DNA Repair Proteins: Efficiently Finding Genome Errors

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.

IOW it is in the software of life- DNA being part of the hardware.

Blind molecules can’t identify anything, let alone correct mistakes.

Assertion without supporting facts.

To identify and correct mistakes requires knowledge.

Assertion without supporting facts.

This knowledge is most likely in the form of a program similar to spellchecker.

Qualified assertion without supporting facts.

IOW it is in the software of life- DNA being part of the hardware.

This sentence I can’t decipher.

Blind molecules can’t identify anything, let alone correct mistakes.

hrun0815:

Assertion without supporting facts.

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.

Assertion without supporting facts.

You think so?

Can you think of any examples to the contrary?

How can you correct a mistake without a- identifying the mistake, which means you have to know one exists and b- know how to correct it, meaning out of all the other possibilities you have to make the correct choice?

This knowledge is most likely in the form of a program similar to spellchecker.

Qualified assertion without supporting facts.

Call it an ID prediction.

IOW it is in the software of life- DNA being part of the hardware.

This sentence I can’t decipher

Nothing to decipher.

You are stuck in a two-dimensional realm.

One that forces you to think that the DNA is the information.

It isn’t. It is 1- a carrier of the information, just as computer disc is a carrier and not the information; 2- it also is used to carry out the instructions.

In computers there are wires and/ or fibers, gates, switches, processors, etc. that make sure the information gets to where it is supposed to go.

In an organism the data is sent via RNA carriers, that can also become a component in the required system.

See also:

Biological Information in 3 Dimensions

It’s funny. I point out statements that are mere assertions. I get back a whole long post in which none of the assertions actually gets supported by fact.

Perhaps you just think they are assertions.

I understand that someone like you understands assertions because that is all your position has.

But unless you can counter my alleged assertions- how do you know they are assertions?

Perhaps your claim of assertion is the real assertion.

I noticed yoiu didn’t even try to answer my questions.

That tells me who is doing the asserting…

But unless you can counter my alleged assertions- how do you know they are assertions?

If they were not simply assertions, you would have supported them by facts about two posts ago.

uh,hrun?

Can you correct a mistake without identifying it though knowledge of what it should be? And then knowing how to correct it?

Wow, that sure would go a long way towards proving your assertion that Joseph is simply making assertions.

Joseph,

I think you make really good points. It seems very unlikely to me that a system that identifies and repairs problems in a complex code could not be designed. Call it personal incredulty maybe. But your argument makes a lot of sense to me. A repair mechanism does not seem likely to be the result of random mutation and natural selection.

Uh, Upright BiPed,

Do you know if ‘blind molecules’ can or can not correct mistakes? Do you know that in order to correct or identify mistakes you need knowledge?

Those are the assertions made by Joseph. Now we have three posts that do not support those assertions with any evidence. My guess is, there will be many more to follow– and none of them will factually support those statements (which is why I call them assertions).

hrun0815:

If they were not simply assertions, you would have supported them by facts about two posts ago.

That is an assertion.

Also I think I did a pretty good job of explaining myself.

Apparently you choked on that explanation.

Thanks Upright Biped and Collin.

I appreciate the support…

If there are repair mechanisms, this implies that RANDOM variations are actively resisted by the organism itself.

It would appear some forms of variation are actively suppressed, others are let through.

Variations therefore, when they happen, could for the most part be NON-RANDOM.

When the repair mechanisms sufficiently fail this often leads to things like cancer. It is unreasonable to believe mechanisms which lead to things like cancer lead to integrated biological complexity. Plenty of empirical proof for this.

With respect to cancer cells, we don’t see natural selection within the organism enabling better and better features in the cell. Group selection fails and the organism dies.

If there are repair mechanisms at the somatic level, there would reasonably be repair like mechanisms at the germline level. Which imply unless the repair mechanism are suppressed, large scale variation will be resisted. However, in general when such repair mechanisms are arrested, we see disasters!

