, doesn't mean that we've explained the thing itself. In the case of the clock this must be considered obvious. Someone could document weights, gear ratios, and pendulum lengths to the utmost detail, and they have still not explained it's existence, only a knowledge of how it operates. For biological organisms, to be perfectly fair, we must consider two distinct and contrasting possibilities: 1) Their existence can be explained purely by natural and physical laws. 2) They are only explicable in terms of design (agency, a mind) and no natural laws of chemistry and physics account for their form. Both explanations require positive evidence. That either should be the "default position" for some private philosophical reason is unwarranted, regardless your justification; and foisting upon proponents of the other the only burden of proof should be considered unacceptable. Herein lies part of the problem. The design hypotheses is ruled out by fiat, even though it's one of the contrasting logical possibilities for the genesis of cell. Regarding error correcting proteins: these molecules may be autonomous in their operation, but not in their existence, which relies on cellular machinery -- machinery which also requires explanation. We can hardly pick some point along a complex chain of molecular dependence and say, "There, see? It's operating all by itself!" The whole interdependent nano-machine requires an explanation; and if you can't show how the thing can exist on its own, or come into existence unaided, you can't very well pick at some part in a chain of complex interdependence and say that it's operating blindly, at least in my view. This invites the semantic argument about what constitutes blind. My apologies if this post rambles a little. There's a lot that can be said and a lot that can be picked at. However as far as I'm concerned, with regard to clocks or combustion motors or autonomous error correcting proteins, there is much more to be explained than just the physical laws by which they operate. There needs to be an account of their origin. Until natural laws can directly account for the contingent specificity of the cell, I see design as the most sufficient explanation.Apollos_{March 17, 2010
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While we wait for Apollos' return:
The operation of a grandfather clock can be explained by physics. You can describe the physical laws which allow the gravity mechanism to convert stored energy into motion, and how the ratios of the gears and the lengths of the pendulums translate into very good timekeeping.
I will politely disagree and offer that the operation of a grandfather clock can only be explained by design. Agency is using physics- directing physics- to do something in the absence of direct/ further agency involvement- mechanics. Set it and forget it- that is until it is time to re-set it...Joseph_{March 17, 2010
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Pan Narrans, I have already provided the evidence. Apparently you don't know what evidence is. Apparently you don't understand how science operates. IOW Pan and hrun, I await your counter-evidence without any evidence at all of you will ever provide any. What can you say? You have already proven that you don't know what you are talking about. Pan's evidence that DNA repair is a blind process is that we have observed the DNA repair mechanism in action. Real deep Pan- and real convincing- not. I have also noticed that you have refused to answer a simple question- Perhaps you missed it- several times- Do you think that spellchecker is a blind process? Or is your intellectual integrity geting in the way?Joseph_{March 17, 2010
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Joseph, I await your evidence with bated breath. Until you provide some, I leave the floor to you.Pan Narrans_{March 17, 2010
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This discussion started out with your unfounded assertion that “Blind molecules can’t identify anything, let alone correct mistakes.” Here we are over 100 messages later and you still haven’t supported that claim.
Funny that my claim stands unrefuted. All you have is the unfounded cry of "assertion".Joseph_{March 17, 2010
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Pans Narrans:
Here we are over 100 messages later and you still haven’t supported that claim.
I have- ALL observations and experiences tell us that every time we see proof-reading and error correction an agency is involved. OTOH you seem to think the evidence that DNA repair is a blind process is that DNA repair can be observed. As for intellectual integrity- you don't know what that is...Joseph_{March 17, 2010
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Pan, I read through your article on the "evolution" of DNA repair mechanisms and it is the same ole, same ole evolutionary tripe passing as science,,, in other words wishful speculation. It will turn out the same for any other article you wish to cite for it is IMPOSSIBLE for material processes to generated "coded" information. DNA Is A Intelligently Designed Code - Perry Marshall - video http://www.metacafe.com/watch/4018241/dna_is_a_intelligently_designed_code_perry_marshall/ In fact Pan, the list of what evolutionists have failed to explain by purely natural processes reaches to the very ends of the roots of biology and includes 1 the origination of the DNA molecule, 2 the origination of the RNA molecule, 3 and the origination of even a single simple protein molecule. Looked at objectively a DNA repair mechanism would be fairly complex mechanism since it would be required to process information of a "optimal" state for which the DNA should be repaired to. To excise the incorrect nucleotides and to reattach correct nucleotides in the correct places. How many proteins are working in concert to perform this task? The article mentions 40 team members, whatever team member means, we can safely surmise that at least 40 distinct proteins are involved in the process. How many of these proteins are unique Pan? Lets say that very conservatively 10 will be found to have no homologies in other mechanisms of the cell. What is the probability of 10 unique proteins occurring at the same place and the same time Pan? conservatively it will be about 1 in 10^770 Pan. Tell you what Pan, I have another machine that is much simpler that a DNA repair mechnism, and in fact is a required precursor for the first photosynthetic life found on earth since it provides the "fuel" for photosynthesis to do its job; Evolution vs ATP Synthase - Molecular Machine - video http://www.metacafe.com/watch/4012706/evolution_vs_atp_synthase_molecular_machine/ Can you please cite the natural process that generated this machine in the first photosynthetic life? or better yet can you go into a lab and produce this machine using all your know how? "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologistbornagain77_{March 17, 2010
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Joseph writes (108):
Look if DNA repair is your only example then you have lost because you cannot use DNA repair- the thing being debated- as evidence that DNA repair is blind.
This discussion started out with your unfounded assertion that "Blind molecules can’t identify anything, let alone correct mistakes." Here we are over 100 messages later and you still haven't supported that claim. You seem to understand that your opponents cannot validly assume their conclusions (although that is not what I'm doing here) but you have great difficulty in applying that criteria to yourself. So, without assuming what you are trying to prove, please show the evidence for your original assertion. If you have none, please demonstrate the minimal intellectual integrity required to retract your claim.Pan Narrans_{March 17, 2010
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Who thinks that spellchecker is a blind process?Joseph_{March 17, 2010
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However every time we have observed proof-reading and error correction it has always been with agency involvement. Pan Narrans:
You are simply asserting your claim again without evidence.
I provided te evidence. You, OTOH, cannot provide anything to counter what I posted. Go figure...Joseph_{March 17, 2010
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