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

Pan said, "He didn’t say anything about control mechanisms evolving, he clearly and unambiguously asserted that “blind molecules can’t identify anything, let alone correct mistakes.”" Fine. It's hard to prove that negative as well. But it is reasonable to take the position that blind molecules cannot identify things. It is similar to the assumption that a machine cannot identify things without having been designed to do so. Otherwise you merely have pieces of metal and stone.Collin_{March 16, 2010
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Collin writes (41)
Hrun is taking advantage of the fact that it is very hard to prove a negative. It is hard to prove that error control mechanisms couldn’t possible ever evolve. So he says that Joseph’s assertions that they did not evolve are baseless.
I've been reading this thread with some bemusement, and I think this is a good point to reiterate Joseph's original claims (1):
Blind molecules can’t identify anything, let alone correct mistakes. To identify and correct mistakes requires knowledge. This knowledge is most likely in the form of a program similar to spellchecker.
He didn't say anything about control mechanisms evolving, he clearly and unambiguously asserted that "blind molecules can't identify anything, let alone correct mistakes." That assertion, which he has still not attempted to support aside from some silliness about talking to his refrigerator, fails to take into account what is currently known about DNA repair mechanisms. Anyone interested in learning more about how these mechanisms work can use the links from that page and also search PubMed for more information on particular genes. Joseph's final assertion is actually a (qualified) positive claim. Supporting that would be as simple as identifying the "spell checker" in an actual cell. It is not unreasonable to expect people who make strong claims in public to support them with evidence. If the claimant is unable to do so, the intellectually honest thing to do is retract the unsupported claim.Pan Narrans_{March 16, 2010
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Hrun is taking advantage of the fact that it is very hard to prove a negative. It is hard to prove that error control mechanisms couldn't possible ever evolve. So he says that Joseph's assertions that they did not evolve are baseless. But let me give a lawyer analogy, because I am one and that's what I know: "Your honor, I was alone in the room with the Mr. Brown and an alien flew in and took the knife that was in my pocket and stabbed him. Then he grabbed me and forced me to touch his bloody shirt. The prosecution has to prove my theory wrong before I'm convicted and since the prosecution can't prove it wrong, I must be acquitted."Collin_{March 16, 2010
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Real world example- I am still waiting for an answer from that glass of water. I picked up my wife's car-keys this morning to get into the SUV and the keys didn't correct my mistake. I wrote 2 + 2 = 5 on a piece of paper and the error is still there.Joseph_{March 16, 2010
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hrun0815:
I see error repair in cells.
That is the thing that needs explaining. You cannot use it to support your position. Noiw if you have evidence outside of biology in which blind molecules correct errors, then by all means, present it so we can have a look.
I can not detect agency anywhere?
The agency is either the cell or the organism in which the cell resides. DNA repair does not occur outside of the cell.Joseph_{March 16, 2010
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hrun0815- When you use the thing that needs explaining as an example for what needs to be explained, you have serious issues. Also it is a fact that every time we have observed proof-reading and error-correction there has always been agency involvement. What do I have to do- find you and take you to every place on the planet to "prove" my point? Oh no there are many other places in the universe to explore! You see error repair in cells- cells either are the agency- as is the case with single-celled organisms- or are part of an agency. IOW you are wrong as agency is obviously present when cells repair their DNA.Joseph_{March 16, 2010
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While some commenters are held up in moderation for hours, days, or never even see some comments get published, there are others who see their points of view treated with respect. I belong in the first group so I am giving up.Toronto_{March 16, 2010
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You are messed up on several levels.
I think that says it all. You make assertions, file to support them, but charge others to support theirs. It's exactly like I predicted.hrun0815_{March 16, 2010
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Yes, particularly in the cases where no supporting facts are provided. Which is not the case here as demonstrated in the OP and by Joseph’s real-world examples and the further biological analysis provided by Scordova, which is far more than you can lay claim to for your own assertions thus far.
What real world examples? I see error repair in cells. I can not detect agency anywhere? Where are the facts?hrun0815_{March 16, 2010
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If I will admit to something that is competely and demonstrably untrue, you will answer my questions, correct?
That Joseph did not support his assertions with facts? That is untrue? I just want to make sure. Could you confirm for me that you believe that to be true?hrun0815_{March 16, 2010
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PaulN @34,
Is there any way to turn the comment preview back on? It was so useful.
It must be something local to you, as the preview works fine for me.Toronto_{March 16, 2010
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Actually what I said is based on the observation and experience that says every time we have observed error correction it has been via agency involvement at some level. hrun0815:
Again, this is an extremely strong assertion.
You apparently have no idea what an assertion is.
There is error repair going on in my body at this moment, yet, nobody has ever observed any agency involved in my DNA repair.
So you are using the thing that needs explaining as an example to explain it? You are messed up on several levels. How many different personalities do you have?
It is your ASSUMPTION, that in my ‘design’ agency was involved.
It is an inference based on all available data. Just as the inference to the design of Stonehenge is based on all available data.
