DNA preserves the integrity of its program

pshun2404

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It is a wonderful curiosity how the program of DNA has within it the means to preserve its own integrity. The production of the very enzymes that preserve the intended program and protect it from random mutations is amazing in that even in the earliest Eukaryotes this protection and repair program is already functional and in place. All laymen should view at least these...

Mechanisms of DNA damage and repair – Professor Dave


Error Corrections in DNA pt 1: Guard Against Random Mutations


In Molecular Biology of the Cell (5th ed.), New York: WH Freeman, p. 963, by Lodish, Berk, Matsudaira, Kaiser, Krieger, Scott, Zipursky, and Darnell (2004), tell us that between 10,000 to 1,000,000 damage or mutation events occur daily in each cell. Of the 6 billion bases these could affect, this constitutes a rate of approximately 0.000165% of the human genome. In response there are over 100 cellular enzymes at work constantly repairing any sequence change leaving resulting damage almost nill.

Permanent base pair mutations are so unlikely, that only around 1 in 10,000,000,000 remain unrepaired. That means there is only a 0.00000001% chance of a single base pair mutation remaining and having its effect! When this does occur (and it does), in almost every case, it is detrimental or neutral.

The numbers of those that possibly remain and have a positive effect that could be “selected” (so to speak) to remain, are even more rare than this incredibly small number. From the perspective of probability it is almost impossible (but can and does occur).

So what we see here is that not only does DNA contain a powerfully effective pre-coded plan to produce all that the organism will become (every organ, system, and their interactions) but has a system in place from its own beginning (enzymes it itself codes for thereafter) to assure that this specific organism will result. DNA fulfills its purpose so predictably that it is not reasonable in my opinion to assume that it came about via random mutations over time. Random mutations are an effect that still occurs and mostly destroys but it is not a cause. The reality had to already exist in order to be mutated.

What are your thoughts?
 
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Speedwell

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It is a wonderful curiosity how the program of DNA has within it the means to preserve its own integrity.
And at the same time it has the means within it to produce random variation. That is even more wonderful, when you think of it.
 
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Sanoy

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How does this affect the evolutionary time line? Is there enough life permitting time on earth to allow for enough random mutations given the natural tendency of life to greatly counteract those mutations? I wonder if anyone has done the calculations.
 
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Speedwell

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As I said they do occur but it is not part of the program (which fights so hard to eliminate them)
Does it? One of the problems which arises with the careless habit of referring to the theory as evolution by mutation and natural selection is that it misrepresents the role of genetic mutations in the process. Natural selection acts on random variation--to which mutations contribute but are not the sole cause. One can easily form the mistaken impression by this careless use that species morphology is static until a mutation strikes a single individual. Even worse, I have seen creationists argue that random heritable variation is distinct from mutation as a source of selectable variants.
 
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pshun2404

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Does it? One of the problems which arises with the careless habit of referring to the theory as evolution by mutation and natural selection is that it misrepresents the role of genetic mutations in the process. Natural selection acts on random variation--to which mutations contribute but are not the sole cause. One can easily form the mistaken impression by this careless use that species morphology is static until a mutation strikes a single individual. Even worse, I have seen creationists argue that random heritable variation is distinct from mutation as a source of selectable variants.

Definitely not thought of as the only cause (but alleged to be significant none the less). So what types of mutations other than genetic mutations are YOU referring to? As in the case of the Blackcap (which has undergone various topical variations) we know these to be mostly the result of speciation (predominately adaptation and geophysical isolation) but in such cases epigenetics most probably effects the genome (but they remain Blackcaps). So what are you referring to?
 
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Speedwell

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Definitely not thought of as the only cause (but alleged to be significant none the less). So what types of mutations other than genetic mutations are YOU referring to? As in the case of the Blackcap (which has undergone various topical variations) we know these to be mostly the result of speciation (predominately adaptation and geophysical isolation) but in such cases epigenetics most probably effects the genome (but they remain Blackcaps). So what are you referring to?
What I am referring to is that genome is not the same as phenome. What Darwin observed, and what is still true is that the evolutionary process is so disposed that each new generation of a species presents a randomly distributed range of variants to the environment for selection. It is that morphology which is subject to selection, not genetics--not directly. Mutations are only one cause of that variation, necessary to it but not the sole cause. There are other subroutines at work; I have already described to you, for instance, how the standard deviation of the random variation changes in response to environmental stress levels. I suppose you would class that among epigenetic phenomena, but the point stands: epigenetics is just one more contributor to the random variation of the phenotype, which is the raw material on which natural selection works.
 
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Tanj

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What are your thoughts?

Thought 1: Error correction of DNA damage in somatic cells != what happens in meiosis.

