DNA Information Evolution and ID

[SailingCyclops]

In a Random Ramblings discussion dadman asserted:

.. since all code derives from an intelligent source . . .
[...]
I do believe the subject is not so much evolution . . . but intelligence . . .
do you know anything about this "evolution coder/de-coder" ??

ref:This post

The assertion is made that since DNA is a code, there must be a coder. Presumably, some intelligent entity.

Questions for debate:

Is the coding, and information transfer we observe in DNA a product of evolution by natural selection? Or does DNA information and it's transfer demand an intelligence?

Does all code derive from an intelligent source?

Bob

[Starboard Tack]

[quote="nygreenguy"][quote="Starboard Tack"]


I think I have said it before, but I'll try one more time. Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. If other scientists disagree with him, they disagree with him.

But I am curious. The last paper states that DNA may have evolved into the non-evolvable form twice. Can you tell me whether you think it plausible that this happened in the duration between the end of frustration events during the Late Heavy Bombardment period about 3.9 billion years ago and when evidence of photosynthetic life is indicated 3.83 billion years ago?

[delcoder]

Where does the article suggest the mutations were not "spontaneous" or "random"?

Cherry picking, always cherry picking. The introduction clause of the article said:

For more than a decade, Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, has solidified her premise that when cells are under stress, the rate of gene changes called mutations goes up
Source: redOrbit (http://s.tt/13Ysv)

Emphasis added.

and:

This time, she used bacteria that had a defective gene for resistance to an antibiotic called tetracycline. If the gene had worked, the cells would be resistant to the antibiotic. Instead, these cells were susceptible. Again, she starved the cells. In response to the starvation, the cells increased their rate of mutation including mutation of the defective gene.
Source: redOrbit (http://s.tt/13Ysv)

and:

In another set of experiments, she and her colleagues attempted to find out how much stress-induced mutagenesis contributed to spontaneous mutation. To do this, they studied starved cells that were not being stimulated with a second stressor, a DNA break.

One by one, they eliminated the stress-response pathways within the cells that they knew contributed to stress-induced mutagenesis.

"When we did that, half of the mutagenesis went away," said Rosenberg. "That means we can say half of spontaneous mutation is stress-inducible.

Source: redOrbit (http://s.tt/13Ysv)

Mutations are still random. Do you understand the underlying genetics on WHY there was increased mutation (or how we get mutations at all)? Stress tends to create more mutations because the cells are working faster. We are getting more activity within the genome increasing the rate of mutations.

If they have a lottery drawing 5 times a day instead of once, the results are still just as random, they just happen more frequently.

Great explanation, but leaves out important facts. Here is what she said:

We discovered that the normally high-fidelity mechanism of DNA double-strand-break repair is switched to a mutagenic version of that mechanism, using a special error-prone DNA polymerase, specifically when cells are stressed, under the control of two cellular stress responses. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then.

http://www.bcm.edu/cmb/?pmid=2391

]The main premise of epigenetic changes is they are environment driven. Obviously, what she has found here is that the rate of mutations is also environmentally driven. Coincidence?

Yes. Can you show otherwise how the two are in any way causally correlated?

No, but I am working on it. nursebenjamin provided me with two avenues of research regarding this phenomenon.

The mundane and hardly proven premise that all mutations are errors has always seemed peculiar to me.

A mutation is, by definition, an error.

Really? Any more gems of wisdom?

]First a mistake has to be made. Considering millions of individual base pair copies are made why do a few get copied wrong.

Because it is imperfect.

Then there is the proof reading mechanism that corrects the errors.

Which is also imperfect.

Who said it wasn't?

It seems strange and highly improbable that this mechanism would fail to correct some of the same errors made previously.

Do you understand the mechanism, the protein complexes involved and how they interact? Once an error gets past the first proofreading, it will not ever be switched back to the "original" because of the nature of the mechanism. The mechanism has no knowledge of what the sequence should be, it only checks for errors through chemical physical incompatibility.