Spetner has speculated that the variation and mutation we see in the germline cells look too purposeful to be random. They seem to be variations by design. So it would seem the repair mechanisms, in those cases are not arrested, but operate in a way to permit some variation.

Can selection sufficiently cull the bad from the good were such repair mechanisms arrested? Doubtful. In human populations, the number of bad trials that can be tolerated without the population being wiped out is about 3 per person on average (and that’s assuming about 40 offspring per female!)

But let’s consider the activity on somatic cells as a guide. If DNA in every cell is being policed so vigrously, maybe millions of variations being actively deleted (not by selecion but by purposeful repair), on what grounds would we expect large scale random variations to result in viable organisms? Deletion and repair of random variation seems to be an essential feature. Evolutionary theories relying on random variation seem to appeal to what is obviously a bad thing for living organisms.

For evolution to progress, the variations would have to be non-random. James Shapiro, one of Sternberg’s colleagues, suggests mechanisms of non-random variation.

Where Shaprio would part company with the ID community is the what created an engineered system that fascilitated non-random variation in the first place.

Ooops, I missed Colin’s post. Again, no supporting facts for the assertions.

Hrun,

Here’s an unsupported assertion: Stonehenge was intelligently designed.

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?

Hrun,

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?

One needs a functional repair system in the first place before the cell will be viable. Selection can’t select for the precursors of a repair system because the cell would be already dead without the repair system already in place!

The classic chicken-and-egg paradox (actully the pardox is solve, you need the chicken first, but that implies design).

hrun “Do you know if ‘blind molecules’ can or can not correct mistakes? Do you know that in order to correct or identify mistakes you need knowledge?”

Thats right hrun, if the potato is too hot, just throw it back.

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?

off topic:

For all our evolutionist friends who go to such great pains to strain out a gnat but so easily swallow a camel. (Matthew 23:24)

I thought you might like this video showing a gnat staining.

Fruit Fly Brains Ramp Up Activity During Flight
http://www.metacafe.com/watch/.....ng_flight/

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.)

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?

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.

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.

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.

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.

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.

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.co.....exity.html

which leads to:

http://darwins-god.blogspot.co.....-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.

That was directed toward Hrun@22

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?

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.

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?

Are there any?

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.

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 @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.

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.

Is there any way to turn the comment preview back on? It was so useful.

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.

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.

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.

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?

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?

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.

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.

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.

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.

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.

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 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 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 writes (47):

But it is reasonable to take the position that blind molecules cannot identify things.

Given the evidence for DNA repair mechanisms, it is not reasonable to take that position. We observe the biochemistry. A quick search turns up over a dozen papers in one issue of just one journal:

http://www.sciencedirect.com/s.....l/15687864

Toronto:

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- you cannot use what requires an explanation as the example for the explanation.

That is just plain dumb.

Pan Narrans,

I have supported my claims.

I can’t help it if you are unable to follow along.

And again you people who try to use the very thing that needs an explanation as an example for your position have serious issues.

IOW you cannot point to DNA repair mechanisms as evidence for blind molecules doing something when it is that very DNA repair that requires an explanation.

But I will tell you what-

If you or anyone else ever demonstrates that a living organism can arsie from non-living matter via blind, undirected (chemical) processes I will retract everything I have ever said about blind molecules.

Until you do that you don’t have any evidence for your position.

IOW your position is based solely of bald assertion after bald assertion.

Clive Hayden writes (52):

To argue as you do is to affirm your conclusion, that since there is DNA repair, there must be blind molecules, which is exactly what is in question.

If you or Joseph have any evidence that there is anything other than chemistry (and physics, of course) taking place as part of the DNA repair mechanisms, please present it. Otherwise Joseph’s claims remain unsupported assertions.

Thanks for taking the time to surface the apparent question being begged Clive.

And thanks Collins for identifying a tactic that was indeed taken advantage of beyond any rational means in order to justify assertions.

I believe the logic is as follows:

Proving that the molecular repair carried out by proteins in DNA correction wasn’t a result of blind/random material chance+necessity follows the same difficulty as proving the stone formation within stonehenge wasn’t a result of a nearby mountain exploding and rock shards falling into the specific pattern that we see today.