In Molecular Biology of the Cell (5th ed.), New York: WH Freeman, p. 963, by Lodish, Berk, Matsudaira, Kaiser, Krieger, Scott, Zipursky, and Darnell (2004), tell us that between 10,000 to 1,000,000 damage or mutation events occur daily in each cell. Of the 6 billion bases these could affect, this constitutes a rate of approximately 0.000165% of the human genome. In response there are over 100 cellular enzymes at work constantly repairing any sequence change leaving resulting damage almost nill.

Permanent base pair mutations are so unlikely, that only around 1 in 10,000,000,000 remain unrepaired. That means there is only a 0.00000001% chance of a single base pair mutation remaining and having its effect!

Thought 2: You are misrepresenting the data. Let's assume the lower bound (10000 mutations/day/cell)
There are 3.7 x10^12 cells in your body, so that is 3.7x10^16 mutation events/body/day. If 1 in 10^10 are not corrected, that leaves 3.7x10^6 (or 3.7 million) mutations that stay, every day.
 
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pshun2404

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What I am referring to is that genome is not the same as phenome. What Darwin observed, and what is still true is that the evolutionary process is so disposed that each new generation of a species presents a randomly distributed range of variants to the environment for selection. It is that morphology which is subject to selection, not genetics--not directly. Mutations are only one cause of that variation, necessary to it but not the sole cause. There are other subroutines at work; I have already described to you, for instance, how the standard deviation of the random variation changes in response to environmental stress levels. I suppose you would class that among epigenetic phenomena, but the point stands: epigenetics is just one more contributor to the random variation of the phenotype, which is the raw material on which natural selection works.

I know, but even Phenotype is based in Genotype...just as Epigenetics influences how or which genes (hence the "GENES") express, though I would not count the Epigenetic effect as "mutation", just influential or resulting from differences between individuals in their different environments.

Random mutations in the genome are not the same, they are errors, disturbances, destructions, new additions (like many of the alleged ERVs), and so on. And for the most part the mechanism we are discussing counter-acts and corrects 99.99999% of these. The numbers that "succussfully" remain are so slight it is just as reasonable to assume these may not transmutate organisms across genera as it is to assume they may.

Secondly, we having never observed a case where this repair process is not also present which evolved first? Could the correction process have evolved first? Then the earlier, assumed to be less, genome would never have sophisticated to this level (not enough time in life-form history). And would not the DNA have to pre-exist in order to produce these enzymes in the first place? Could a cell produce the DNA without a translation transcription process already in place? Or the DNA already exist to produce the cell it resides in?

In my opinion, the pre-coded instructions of the DNA, and its repair mechanism (to preserve the encoded program) had to have arisen simultaneously. Neither occurred through natural selection of such a miniscule number of alleged positive or useful random mutations. I don't see any, cannot show ones that were not there and now are which produced a positive effect, we have never found any...so why should I accept them as real or true?
 
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Speedwell

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The numbers that "succussfully" remain are so slight it is just as reasonable to assume these may not transmutate organisms across genera as it is to assume they may.
Do you have any examples of organisms which have "transmutated across genera?" I am not aware of any, and as I understand it such an occurrence would falsify the ToE.
 
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pshun2404

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Do you have any examples of organisms which have "transmutated across genera?" I am not aware of any, and as I understand it such an occurrence would falsify the ToE.

That was a mere example that I was saying was not a possibility in my opinion (apparently you agree), but yet many believe that transmutation crosses over classes (do you agree many believe this?).
 
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Speedwell

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That was a mere example that I was saying was not a possibility in my opinion (apparently you agree), but yet many believe that transmutation crosses over classes (do you agree many believe this?).
No. If a new species splits off from an existing species, the two of them will remain members of the same genus. Only if the member species of the genus grow more numerous and it becomes convenient to split one genus into two will a species become a member of a new genus (but it is still a member of the original genus, promoted now to family). This is the nested hierarchy we have been trying to tell you about, and the same applies at any level of the taxonomy. No species will ever evolve from one existing genus to another existing genus, just as no order will move from one existing class to another. All evolution can do is branch; there are no crossovers.
 
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pshun2404

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No. If a new species splits off from an existing species, the two of them will remain members of the same genus. Only if the member species of the genus grow more numerous and it becomes convenient to split one genus into two will a species become a member of a new genus (but it is still a member of the original genus, promoted now to family). This is the nested hierarchy we have been trying to tell you about, and the same applies at any level of the taxonomy. No species will ever evolve from one existing genus to another existing genus, just as no order will move from one existing class to another. All evolution can do is branch; there are no crossovers.

I see! So you are saying fish (one class) never became reptiles (another class) or reptiles never eventually became birds or mammals and so on?
 
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pshun2404

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Nested Hierarchies are just a masterful application of set theory where man decides criteria to group particular items in question, so they carry the concept of being related as in being similar but in fact they do not automatically imply lineage in any way. Nested Hierarchies are applied in many fields for many purposes but they are all the stuff of man's mind.