Can it not make mistakes when checking for "errors through chemical physical incompatibility?" Is it possible that mechanism could determine there was an incompatibility when there was no incompatibility? If so would it not be logical the mechanism would attempt to correct an error where no error exists?

Again the question needs to be asked why is the proof reading mechanism 100% efficient on millions of base pairs and then goof on the very few miss copied base pairs.[/quote]

This statement doesnt make sense. It is like me looking at a test where I got 2 problems wrong and saying "I got a 100% expect for these 2 problems!"

Not at all. It is more like looking at a test where all the problems were answered correctly and two were marked wrong. Why? Because the comparison model was misread.

Of course I am looking at all this from a purely logical standpoint, but it seems to me that scientists are blindly accepting a premise just as they blindly accepted "junk DNA."

Instead of criticizing the people who spend their lives doing this, and doing this pretty effectively, have you considered the fact you may be wrong?

Very definitely. In fact the number of times I have been wrong when I was absolutely sure I was right that makes me wonder about the infallible "people who spend their lives doing this." Look at what the Darwin followers did to Lamark.

Also, you cant do science by logic alone. All logic does is analyze statements. If you dont have the scientific background to make, understand, or interpret the facts and concepts, logic is useless.

Who said doing science was by logic alone? It is my position that one should view all evidence logically. If you don't think logically all the scientific background to make, understand, or interpret the facts and concepts are useless.

[nursebenjamin]

... Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. ...

Can you provide a source for this quote please. My impression is that you have a habit in these threads of quote-mining and misquoting scientists. This isn't the first unsourced "quote" that you have posted.

[nygreenguy]

... Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. ...

Can you provide a source for this quote please. My impression is that you have a habit in these threads of quote-mining and misquoting scientists. This isn't the first unsourced "quote" that you have posted.

He sourced it a while back. He just misinterprets the paper over and over.
http://profiles.nlm.nih.gov/SC/B/C/C/B/_/scbccb.pdf

Our discussion of it is here:
http://debatingchristianity.com/forum/v ... 023#414023

[nygreenguy]

I think I have said it before, but I'll try one more time. Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. If other scientists disagree with him, they disagree with him.

No no no no no. He NEVER said that. I even explained this all the way down to the specific mechanisms and proteins involved.

But I am curious. The last paper states that DNA may have evolved into the non-evolvable form twice. Can you tell me whether you think it plausible that this happened in the duration between the end of frustration events during the Late Heavy Bombardment period about 3.9 billion years ago and when evidence of photosynthetic life is indicated 3.83 billion years ago?

First, there is no "non-evolveable form" so I cant speak to that part. Also, I still question the accuracy of your dates, but ignoring all of this, this event would have began at (b) of their Figure 2 at a point when cells were using both RNA and DNA. It is a pretty interesting paper with good graphs and figure for non-molecular biologists but I am not so sure how exactly it has help up over the past 12 years. Either way, if you have more specific questions about the paper, I am happy to respond.

[nygreenguy]

Where does the article suggest the mutations were not "spontaneous" or "random"?

Cherry picking, always cherry picking. The introduction clause of the article said:

For more than a decade, Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, has solidified her premise that when cells are under stress, the rate of gene changes called mutations goes up
Source: redOrbit (http://s.tt/13Ysv)

Emphasis added.

and:

This time, she used bacteria that had a defective gene for resistance to an antibiotic called tetracycline. If the gene had worked, the cells would be resistant to the antibiotic. Instead, these cells were susceptible. Again, she starved the cells. In response to the starvation, the cells increased their rate of mutation including mutation of the defective gene.
Source: redOrbit (http://s.tt/13Ysv)

and:

In another set of experiments, she and her colleagues attempted to find out how much stress-induced mutagenesis contributed to spontaneous mutation. To do this, they studied starved cells that were not being stimulated with a second stressor, a DNA break.

One by one, they eliminated the stress-response pathways within the cells that they knew contributed to stress-induced mutagenesis.

"When we did that, half of the mutagenesis went away," said Rosenberg. "That means we can say half of spontaneous mutation is stress-inducible.