While it’s nearly impossible to actually prove the negative, it certainly is well within rational means to infer a more likely scenario for the positive, being that intelligence was the source of said phenomena according to real-world observations of what intelligence is able to create.

The hypothetical alien vs. a force well known to commit murder according to direct and historical observation is a good analogy. The only thing I would change to make it more relevant with respect to the topic at hand is to change the hypothetical to something we know is much less capable of murdering someone and then framing them. For this I would change the story from an alien to a cockroach as the responsible party, which would further widen the rational gap between the conceivable possibilities.

Pan Narrans,

I have supported my claims.

I cannot help it if you cannot understand what I post.

Ya see Pan you don’t have any evidence that living organisms are reducible to chemistry and physics.

All you can do is use the example of DNA repair as evidence that DNA repair is carried out by blind molecules.

Do you even realize how messed up that is?

Apparently not- but it does expose your agenda…

Clive Hayden writes (55):

Pan,

If you or Joseph have any evidence that there is anything other than chemistry (and physics, of course) taking place as part of the DNA repair mechanisms, please present it. Otherwise Joseph’s claims remain unsupported assertions.

There is clearly information, just as when the body repairs itself, and a reductionist viewpoint such as chemistry and physics cannot be the whole show or the entire story. It would be like saying that a computer is clearly only chemistry and physics. This is all that really has to be shown, evidence using sense, it doesn’t have to be physical evidence, unless you’re steeped in materialism, which I am not, but presume you are.

Steeping? I’m positively bathing in the stuff!

What I’m hearing, and please correct me if I’m misconstruing your position, is that biologists and biochemists have discovered a wide variety of repair mechanisms that use pretty well understood chemistry and physics to fix certain kinds of errors that occur when DNA replicates. Joseph comes along and, without demonstrating any knowledge of this work or any background in biology, chemistry, or physics, and simply states the equivalent of “That’s just not possible.”

Surely you can understand that those of us with a background in one or more of those disciplines would require more than such a bare assertion to take the claim seriously.

Now, as you note, reductionism isn’t useful when discussing certain features of complex systems. It makes no more sense to talk about chemical reactions in terms of quantum mechanics (usually) than it does to talk about software in terms of electricity. However, noting that provides no evidence for the assertion that anything more than the laws of chemistry and physics are required to explain the observed DNA repair mechanisms.

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. A good way to tell when you’re reaching the necessary levels of evidentiary support is when you can start making testable predictions about your claims.

Joseph writes (56):

Apparently not- but it does expose your agenda…

My only agenda is that I like to see debates like these proceed rationally. Failing to support one’s assertions, and then failing to retract them, detracts from rational debate.

If you have real support for your positions I would be very interested to hear it.

I don’t think the points made in this thread have been well communicated. It seems clear that everyone agrees proteins are involved in DNA repair.

Joseph is really contending that a mind is required to create the molecules (proteins) to repair DNA. Opponents are contending that is not the case.

The fact that chemistry ultimately does the work and no intelligent agent is directly present coordinating the repair process is irrelevant. That would be like finding a clock and stating that since no one was directly turning the hands the cause was not an intelligent agent.

Joseph’s assertion – based on experience, intuition and inference – is that any repair process requires foreknowledge of what is being repaired. Foreknowledge implies a designer. This is reasonable since this is always the case as we experience the world. We know from experience before we can fix something we must know what is wrong with it and in order to do that we must know what it is supposed to look like or work.

A quick aside, up until fairly recently Fermats last theorom was unsolved. Prior to that would it have been reasonable to assert its validity?

Quickly an example. Lets look at a DVD. It contains the encoded video stream but it also contains all error detection information and enough extra information so that even though it becomes scratched it can still be played. The software that decodes the stream of bytes needs to know the scheme being used in order to correct the video stream.

