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 Narrans:
I see nothing in those observations that suggests that anything other than well-understood chemistry and physics are at work.
And if living organisms are reducible to chemistry and physics you would have a point. However there isn't any evidence for that. Spellchecker does not violate any laws of physics. Is it a blind process? Pan Narrans:
We observe error correction of DNA.
Yes I know. That is what we are discussing.
We have not observed any agency other than evolution involved.
"Evolution" has several meanings. Only one excludes agency. We have never observed error correction evolve via blind, undirected processes starting from an organism that never had one. 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. What part of that don't you understand?Joseph_{March 17, 2010
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hrun0815:
I’m saying that you have no idea if or if not detecting an error requires ‘knowledge’ (depending on how you define knowledge, of course).
Yes I do. Ya see in order to detect an error there must be some knowledge that an error exists.
My guess is, that it, yet again, depends on how you define ‘blind’.
I have presented four definitions that apply. What is your problem?Joseph_{March 17, 2010
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Joseph writes (96):
Pan Narrans:
Scientists observe DNA repair mechanisms in real organisms.
I know. That is what we are discussing.
You recognize the validity of those observations. That's a good starting point.
You seem to think that just saying that means the molecules are blind.
I'm not sure exactly what you mean by "blind" in this context. I see nothing in those observations that suggests that anything other than well-understood chemistry and physics are at work.
I find that very funny.
I'm glad to have brought some joy into your day. There is no need for these debates to be acrimonious.
No one has observed any intelligent agent creating those mechanisms.
No one observed blind, undirected processes creating them either.
There is ongoing research that is discovering how such mechanisms can evolve. See here for just one summary: http://www.landesbioscience.com/curie/chapter/1108
However every time we have observed proof-reading and error correction it has always been with agency involvement.
You are simply asserting your claim again without evidence. We observe error correction of DNA. We have not observed any agency other than evolution involved. You can't simply assert your conclusion and expect to be taken seriously.Pan Narrans_{March 17, 2010
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The short answer is no, but with some qualifications; and I’d like to give more detail, but I’m on my way out and won’t be back until this evening. I’ll post a followup later.
I'll wait till then. My guess is, that it, yet again, depends on how you define 'blind'. However, your post at #64 is pretty clear. Maybe you should read it again and see what it means for DNA repair enzymes.hrun0815_{March 17, 2010
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Are you saying detecting an error does not require knowledge?
I'm saying that you have no idea if or if not detecting an error requires 'knowledge' (depending on how you define knowledge, of course).hrun0815_{March 17, 2010
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OK how can something (or someone) correct an error without the knowledge that A) an error exists and B) without the knowledge of how to correct it? hrun0815:
You have to be able to detect error.
Are you saying detecting an error does not require knowledge? "evolutiondidit"!Joseph_{March 17, 2010
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andrewjg @78 and Upright Biped @79 thanks. ;-) andrewjg, likewise @ 59
hrun @ 80 - Re #64: So, Apollo, you (and I might guess also andrewjg and Upright BiPed) actually believe that Joseph is very wrong when he writes that ‘blind molecules can’t identify anything, let alone correct mistakes’... Joseph @ 94 - Apollo- do you think that I am wrong?
The short answer is no, but with some qualifications; and I'd like to give more detail, but I'm on my way out and won't be back until this evening. I'll post a followup later.Apollos_{March 17, 2010
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Strange that you cannot provide any examples beyond the one being debated. hrun0815:
How could I provide examples, there is no such fact.
Then it appears my original claim is not unfounded. If the only example of blind molecules identifying and correcting errors is the DNA repair mechanism, then you lose. You cannot use the DNA repair mechanism as evidence the DNA gets repaired by blind molecules. Do you think that spellchecker is a blind process?Joseph_{March 17, 2010
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hrun0815:
Now you are just posting multiple definitions, without defining what you actually mean by ‘blind’ molecules.
That was to refute your nonsensical claim that my use of the word "blind" is "out of line with how any other person defines blind" As for which applies- well it appears they all do. 2 a : unable or unwilling to discern or judge b : unquestioning Check 3 a : having no regard to rational discrimination, guidance, or restriction (blind choice) b : lacking a directing or controlling consciousness (blind chance) c : drunk 1a Oops not "drunk" otherwise Check. 4 a : made or done without sight of certain objects or knowledge of certain facts that could serve for guidance or cause bias (a blind taste test) — compare double-blind, single-blind b : having no knowledge of information that may cause bias during the course of an experiment or test Big Check. So apparently you are the problem.Joseph_{March 17, 2010
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I have only been saying that for how many posts? Strange that you cannot provide any examples beyond the one being debated. There isn’t any evidence that DNA is blind.