Source: redOrbit (http://s.tt/13Ysv)

Mutations are still random. Do you understand the underlying genetics on WHY there was increased mutation (or how we get mutations at all)? Stress tends to create more mutations because the cells are working faster. We are getting more activity within the genome increasing the rate of mutations.

If they have a lottery drawing 5 times a day instead of once, the results are still just as random, they just happen more frequently.

Great explanation, but leaves out important facts. Here is what she said:

We discovered that the normally high-fidelity mechanism of DNA double-strand-break repair is switched to a mutagenic version of that mechanism, using a special error-prone DNA polymerase, specifically when cells are stressed, under the control of two cellular stress responses. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then.

http://www.bcm.edu/cmb/?pmid=2391

I know what she said, Ive read her actual paper and other like it. The process is still random. The rate has changed, but the process is still random.

The mundane and hardly proven premise that all mutations are errors has always seemed peculiar to me.

A mutation is, by definition, an error.

Really? Any more gems of wisdom?

If you would use the definitions properly, I wouldnt be forced to correct you.

It seems strange and highly improbable that this mechanism would fail to correct some of the same errors made previously.

Do you understand the mechanism, the protein complexes involved and how they interact? Once an error gets past the first proofreading, it will not ever be switched back to the "original" because of the nature of the mechanism. The mechanism has no knowledge of what the sequence should be, it only checks for errors through chemical physical incompatibility.

Can it not make mistakes when checking for "errors through chemical physical incompatibility?" Is it possible that mechanism could determine there was an incompatibility when there was no incompatibility? If so would it not be logical the mechanism would attempt to correct an error where no error exists?[/quote] Yes and no. DNA polymerase tends to do most of the work. It does the replication, proofing, AND the fixing and it is doing this all at the same time. If you knew the process you would see why your question doesnt seem to make any sense. The mechanism (protein) which creates the errors is also the one that fixes it all usually in the same "time" so you cant really differentiate between a mismatch from replication vs. a mismatch from proofing.

Again the question needs to be asked why is the proof reading mechanism 100% efficient on millions of base pairs and then goof on the very few miss copied base pairs.

This statement doesnt make sense. It is like me looking at a test where I got 2 problems wrong and saying "I got a 100% expect for these 2 problems!"

Not at all. It is more like looking at a test where all the problems were answered correctly and two were marked wrong. Why? Because the comparison model was misread.

Except in this case, the teacher IS the student. It tries to copy the other strand but it just makes mistakes. To even think about it being 100% "efficient" is not accurate. I would suggest watching some of the youtube videos on DNA replication to understand the process in more detail.

Very definitely. In fact the number of times I have been wrong when I was absolutely sure I was right that makes me wonder about the infallible "people who spend their lives doing this." Look at what the Darwin followers did to Lamark.

Scientists readily admit they can be wrong. Anytime anyone thinks they are absolutely right is when you should be skeptical.

Who said doing science was by logic alone? It is my position that one should view all evidence logically. If you don't think logically all the scientific background to make, understand, or interpret the facts and concepts are useless.

Correct, the two are inseparable. However, you must HAVE the background FIRST before you can logically analyze it.

[delcoder]

Where does the article suggest the mutations were not "spontaneous" or "random"?

Cherry picking, always cherry picking. The introduction clause of the article said:

For more than a decade, Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, has solidified her premise that when cells are under stress, the rate of gene changes called mutations goes up
Source: redOrbit (http://s.tt/13Ysv)

Emphasis added.

and:

This time, she used bacteria that had a defective gene for resistance to an antibiotic called tetracycline. If the gene had worked, the cells would be resistant to the antibiotic. Instead, these cells were susceptible. Again, she starved the cells. In response to the starvation, the cells increased their rate of mutation including mutation of the defective gene.
Source: redOrbit (http://s.tt/13Ysv)

and:

In another set of experiments, she and her colleagues attempted to find out how much stress-induced mutagenesis contributed to spontaneous mutation. To do this, they studied starved cells that were not being stimulated with a second stressor, a DNA break.