Thus, it is your ASSUPTION, that part of that ‘design’ also involves ‘agency at some level’ for my error repair.
It's called an inference. It appears the only time we see proof-reading and error-correction are when agency is involved. Ya see DNA, it resides inside of an agency. Even you, a troll, are an agency. The DNA inside of you would not get repaired if we took it out of you. It wouldn't do anything but start to decay- no hope for repair.Joseph_{March 16, 2010
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Upright BiPed@30,
If I will admit to something that is competely and demonstrably untrue, you will answer my questions, correct?
If you can demonstrate that a statement is untrue, simply do it and you win that point and maybe the argument. I hope we can have scientific debates here, not political ones. A scientist would prove that the statement was untrue.Toronto_{March 16, 2010
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Is there any way to turn the comment preview back on? It was so useful.PaulN_{March 16, 2010
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Hi Frank.
Clever.
As you can see from others, it is quite common to demand supporting facts for assertions.
Yes, particularly in the cases where no supporting facts are provided. Which is not the case here as demonstrated in the OP and by Joseph's real-world examples and the further biological analysis provided by Scordova, which is far more than you can lay claim to for your own assertions thus far. According to Joseph:
OK I just asked a glass of water if it could identify anything in the room and did not receive a response- yet. :) How long should I wait? I also told it that the regrigerator was a washing machine to see if it would correct my mistake. :) Heck the two aren’t even the same color! To identify and correct mistakes requires knowledge.</blockquote You retorted with more unsubstantiated allegations to which he replied:
Also I think I did a pretty good job of explaining myself. Apparently you choked on that explanation.
And this is the true position to which we still stand as the progress of this discussion has yet to go further than its initial conditions. It's your turn to provide something useful, otherwise your allegations will remain allegations.
PaulN_{March 16, 2010
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Upright BiPed @29, An intelligent agency, in this case a patient in a hospital, scratches herself every day causing wounds on her arm. Every night, her body repairs the damage done by her intelligent actions during the day. No one has told the body what was injured or how to repair it, yet every night, her unintelligent biology repairs what her intelligent and concious actions have done.Toronto_{March 16, 2010
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Let me get this straight: If I will admit to something that is competely and demonstrably untrue, you will answer my questions, correct? Okay, I admit it. Now answer my questions. All of them if you please.Upright BiPed_{March 16, 2010
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hrun, are you going to answer any of the questions I asked yesterday.
Are you going to admit that Joseph's comments (which, by the way, started this whole mess) are not at all based on facts and are indeed not supported by a single shred of evidence.hrun0815_{March 16, 2010
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hrun, are you going to answer any of the questions I asked yesterday. - - - - - - - Can you even conceptualize how a mistake could be corrected without first being identified as incorrect? Can you conceptualize how it might be reverted back to the correct value without having a correct value? Moreover, can you tell me which of the four grand theories of matter is responsible for initiating such a process by where mistakes are identified as being incorrect and a means to revert them back to correct values is set in motion? Is it Einstien’s Relativity? How about quantum mechanics? Newtonian mechanics? Maxwell’s eletromagnetic field? Is it an emergent property of matter that such a process comes about? What other examples of such material processes can we compare this to? Given that our universal experience with such systems only comes about as the product of an agent, what do we have as an contrary example so that we may have confidence that this system is merely a property of matter – as oppossed to just an assertion that it is? I’m genuinely asking for an answer here – what examples do we have that such systems come about without agency input? Are there any? Upright BiPed_{March 16, 2010
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Actually what I said is based on the observation and experience that says every time we have observed error correction it has been via agency involvement at some level. Again, this is an extremely strong assertion. There is error repair going on in my body at this moment, yet, nobody has ever observed any agency involved in my DNA repair. It is your ASSUMPTION, that in my 'design' agency was involved. Thus, it is your ASSUPTION, that part of that 'design' also involves 'agency at some level' for my error repair. Yet again, assertion-- but not a single shred of supporting fact.
hrun0815_{March 16, 2010
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My claims are based on facts.
If that is so, then you should be able to cite these facts to support your assertions. You have failed.
I’m going to be Frank, are you being a troll on purpose? The inanity of your posts in combination with your cocky demands while refusing to submit to any form of intellectually responsible discourse screams that you came from under a bridge somewhere.
Hi Frank. I am actually not being a troll on purpose. As you can see from others, it is quite common to demand supporting facts for assertions. In fact, Joseph himself wants such supporting facts for assertions he does not believe to be true. In any case, how about the UV repair system? Could you imagine how a blind molecule system without any additional input or template could revert an error to the original base?hrun0815_{March 16, 2010
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That was directed toward Hrun@22PaulN_{March 16, 2010
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I would guess that those people have not read about all the things that are known about the DNA repair system.
My goodness, did you completely miss the link provided in the OP? http://darwins-god.blogspot.com/2009/07/another-layer-of-dna-repair-complexity.html which leads to: http://darwins-god.blogspot.com/2009/06/new-dna-damage-repair-mechanism-must.html I'm going to be Frank, are you being a troll on purpose? The inanity of your posts in combination with your cocky demands while refusing to submit to any form of intellectually responsible discourse screams that you came from under a bridge somewhere.PaulN_{March 16, 2010
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Somebody points out that Joseph states utterly baseless assertions as fact.