Finally I agree Hrun and Pan. At least theoretically it would be possible for mutation to stumble upon a protein capable of repairing some kind of defect in the DNA even though this capability is likely never to be demonstrated. But I think the author of the original article says it best,

“It would be extremely unlikely for blind variations to stumble upon such protein designs. With evolution we must believe that such proteins just happened to arise and then were selected because they helped in the DNA repair system. If you believe that then I have a bridge to sell you.”

Way too many comments for me to reply to. Just real quick, I’ll go with this one:

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.

In fact, Joseph didn’t claim that and I did not ask for factual support for this assertion. Joseph made two specific claims, one positive and one negative (Blind molecules can’t identify anything, let alone correct mistakes. To identify and correct mistakes requires knowledge.) Nowhere are we talking about evolution. And nowhere is their factual support, positive or negative claim.

Hrun @59,

The fact that knowledge of what to correct and how to correct it are necessarily required to actually carry out correction is damn near axiomatic.

If one of those two conditions isn’t met, then please offer a better alternative for how correction takes place, and how this proposal is substantiated with respect to reality.

You seem to be completely bypassing one of the core tenets of science, that the person proposing a positive statement bears the burden of proof. Joseph’s statement that correction requires prior knowledge of what and how to carry it out, as a principal, is confirmed on a daily basis in the real world. His burden of proof is fulfilled. Now it’s your turn.

Nowhere are we talking about evolution. And nowhere is their factual support, positive or negative claim.

Your inability to recognize what constitutes proof for positive and negative claims (especially in light of a materialist predisposition) by no means objectively trivializes what you continuously refuse to accept. It moreso shows your own density as opposed to a true lack of proof as you continue to assert.

Pan, it is not a matter of the present existence of molecular machines and their obeying the laws of physics and chemistry in the present, it is a matter of the origination of these machines. i.e. Where did the functional information come from to build these machines in the first place?

The Capabilities of Chaos and Complexity: David L. Abel – Null Hypothesis For Information Generation – 2009
To focus the scientific community’s attention on its own tendencies toward overzealous metaphysical imagination bordering on “wish-fulfillment,” we propose the following readily falsifiable null hypothesis, and invite rigorous experimental attempts to falsify it: “Physicodynamics cannot spontaneously traverse The Cybernetic Cut: physicodynamics alone cannot organize itself into formally functional systems requiring algorithmic optimization, computational halting, and circuit integration.” A single exception of non trivial, unaided spontaneous optimization of formal function by truly natural process would falsify this null hypothesis.

The Cell as a Collection of Protein Machines
“We have always underestimated cells. Undoubtedly we still do today,,, Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each which is composed of a set of large protein machines.”
Bruce Alberts: Former President, National Academy of Sciences;

The Cell – A World Of Complexity Darwin Never Dreamed Of – Donald E. Johnson – video
http://www.metacafe.com/watch/.....e_johnson/

Cells Are Like Robust Computational Systems, – June 2009
Excerpt: “We now have reason to think of cells as robust computational devices, employing redundancy in the same way that enables large computing systems, such as Amazon, to keep operating despite the fact that servers routinely fail.”
http://www.sciencedaily.com/re.....103205.htm

Simulations reveal new information about the gateway to the cell nucleus
Excerpt: “There are whole machines in living cells that are made of hundreds or thousands of proteins,” says Schulten, “and the nuclear pore is one of those systems. It’s actually one of the most magnificent systems in the cell.”,,,Hundreds to thousands of NPCs are embedded in the nuclear envelope of each cell,”… http://www.psc.edu/science/2006/schulten/

Articles and Videos on Molecular Motors
http://docs.google.com/Doc?doc.....&hl=en

“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 Biologist

William Bialek – Professor Of Physics – Princeton University:
Excerpt: “A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.”

Pan, since you mentioned quantum physics, are you aware that transcendent information is now shown to be independent of matter and energy? As well, are you aware transcendent information is shown to excercise dominion of matter and energy in quantum teleportation experiments?