One by one, they eliminated the stress-response pathways within the cells that they knew contributed to stress-induced mutagenesis.

"When we did that, half of the mutagenesis went away," said Rosenberg. "That means we can say half of spontaneous mutation is stress-inducible.

Source: redOrbit (http://s.tt/13Ysv)

Mutations are still random. Do you understand the underlying genetics on WHY there was increased mutation (or how we get mutations at all)? Stress tends to create more mutations because the cells are working faster. We are getting more activity within the genome increasing the rate of mutations.

If they have a lottery drawing 5 times a day instead of once, the results are still just as random, they just happen more frequently.

Great explanation, but leaves out important facts. Here is what she said:

We discovered that the normally high-fidelity mechanism of DNA double-strand-break repair is switched to a mutagenic version of that mechanism, using a special error-prone DNA polymerase, specifically when cells are stressed, under the control of two cellular stress responses. The stress responses increase mutagenesis specifically when cells are maladapted to their environments, i.e. are stressed, potentially accelerating evolution then.

http://www.bcm.edu/cmb/?pmid=2391

I know what she said, Ive read her actual paper and other like it. The process is still random. The rate has changed, but the process is still random.

I don't think you and I are on the same page with this random business. What I have read about "Directed Mutations" and "Adaptive Mutations" indicates the vast increase of mutations in the genome area where help is to be found is not random. The specific mutations are, obviously, random. It seems to me that living organisms are equipped with a mechanism (epigenetics) which allows for existing genes to be expressed or suppressed to provide adaptive responses. When no genes are present that can be expressed or suppressed which will allow adaptive responses then directed mutations attempt to produce beneficial mutations. Having no template to work with they must be random attempts, but not random as to where they occur.

This, sir, is the product of logic. It is not a religious clutching to spontaneous and random mutations in an attempt to defend Darwinism. Purely random mutations and natural selection has never been a logical approach to survival. It is inane and flies in the face of the basic reasoning that there must be a cause and effect relationship with respect to genetics as well as any other aspect of knowledge.

It seems strange and highly improbable that this mechanism would fail to correct some of the same errors made previously.

Do you understand the mechanism, the protein complexes involved and how they interact? Once an error gets past the first proofreading, it will not ever be switched back to the "original" because of the nature of the mechanism. The mechanism has no knowledge of what the sequence should be, it only checks for errors through chemical physical incompatibility.

Can it not make mistakes when checking for "errors through chemical physical incompatibility?" Is it possible that mechanism could determine there was an incompatibility when there was no incompatibility? If so would it not be logical the mechanism would attempt to correct an error where no error exists?[/quote]

Yes and no. DNA polymerase tends to do most of the work. It does the replication, proofing, AND the fixing and it is doing this all at the same time. If you knew the process you would see why your question doesnt seem to make any sense. The mechanism (protein) which creates the errors is also the one that fixes it all usually in the same "time" so you cant really differentiate between a mismatch from replication vs. a mismatch from proofing.

I will chew on that for a while, but it still doesn't sit well. Spontaneous and random mutations at any point in DNA makes no sense. First, they are extremely infrequent. Second, the fact they are said to occur anywhere in DNA indicates the odds are even more reduced they could have a beneficial effect as most of the DNA is non coding. (Junk) The odds of non directed mutations actually aiding a species to survive are insurmountable.

[Starboard Tack]

... Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. ...

Can you provide a source for this quote please. My impression is that you have a habit in these threads of quote-mining and misquoting scientists. This isn't the first unsourced "quote" that you have posted.

Really? Could you name another?

This is from Crick's 1968 paper in J. Molecular Biology "The Origin of the Genetic Code", referenced in "Creating Life in the Lab" by F. Rana. The reason for believing that DNA could not have evolved once developed was because any change in codon assignments would result in change in amino acids in every protein made by the cell. Since this would yield a very large number of defective proteins the results would be death for the cell. Changes that result in death are generally considered to be dead ends, evolution wise.

