Can mutations produce mutation repair systems?

[Jonathan_Burke (Jon)]

@WilliamDJ

Step 1 in the scientific method is to reject a theory immediately if it is in conflict with natural laws.

Here’s the problem.

1. You have not proved it is in conflict with natural laws.
2. In order to prove it is in conflict with natural laws, you must apply the scientific method. To date you have not done this. Let me know when you have.
3. You also need to address all the evidence which does not agree with your theory. In this case, that constitutes the several lines of independent evidence for evolution, none of which you have addressed.

All you’re doing is the same thing as Ken Ham does; make unsubstantiated claims while using scientific language to give pseudo-scientific arguments a veneer of credibility.

[Bill_II]

@WilliamDJ

You are wrong. Step 1 in the scientific method is to reject a theory immediately if it is in conflict with natural laws.

Good to know. Then we can throw out General Relativity because it was in conflict with Newton’s natural laws? We wouldn’t want to waste any time trying to prove that would we.

@Jonathan_Burke

All you’re doing is the same thing as Ken Ham does; make unsubstantiated claims while using scientific language to give pseudo-scientific arguments a veneer of credibility.

Jon I wouldn’t say @WilliamDJ has risen to the level of “a veneer of credibility” yet. It is more like smoke and mirrors.

[John_Dalton]

@WilliamDJ

Either of you is convinced that organic molecules possess the magical property of spontaneous self-organization, which allows them to form increasingly complex structures with an increasingly higher energy level. This pre-Victorian alchemist faith is diametrically in conflict with empirical science. Molecules possess the natural property of spontaneous disintegration.

This comes up pretty often. My understanding is that it can’t be strictly said to apply in such cases, as the Earth’s surface receives constant inputs of energy from sunlight and underground.

I can’t see why a mutation repair system is any different from anything else that might evolve through natural selection, except that it happens to have the word “mutation” in it.

[gbrooks9 (George Brooks)]

@WilliamDJ

1. Either of you is convinced that organic molecules possess the magical property of spontaneous self-organization, which allows them to form increasingly complex structures with an increasingly higher energy level. This pre-Victorian alchemist faith is diametrically in conflict with empirical science.

@WilliamDJ

I’m waiting for you to send a diatribe to the world’s greatest physicists… that there is no way that the chaotic and unpredictable movement of Hydrogen atoms could ever create a nuclear furnace run on Fusion, and which actually constructs a broad range of new elements in its core. That would be crazy, right?

I’ve said my piece… and you continue to ignore principles of science in favor of poetic ideologies. Enjoy!

[T_aquaticus]

@WilliamDJ

The Miller-Urey experiments proves that a (simple) factory must be built to produce an ever growing amount of amino-acids.

Why would it require a factory? If the same conditions existed in nature the same results would occur.

@WilliamDJ

The physical differences between chimps and humans are caused by differences in their DNA.

Then your claim that DNA can’t change without causing harm is false. Humans and chimps are separated by ~40 million mutations and both species are doing just fine. In fact, both species rely on some of those mutations for function.

@WilliamDJ

These differences are found both in the parts that code for proteins and in the other parts, which appear to be functional as well and are not junk as Darwinists and Naturalists still believe. The progress of science has dismissed this belief to the domain of fairy tales. See: ENCODE, the Encyclopedia of DNA Elements at: https://www.encodeproject.org/. ENCODE makes clear that the DNA is a book, made up of chapters, paragraphs, sentences, words, and letters. Please educate yourself.

Even the ENCODE studied demonstrated that the vast majority of the human genome has no sequence specific function. Their definition of function is so loose that they classified introns as having function.

@WilliamDJ

Indeed, opposed processes can happen simultaneously. But they cannot produce one another.

Why can’t mutations produce a protein that binds to DNA and alters DNA?

[WilliamDJ (William DeJong)]

@Jonathan_Burke

All you’re doing is the same thing as Ken Ham does; make unsubstantiated claims while using scientific language to give pseudo-scientific arguments a veneer of credibility.

What I am doing is defending empirical science against people who do not care for natural laws and logic, blinded by their pre-Victorian Alchemist faith that organic molecules possess the magical property of spontaneous self-organization, which allows them to form increasingly complex structures with an increasingly higher energy level.

@Bill_II

Then we can throw out General Relativity because it was in conflict with Newton’s natural laws?

You are wrong. Newton’s laws are not in conflict with General Relativity. Newton’s laws describe our physical reality for speeds that are not close to the speed of light.

@Bill_II

Jon I wouldn’t say @WilliamDJ has risen to the level of “a veneer of credibility” yet. It is more like smoke and mirrors.

You are wrong. The basic empirical fact of chemistry that oxidation cannot produce reduction (e.g.: rusting of iron cannot produce the transformation of rust into iron) is the basis of chemical industries. Only enemies of science throw out empirical facts as smoke and mirrors.