To top it all off Pan, materialists insist that consciousness has somehow arisen from a 3-dimensional material basis. Yet the double slit experiment, of quantum mechanics, shows that the “infinite quantum information waves” will not collapse to their “uncertain 3-D material particle states” until a conscious observer is present. So Pan, can you please explain how 3-D material reality gave rise to the consciousness that is required for its own existence? The only logical answer, for me, is that consciousness precedes the 3-D material realm and that consciousness resides within the infinite transcendent information realm.

bornagain77 writes (61):

Pan, it is not a matter of the present existence of molecular machines and their obeying the laws of physics and chemistry in the present, it is a matter of the origination of these machines. i.e. Where did the functional information come from to build these machines in the first place?

Do you have a definition of “functional information” that would allow one to calculate it for, say, a strand of human DNA, a yeast cell, and a snowflake?

Do you have any evidence that anything other than chemistry and physics was involved in the evolution of DNA repair mechanisms?

Perhaps we’ll get to the remainder of your post when these two issues are resolved.

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.

What natural laws can’t explain is the presence of the clock itself with its precisely arranged parts, nor why it should keep time at all. The clock defies a natural explanation because no laws describe its assembly nor its purpose.

We know that the clock does not form itself by any known physico-chemical process. That we can understand the physics of its operation does nothing to explain its presence.

So it seems for biochemical mechanics. The physics and chemistry may explain the interactions, but they do not explain the system itself. Physics can explain the interaction between the parts of the grandfather clock, but the clock itself also needs explaining. The precise design and arrangement of parts cannot be explained by physics and chemistry.

It’s not the chemical interactions that design proponents have a problem with; it’s the specific arrangement of protein parts that serve a purpose toward functional interaction. The parts and their composition defy natural explanation, not their chemical (or physical) interactions.

This whole thread seems to be about semantics. I say that a computer doesn’t actually perform facial recognition by itself. Someone else says that clearly it does, and that they can describe physically how it all takes place. What still needs explanation however is the computer itself, the algorithm, and the programming that made it happen. The mind performed the facial recognition, and used the computer as a tool to develop a set of rules for solving these types of problems autonomously. Much in the same way, a mind designed the clock and made use of physical laws to reproduce reliable behavior for the purpose of timekeeping. Natural laws are wholly inadequate as an explanation for either.

Design proponents claim that the cell is in the same category as the clock (or the computer, with its software) — that natural laws are inadequate to explain the intricate nano-machinery of biological organisms. This claim is refuted by showing by what natural laws govern the generation of such systems, absent intelligent design — and not simply by demonstrating the physical laws by which they operate.

It has now been demonstrated Irreducible Complexity can be mathematically quantified as functional information bits(Fits).

Functional information and the emergence of bio-complexity:
Robert M. Hazen, Patrick L. Griffin, James M. Carothers, and Jack W. Szostak:
Abstract: Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define ‘functional information,’ I(Ex), as a measure of system complexity. For a given system and function, x (e.g., a folded RNA sequence that binds to GTP), and degree of function, Ex (e.g., the RNA-GTP binding energy), I(Ex)= -log2 [F(Ex)], where F(Ex) is the fraction of all possible configurations of the system that possess a degree of function > Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of functions.
http://genetics.mgh.harvard.ed.....S_2007.pdf

Mathematically Defining Functional Information In Molecular Biology – Kirk Durston – short video
http://www.metacafe.com/watch/.....k_durston/
Entire video:
http://vimeo.com/1775160

for your second question, do you have any proof whatsoever, besides wishful speculation, that these machines arose from purely materialistic processes?

“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 Biologist

Pan Narrans:

What I’m hearing, and please correct me if I’m misconstruing your position, is that biologists and biochemists have discovered a wide variety of repair mechanisms that use pretty well understood chemistry and physics to fix certain kinds of errors that occur when DNA replicates.

Except they haven’t done that.

Ya see there isn’t anything at all that demonstrates living organisms are reducible to chemistry and physics.

If you have real support for your positions I would be very interested to hear it.

Other than the fact that every time we observe proof-reading and error correction an agency is involved?