Nobody refuted you. How could I provide examples, there is no such fact. Again that would depend on your definition of blind... that you still have not provided.
Decisions, decisions. More knoweldge required- or is it just a toss-up?
Depends on whether the DNA has just divided or not.hrun0815_{March 17, 2010
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Only the first definition is about sight. IOW if hrun0815 can’t even understand the basic definitions of the words being used what else can I do?
Now you are just posting multiple definitions, without defining what you actually mean by 'blind' molecules. This is just useless.hrun0815_{March 17, 2010
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OK how can something (or someone) correct an error without the knowledge that A) an error exists and B) without the knowledge of how to correct it? hrun0815:
You have to be able to detect error.
I have only been saying that for how many posts?
But there is no fact that shows that ‘blind’ molecules are not capabale of doing so.
Strange that you cannot provide any examples beyond the one being debated.
And the blueprint to correct erros comes from the fact that there are two strands of DNA (another ‘blind’ molecule).
There isn't any evidence that DNA is blind. Now if you can demonstrate that living organisms can arise from non-living matter via blind, undirected (chemical) processes, then you will have that evidence. You will also have falsified ID.
The error will, in general, be in only one of them.
Decisions, decisions. More knoweldge required- or is it just a toss-up?Joseph_{March 17, 2010
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Pan Narrans:
Scientists observe DNA repair mechanisms in real organisms.
I know. That is what we are discussing. You seem to think that just saying that means the molecules are blind. I find that very funny.
No one has observed any intelligent agent creating those mechanisms.
No one observed blind, undirected processes creating them either. However every time we have observed proof-reading and error correction it has always been with agency involvement. Beavers correct the faults in their dams. Ants correct the faults in their "ant hill". Termites correct faults in their mounds. Bees correct faults in their hive. DNA does not get repaired outside of a living organism. Take the DNA and proteins out. Induce mistakes in the DNA- see if the proteins rush to it to repair it. If it were pure physics and chemistry we should observe at least an attempt at repair the damage. However that the ONLY example you have for your position is the very thing being debated is hilarious. Do you think that continuing to do so really helps your case?Joseph_{March 17, 2010
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The same with spellchecker- it isn’t blind- it is a directed process. hrun0815:
If that is the case, then you have a definition of blind that is simply out of line with how any other person defines blind.
So hrun thinks ignorance is a refutation: blind:
2 a : unable or unwilling to discern or judge (blind to a lover's faults) b : unquestioning (blind loyalty) 3 a : having no regard to rational discrimination, guidance, or restriction (blind choice) b : lacking a directing or controlling consciousness (blind chance) c : drunk 1a 4 a : made or done without sight of certain objects or knowledge of certain facts that could serve for guidance or cause bias (a blind taste test) — compare double-blind, single-blind b : having no knowledge of information that may cause bias during the course of an experiment or test
Only the first definition is about sight. IOW if hrun0815 can't even understand the basic definitions of the words being used what else can I do?Joseph_{March 17, 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.
Let's ask: Apollo- do you think that I am wrong?Joseph_{March 17, 2010
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re#92: Restating the assertion in other words apparently counts for some as stating facts supporting said assertion.hrun0815_{March 17, 2010
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Joseph writes (82):
Every time we have observed proof-reading and error-correction there has always been an agency involved.
Assuming your conclusion is assuming your conclusion, even when the second time you do it in a bold font. Scientists observe DNA repair mechanisms in real organisms. No one has observed any intelligent agent creating those mechanisms. You have provided no evidence for your assertion that such an agent is required.Pan Narrans_{March 17, 2010
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OK how can something (or someone) correct an error without the knowledge that A) an error exists and B) without the knowledge of how to correct it?
You have to be able to detect error. But there is no fact that shows that 'blind' molecules are not capabale of doing so. And the blueprint to correct erros comes from the fact that there are two strands of DNA (another 'blind' molecule). The error will, in general, be in only one of them.hrun0815_{March 17, 2010
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If the designer(s) put those molecules there to identify and correct mistakes then it is obvious those molecules are not blind. The same with spellchecker- it isn’t blind- it is a directed process.