@John_Dalton

This comes up pretty often

The fundamental properties of physical reality come up pretty often in physical reality.

@John_Dalton

I can’t see why a mutation repair system is any different from anything else that might evolve through natural selection, except that it happens to have the word “mutation” in it

In your fantasy world, shaped by the doctrines of Naturalism and Darwinism, anything can happen. Not in the real world: apples cannot fall downwards and upwards at the same time; a phenomenon P cannot produce M and Opposite-M at the same time; oxidation cannot produce reduction; and mutation cannot produce mutation repair.

@gbrooks9

I’m waiting for you to send a diatribe to the world’s greatest physicists… that there is no way that the chaotic and unpredictable movement of Hydrogen atoms could ever create a nuclear furnace run on Fusion, and which actually constructs a broad range of new elements in its core.

Indeed, inside the furnace of every star, hydrogen atoms can merge together into more complicated atoms. However, sooner or later these more complicated atoms, or even molecules, will fall apart again by radiation that hits them; the bigger they are the sooner. This is what Miller found out in 1953, when trying to produce an ever more concentrated primordial soup. He could only succeed by building a factory where the produced amino acids were transported to a second flask where they were safe for destruction by lightning.

@T_aquaticus

Why would it require a factory? If the same conditions existed in nature the same results would occur.

Factories can only emerge in the fantasy world of Naturalists and Darwinists, not in the real word. If such a thing would happen, an ever growing amount of complex molecules, and thus an ever growing amount of energy, would become available for free.

@T_aquaticus

Humans and chimps are separated by ~40 million mutations and both species are doing just fine. In fact, both species rely on some of those mutations for function.

You are trapped in circular reasoning: First, you claim that the differences between the DNA of humans and chimps are produced by mutations. From that you prove that mutations of the DNA are beneficial and have shaped the differences between the DNA of humans and chimps. Please release yourself from the doctrines of Darwinism and Naturalism, and start thinking logically, critically and independently again.

@T_aquaticus

Even the ENCODE studied demonstrated that the vast majority of the human genome has no sequence specific function. Their definition of function is so loose that they classified introns as having function.

You are wrong. The ENCODE project has yet discovered the function of more than 80% of the DNA. Please throw out the fairy tale of Darwinists and Naturalists that 90% of the DNA is junk.

@T_aquaticus

Why can’t mutations produce a protein that binds to DNA and alters DNA?

In the fantasy world of Naturalists and Darwinists, anything can happen. But in the real world, mutations cause cancer and hereditary diseases. Mutations, which are oxidation processes, cannot produce mutation repair systems, which consist of a multitude of interconnected chemical reduction processes, by which the decay of information is recovered using the redundancy of information in the DNA by pairs of chromosomes, pairs of chromatids and pairs of DNA-strands.

As a service to those who follow this discussion on “Can mutations produce mutation repair systems?”, below a summary of the conclusions drawn so far.

SUMMARY OF CONCLUSIONS

1. Mutations are not the friend of the DNA, but its enemy because mutations cause cancer and hereditary diseases. No one will put his/her genitals under an X-ray machine to bless his/her children with improved DNA.

2. Living nature continuously adapts to its environment, NOT by mutations but by the mechanism of recombination of gene-variants (‘alleles’) and selection, and by gene regulation.

(http://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf )

3. In every cell, every day hundreds of thousands of mutations of the DNA occur. Fortunately, these mutations are largely repaired by mutation repair systems, for the discovery of which the Nobel Prize in Chemistry was awarded in 2015 http://bit.ly/1LhCGGC . The mutation repair systems prevent the DNA in every cell to turn into complete chaos within a lifetime.

4. Most of the mutations of the DNA consist of oxidative deamination, causing the information recorded by the DNA to ‘rust away’, like the information on a page of inkjet print rusts away by the oxidation of the ink. The mutation repair systems recover the damaged information by a multitude of interconnected chemical reduction processes, using the redundancy of information in pairs of chromosomes, pairs of chromatids and pairs of DNA-strands.

5. Mutations cannot produce mutation repair systems, because the laws of logic and of chemistry contradict this theory: a phenomenon P cannot produce M and Opposite-M at the same time (for example: apples cannot fall downwards and upwards at the same time) and oxidation cannot produce reduction (for example rusting of iron, or rusting of DNA, cannot produce the de-rusting of iron, or the de-rusting of DNA). According to the playing rules of empirical science, the theory that mutations can produce mutation repair systems is nonsense and must be removed from the domain of science and transported to the domain of ‘Dark Ages illogical beliefs’.

6. Naturalists and Darwinists are convinced that organic molecules possess the magical property of spontaneous self-organization, which allows them to form increasingly complex structures with an increasingly higher energy level. This pre-Victorian alchemist faith is diametrically in conflict with empirical science. Molecules possess the natural property of spontaneous disintegration. Natural physical processes are decay processes. The production of increasingly complex structures with an increasingly higher energy level requires the building and running of a factory, as Miller and Urey have demonstrated in 1953 yet. If not, energy would become available for free.