That is enough for rational people.

If all you have is the thing being discussed as evidence for a mechanism for the thing being discussed, then you are not rational.

I am sure that spellchecker does not violate any laws of physics- IOW it procedes via understood physics.

Does that mean it is a blind, undirected process?

And why can’t you find any support for your position- that blind molecules can correct errors- outside of biology?

I find that lack of support very telling.

And as if you can use the thing being debated as supporting your side of the debate- talk about circular…

hrun0815:

And nowhere is their factual support, positive or negative claim.

Factual support-

Every time we have observed proof-reading and error-correction there has always been an agency involved.

What else do you need?

Are you kind of person who thinks the Sun might “rise” in the West tomorrow?

Apollos-

Are you trying to say that clocks are supernaturally Created?

PaulN:

The fact that knowledge of what to correct and how to correct it are necessarily required to actually carry out correction is damn near axiomatic.

What if one doesn’t understand the meaning of “axiomatic”?

Joseph, actually I’m saying that clocks are an emergent property of agency.

Apollos-

Obviously you have never heard of the “biological clock”…

heh-heh

Biological clocks are evidence that clocks are an emergent property of chemistry and physics…

Paley’s Watch Found in Bacteria
The conjunction of structural, biophysical, and biochemical approaches to this system reveals molecular mechanisms of biological timekeeping. http://creationsafaris.com/cre.....#20081031a

Biological Clock Excerpt:

The high-resolution structures of these proteins suggest a ratcheting mechanism by which the KaiABC oscillator ticks unidirectionally. This posttranslational oscillator may interact with transcriptional and translational feedback loops to generate the emergent circadian behavior in vivo.

BA77, to the first sentence of your [64], Zachriel replies:

No. The Functional Information in the paper has nothing to do with Irreducible Complexity, but “Functional Information as a Measure of System Complexity.” The measure is dependent on the function x being considered, and a minimum specified degree of function Ex. A certain fraction F(Ex) will have the minimum specified degree of function, yielding the Functional Information -log2F(Ex).

So a highly complex structure that has a function y may have zero (or undefined) Functional Information for function x. And everything has zero Functional Information if the minimum specified degree of function is zero. In other words, the measure, being highly dependent on the assumptions, is not an unambiguous metric.

Factual support-

Every time we have observed proof-reading and error-correction there has always been an agency involved.

What else do you need?

That is your factual support? We have error correction by humans and not by humans. Of one we know that it requires human-mental processes. Of the other, we don’t know. So you simply assume that because in one agency is involved, it must also be true for the other?

That’s not factual support. That’s simply another assertion of the same fact.

Re#64: You say that the Szostak lab has defined functional information. Not that anybody has actually produced the functional information of complex biological systems, but that is besides the point. You seem to indicate that there is a connection of this type of ‘functional information’ to quantifying ‘Irreducible Complexity’. I personally don’t see the connection.

Could you explain so that we can once and for all have an objective way to defining and assigning ‘Irreducible Complexity’?

Apollos@64

Thanks very clearly stated.

Apollos,

Nice!

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).

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.

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.

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.

David Kellogg-

Do you really think that Zachriel has something relevant to say?

Do you take her laundry to the cleaners also?

Too funny…

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.

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.

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.

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.

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.

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.

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.

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.

re#92: Restating the assertion in other words apparently counts for some as stating facts supporting said assertion.

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?

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?

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?

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?

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.

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:

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.

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?

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.

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”!

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).

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.

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.

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?

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?

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…

Who thinks that spellchecker is a blind process?

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,
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/....._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/.....r_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 Biologist

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…

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,

I await your evidence with bated breath. Until you provide some, I leave the floor to you.

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?

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 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.

To clarify the above: only the first sentence was meant to address Joseph’s comment. The remainder is just me spouting off in general.

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…

Re #114: All unicorns are pink.

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?

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….

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?

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.

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.

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.

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.

Joseph

All unicorns are pink.

http://www.homestarrunner.com/crystal.html

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.

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-

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 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:

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.