If that is the case, then you have a definition of blind that is simply out of line with how any other person defines blind.hrun0815_{March 17, 2010
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Not one IDist thinks my claims are false.
Read the statement by Appolo in #64 and read the approving messages by andrewjg and Upright BiPed. They believe you are wrong.hrun0815_{March 17, 2010
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hrun0815:
You might believe that a designer is necessary to put such molecules there, but once present, those molecules are indeed blind, and they can indeed correct mistakes.
If the designer(s) put those molecules there to identify and correct mistakes then it is obvious those molecules are not blind. The same with spellchecker- it isn't blind- it is a directed process.Joseph_{March 17, 2010
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OK how can something (or someone) correct an error without the knowledge that A) an error exists and B) without the knowledge of how to correct it? I am asking hrun, Pan or any anti-IDist to answer that.Joseph_{March 17, 2010
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hrun0815:
Re #64: So, Apollo, you (and I might guess also andrewjg and Upright BiPed) actually believe that Joseph is very wrong when he writes that ‘blind molecules can’t identify anything, let alone correct mistakes’, which by the way is the very first sentence of this thread.
If that is what you took away from that post then I understand why you think my claims are assertions. Not one of thsoe people even implied that was the case.Joseph_{March 17, 2010
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hrun0815- Not one IDist thinks my claims are false. The only people who think my claims are false are those who are wed to teh anti-ID position. Look up the word "axiomatic" and buy a vowel.Joseph_{March 17, 2010
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David Kellogg- Do you really think that Zachriel has something relevant to say? Do you take her laundry to the cleaners also? Too funny...Joseph_{March 17, 2010
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Re #81: I very carefully looked at your post, yet, I am still as unable to objectively define if a structure has ‘Irreducible Complexity’ and how to quantify it. There are two options: 1) I am too dense to understand. Maybe, in this case, you could use the methodology to give an object quatification of ‘Irreducible Complexity’ or maybe the spindle, flagellum, ribosome, or any other superstructure found in biology. 2) The paper actually does not enable anybody to give an object quatification of ‘Irreducible Complexity’ of any biological superstructure. My feeling is that option #2 is correct. But you should be very readily be able to prove to me and the rest of the world that it is actually #1.hrun0815_{March 17, 2010
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Every time we have observed proof-reading and error-correction there has always been an agency involved. What else do you need? hrun0815:
That is your factual support?
Yes- answer the question. We have NEVER observed proof-reading and error-correction without agency involvement- never. IOW hrun you have nothing at all to support your position. I have observations and experience.Joseph_{March 17, 2010
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Re Kellogg and Hrun; Nobel prize winner Jack Szostak is very clear about the relevance of the definition of functional information, presented in the paper, to the concept of Irreducible Complexity, in the very first line of the paper he co-authored: Szostak states: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. He then goes on to quantify those functional elements of those interacting components. I listed a video by Kirk Durston which goes into detail of how to derive functional Information (FITS) for a amino acid (protein) string or a DNA string. Since the probability of a functional protein is known (Axe; Sauer) to a high degree of certainty, The assumptions that you presume would render the calculations mute are gone!~ And in the case of the Venter hiding his watermark, in "his" genome, it is simply ridiculous to claim otherwise. All of this is straightforward and clearly explained in the videos by Kirk Durston that I listed. Frankly I feel that if any of you atheists have a problem with how the equation is set up, or how the probability of proteins are derived, you should write Jack Szostak, or Doug Axe, and tell them of your concerns and have them retract their peer reviewed papers. If that does you no good, which it won't, I suggest you write up a peer reviewed paper yourself, have it published and tell the world of your insight. Until then, in my eyes, you guys are merely stating your extremely biased opinions. Extremely biased opinions which are never based upon any empirical evidence, but only upon irrational levels of hyper-skepticism.bornagain77_{March 17, 2010
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Re #64: So, Apollo, you (and I might guess also andrewjg and Upright BiPed) actually believe that Joseph is very wrong when he writes that 'blind molecules can’t identify anything, let alone correct mistakes', which by the way is the very first sentence of this thread. You might believe that a designer is necessary to put such molecules there, but once present, those molecules are indeed blind, and they can indeed correct mistakes. It is extremely surprising, that many people actually believe this assertion by Joseph to be false, yet I was vehemently attacked for simply asking for factual support of his statement (which you and I know he is impossible to give).hrun0815_{March 16, 2010
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Apollos, Nice!Upright BiPed_{March 16, 2010
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