All such systems of classification, though intelligently designed, have been around for eons and some are more practical than others, but rarely would one assume they imply lineage but rather similarity. All citrus fruits for example are similar in many ways and are certainly different from non-citrus fruits and yes they are all fruits but this does not imply that lemons became oranges or apples over long periods of time (and certainly not vegetables).
 
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Speedwell

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I see! So you are saying fish (one class) never became reptiles (another class) or reptiles never eventually became birds or mammals and so on?
No, I am saying no such thing. What I am saying is that no species ever moved from one existing genus to another existing genus. The classes were named post hoc to describe convenient groupings of multiple branching speciation events. There would have been (if somebody had been around to name them) no classes until enough species had formed to justify that taxonomic rank. Keep in mind that the taxonomy is purely descriptive. It is not a pre-existing system of categories into which species evolve. Re-read my previous post. If the species of a genus proliferate and become very numerous, the genus may become a family and the member species split into two or more genera. That is not the same as a species "crossing over" from one pre-existing genus to another one, which according to the theory of evolution can never happen. If a species becomes a member of a new genus it is because one has been created for it. The same principle applies at all levels of the taxonomy.
 
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Speedwell

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Nested Hierarchies are just a masterful application of set theory where man decides criteria to group particular items in question, so they carry the concept of being related as in being similar but in fact they do not automatically imply lineage in any way. Nested Hierarchies are applied in many fields for many purposes but they are all the stuff of man's mind.
Correct.

All such systems of classification, though intelligently designed, have been around for eons and some are more practical than others, but rarely would one assume they imply lineage but rather similarity. All citrus fruits for example are similar in many ways and are certainly different from non-citrus fruits and yes they are all fruits but this does not imply that lemons became oranges or apples over long periods of time (and certainly not vegetables).
That's a joke, right? Because otherwise you really don't understand evolution at all.
 
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DogmaHunter

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That means there is only a 0.00000001% chance of a single base pair mutation remaining and having its effect! When this does occur (and it does), in almost every case, it is detrimental or neutral.

The numbers of those that possibly remain and have a positive effect that could be “selected” (so to speak) to remain, are even more rare than this incredibly small number. From the perspective of probability it is almost impossible (but can and does occur).

These are the numbers for a single individual. I'll go ahead and accept them at face value, for the sake of argument.

What's the central idea of any probability figure? Answer: that in a single trial you have x chances out of Y that it happens.

The single trial here, is a single instance.
Now, what happens with the probability figure if you raise the amount of instances?

1 chance in a trillion is really small. So small, you might just as well call it "practically" impossible.

However... Consider 100 trillion trials. Is it still "practically impossible"? Or would it rather mean that theoretically, it will occur 100 times?


DNA fulfills its purpose so predictably that it is not reasonable in my opinion to assume that it came about via random mutations over time.

That's nice.
The thing is though, it isn't based on assumption and your personal opinion is rather irrelevant.

What are your thoughts?

My thoughts are that your argument is self-defeating.
 
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FrumiousBandersnatch

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... not only does DNA contain a powerfully effective pre-coded plan to produce all that the organism will become (every organ, system, and their interactions) but has a system in place from its own beginning (enzymes it itself codes for thereafter) to assure that this specific organism will result.
Early genomes would have been tiny, with no means to correct errors - such a genome would be very mutable and subject to very strong selection - ideal conditions for rapid evolution to produce novel proteins - eventually including simple repair enzymes. With each stabilising development, the rate of novelty production would drop, and that particular selection pressure would ease a little. So you'd expect an initial burst of extremely rapid innovation and die-off, reducing slowly until the genomes were stable enough to produce differentiated populations adapted for different niches.

DNA fulfills its purpose so predictably that it is not reasonable in my opinion to assume that it came about via random mutations over time.
Classic argument from incredulity.

Random mutations are an effect that still occurs and mostly destroys but it is not a cause. The reality had to already exist in order to be mutated.
Gibberish.
 
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pshun2404

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No, I am saying no such thing. What I am saying is that no species ever moved from one existing genus to another existing genus. The classes were named post hoc to describe convenient groupings of multiple branching speciation events. There would have been (if somebody had been around to name them) no classes until enough species had formed to justify that taxonomic rank. Keep in mind that the taxonomy is purely descriptive. It is not a pre-existing system of categories into which species evolve. Re-read my previous post. If the species of a genus proliferate and become very numerous, the genus may become a family and the member species split into two or more genera. That is not the same as a species "crossing over" from one pre-existing genus to another one, which according to the theory of evolution can never happen. If a species becomes a member of a new genus it is because one has been created for it. The same principle applies at all levels of the taxonomy.

So then Speciation is what eventually brings fish to become reptiles and so on, all the way to humans?
 
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