Actually what I said is based on the observation and experience that says every time we have observed error correction it has been via agency involvement at some level. If you have any evidence to the contrary now would be a good time to post it. Otherwise your claim of assertion is meaningless.Joseph_{March 16, 2010
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My claims are based on facts. Have you ever observed an error being corrected via a blind molecule? EVER? Every time we have observed error correction it has been via agency involvement at some level- EVERY TIME. hrun0815:
I would guess that those people have not read about all the things that are known about the DNA repair system.
One thing that is not known is how can blind, undirected processes produce such a thing.
Then I’ll be happy to answer any question you might have.
Bold claim- however you have never demonstrated any capacity to do so.Joseph_{March 16, 2010
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Your claim of assertion is the real assertion.
As I predicted, yet another post without any support for you claims.
The questions were asked to see if you could support your claim.
So after unsupported claims, you are now asking ME to support MY CLAIMS with facts?
I have explained my position and you just ignored it as if your ignorance is some sort of refutation.
You might have explained your position. Yet, you have not posted a single shred of evidence to support your original assertions.
And people who have read about the DNA repair system have no idea how blind molecules can pull off such a thing- “evolutiondidit”- is all we get for an answer.
I would guess that those people have not read about all the things that are known about the DNA repair system. If you like, we can talk about it: Just either admit that your original assertions are not based in fact or post some facts to support them. Then I'll be happy to answer any question you might have.hrun0815_{March 16, 2010
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hrun0815- Your claim of assertion is the real assertion. The questions were asked to see if you could support your claim. You obviously cannot. You say you can conceptualize something about error correction via blind molecules- well man-up and post it. I have explained my position and you just ignored it as if your ignorance is some sort of refutation. And people who have read about the DNA repair system have no idea how blind molecules can pull off such a thing- "evolutiondidit"- is all we get for an answer.Joseph_{March 16, 2010
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scordova
It is unreasonable to believe mechanisms which lead to things like cancer lead to integrated biological complexity. Plenty of empirical proof for this.
You may want to check your assertion by reading
O'Brien PJ (2006): Catalytic promiscuity and the divergent evolution of DNA repair enzymes Chem Rev 106(2):720-52
which cites another 333 articles on DNA repair and the evolution of such systems, respectively. The author concludes:
As a biological system, DNA repair exhibits several of the hallmarks of an evolvable system. As evolution takes place on the level of a population, it is reasonable to consider that evolution has shaped a system that is inherently amenable to evolution. First, many DNA repair activities are redundant. This could allow greater flexibility in recruiting any given enzyme to a new function because gene duplication would not necessarily be required, as mutation of any one enzyme would be buffered by the activity of a functionally redundant enzyme. Second, the majority of DNA repair enzymes appear to have broad substrate specificity and reasonably large rate enhancements. This provides an abundant source of enzymes with low levels of promiscuous activities that could be improved n response to a biological selection for new or increased DNA repair activity. Finally, the relatively simple structure of DNA ensures that few types of catalytic reactions are required to repair any damage. As evolutionary pathways for changes in substrate specificity are likely to be more favorable than the pathways for creation of new catalytic mechanisms, this is expected to provide increased capacity for new DNA repair pathways. Thus, the catalytic promiscuity and broad substrate specificity of DNA repair enzymes are consistent with their apparently complex evolutionary histories and further suggest that there is considerable potential for future evolutionary diversification of enzymatic function in response to changing levels and sources of DNA damage.
osteonectin_{March 15, 2010
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If ever there might be such a thing as "settled science," it is that the Darwinian mechanism of random errors filtered by natural selection is hopelessly impotent as an explanation for this technology. Who are the "deniers" and "enemies of science" now?GilDodgen_{March 15, 2010
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Do you disagree? If you agree, can you please explain the scientific principles you used to come to the conclusion that Stonehenge was designed? Can those same principles be used to determine whether or not DNA repair proteins were designed. Why or why not?
and
Also, can you please explain why scientific skepticism is employed in science? What support does scientific skepticism have? Can assertions be made when only based on skepticism?
and
Can you even conceptualize how a mistake could be corrected without first being identified as incorrect? Can you conceptualize how it might be reverted back to the correct value without having a correct value?
and
Is it Einstien’s Relativity? How about quantum mechanics? Newtonian mechanics? Maxwell’s eletromagnetic field? Is it an emergent property of matter that such a process comes about?
I love it. Somebody points out that Joseph states utterly baseless assertions as fact. Instead of supporting those baseless assertions, the person pointing them out gets buried in heaps of questions. I will answer one thing, though: Yes, I can conceptualize both (how an error could be corrected without identifying if it is incorrect and how an error might revert back to the correct value without actually having the correct value). (And anybody who has read about the DNA repair system should be able to conceptualize both.)hrun0815_{March 15, 2010
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