From http://www.thefreeresource.com/the-gene ... cs-dna-rna: "Woeses theory states that the code is universal for stereochemical reasons, while Cricks theory states that the genetic code is universal because changing anything in the code would be damaging or deadly. Both theories continue to be debated among scientists today."

The combination of the appearance as soon as the earth cooled of a coding system that is unimaginably complex while still be optimixed, and which could not change and still produce functional living organisms is what led Crick and Orgel to theorize that life must have been brought to earth by aliens, a.k.a. directed panspermia. In their view there simply wasn't enough time on earth for such a coding system to appear through unguided processes. As Crick said in his book "Life Itself", "The origin of life appears...to be almost a miracle, so many are the conditions which would have had to be satisfied to get it going." He later thought he was too pessimistic on the possibility of life appearing on earth with the development of the RNA world theory. However, since the RNA world theory now appears to be a dead end, with researchers looking for some mechanism whereby RNA could itself come into existence (a pre-pre-DNA world), Crick seems to have got it right the first time. Some intelligence is required to account for the existence and nature of the universal DNA code. Like Crick, Hoyle, Wickramsinghe and Orgel, you may prefer Dr. Spock as the source of that intelligence, what with that being a scientific conclusion and all. Myself, I think a simpler explanation is worth considering. Since the universe itself has a cause since it came into being, and since the nature of the thing caused displays intelligent design for life, perhaps that intelligence is responsible not only for creating the precise conditions where life could exist, but is also responsible for bringing life into existence in the first place.

Or maybe Spock didit.

Is it really necessary for you to try to validate your position by accusing others of lying, even if done so politely?

[Starboard Tack]

I think I have said it before, but I'll try one more time. Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. If other scientists disagree with him, they disagree with him.

No no no no no. He NEVER said that. I even explained this all the way down to the specific mechanisms and proteins involved.

We'll have to agree to disagree on what Crick meant in his paper on the origin of the genetic code, or why he concluded that aliens must have brought it to earth.

But I am curious. The last paper states that DNA may have evolved into the non-evolvable form twice. Can you tell me whether you think it plausible that this happened in the duration between the end of frustration events during the Late Heavy Bombardment period about 3.9 billion years ago and when evidence of photosynthetic life is indicated 3.83 billion years ago?

First, there is no "non-evolveable form" so I cant speak to that part. Also, I still question the accuracy of your dates, but ignoring all of this, this event would have began at (b) of their Figure 2 at a point when cells were using both RNA and DNA. It is a pretty interesting paper with good graphs and figure for non-molecular biologists but I am not so sure how exactly it has help up over the past 12 years. Either way, if you have more specific questions about the paper, I am happy to respond.

I grant that there are disputes about whether chemical signatures in Isua green belt formations that are consistent with life might be explained otherwise, but dating photosynthesizing cyanobacteria to a least 3.5 billion years is not in question. My question related to the likelihood that DNA could have evolved twice, as I gather the paper suggests. Given its complexity, and the chicken and egg nature of a molecule that is made of protein that can't exist without the molecule existing in the first place, and the fact that no one has a plausible scenario for a pre-DNA world that can exist on early earth, doesn't the idea of this compound chemically 'evolving' twice seem a bit far fetched to you?

[Starboard Tack]

...

Crick stated that once formed, DNA could not have evolved. It has to stop evolving because any change would affect every protein in every cell and that would be catastrophic. ...

Can you provide a source for this quote please. My impression is that you have a habit in these threads of quote-mining and misquoting scientists. This isn't the first unsourced "quote" that you have posted.

He sourced it a while back. He just misinterprets the paper over and over.
http://profiles.nlm.nih.gov/SC/B/C/C/B/_/scbccb.pdf

Our discussion of it is here:
http://debatingchristianity.com/forum/v ... 023#414023

Yes, silly me. When Crick writes: "This (Crick's)theory states that the code is universal because at the present time any change would be lethal, or at least very strongly selected against." I clearly misunderstood him. I thought he was saying that any change would be lethal, therefore no change would have likley survived the process of natural selection.

Thank you for the correction.