7. Naturalists and Darwinist strongly believe that mutations can do anything, including the production of mutation repair systems. They value their precious and unshakable faith in de doctrines of Naturalism and Darwinism higher than the laws of logic and chemistry. This attitude makes them an enemy of empirical science and revives the Dark Ages.

Dr. William DeJong
(Evoskepsis)

[Jonathan_Burke (Jon)]

@WilliamDJ

What I am doing is defending empirical science against people who do not care for natural laws and logic, blinded by their pre-Victorian Alchemist faith that organic molecules possess the magical property of spontaneous self-organization, which allows them to form increasingly complex structures with an increasingly higher energy level.

No you aren’t. If your arguments were based on empirical science, you would be following the scientific method. You would have hypotheses, experiments, and evidence based conclusions. You’re just writing special creationist rhetoric, dressed up in a little scientific jargon. The fact that you keep repeating your arguments almost word for word, without once addressing the evidence against them, shows you’re an apologist, not someone involved in scientific investigation.

[Bill_II]

@WilliamDJ

You are wrong.

No you are wrong.

@WilliamDJ

You are wrong.

No you are wrong.

Which pretty well summarizes how this particular discussion is progressing.

[gbrooks9 (George Brooks)]

@WilliamDJ

Indeed, inside the furnace of every star, hydrogen atoms can merge together into more complicated atoms. However, sooner or later these more complicated atoms, or even molecules, will fall apart again by radiation that hits them; the bigger they are the sooner.

@WilliamDJ

But if it takes 10 billion years for the sun to fall apart, that’s more than enough time for 5 billion years of evolution on Earth.

So… your point about chaotic things cannot self-organize into something organized falls flat on its face.

[glipsnort (Steve Schaffner)]

@WilliamDJ

What I am doing is defending empirical science

When a nonscientist tells the world’s scientists that they don’t know how to do science, he’s not defending empirical science.

[BoltzmannBrain]

@WilliamDJ

Mutations, which are oxidation processes, cannot produce mutation repair systems, which consist of a multitude of interconnected chemical reduction processes

5. Mutations cannot produce mutation repair systems, because the laws of logic and of chemistry contradict this theory: a phenomenon P cannot produce M and Opposite-M at the same time (for example: apples cannot fall downwards and upwards at the same time) and oxidation cannot produce reduction (for example rusting of iron, or rusting of DNA, cannot produce the de-rusting of iron, or the de-rusting of DNA). According to the playing rules of empirical science, the theory that mutations can produce mutation repair systems is nonsense and must be removed from the domain of science and transported to the domain of ‘Dark Ages illogical beliefs’.

There are lots of intermediary steps which you are dismissing here. Mutations cause changes in the DNA sequence, which will cause changes in protein sequences, which will in turn carry the new function. There are lots of enzymes which catalyze reduction processes, so the reason why you think that the emergence of an enzyme which catalyzes the reduction of DNA is impossible is beyond me. You seem to think that the oxidation that generated the mutation in the first place is somehow being ultimately used in the reduction reaction…which again, doesn’t make any sense, why someone would think that? It is like saying that I can’t use a soldering machine to build a refrigerator because it generates heat, while the refrigerator cools things down, do you see how weird that idea sounds?

[T_aquaticus]

@WilliamDJ

Factories can only emerge in the fantasy world of Naturalists and Darwinists, not in the real word. If such a thing would happen, an ever growing amount of complex molecules, and thus an ever growing amount of energy, would become available for free.

You haven’t shown that factories are required.

@WilliamDJ

You are trapped in circular reasoning: First, you claim that the differences between the DNA of humans and chimps are produced by mutations. From that you prove that mutations of the DNA are beneficial and have shaped the differences between the DNA of humans and chimps. Please release yourself from the doctrines of Darwinism and Naturalism, and start thinking logically, critically and independently again.

You have already agreed that the beneficial adaptations in both the chimp and human lineages are due to the genetic differences between them. Obvioulsy, those mutations responsible for the beneficial differences in morphology are the beneficial mutations.

@WilliamDJ

You are wrong. The ENCODE project has yet discovered the function of more than 80% of the DNA. Please throw out the fairy tale of Darwinists and Naturalists that 90% of the DNA is junk.

Their definition of functional includes junk DNA. They even consider introns to be functional, for crying out loud. If a stretch of DNA is transcribed into just one copy RNA in one cell type they consider that DNA to be functional, which is a joke. We would absolutely expect junk DNA to be transcribed into RNA at low levels, so they have not shown that 80% of the human genome has sequence specific function. There is also the fact that 90% of the human genome appears to be accumulating mutations at a rate consistent with neutral drift. If that DNA is functional then we should see evidence of sequence conservation, but no such evidence is there.

@WilliamDJ

In the fantasy world of Naturalists and Darwinists, anything can happen. But in the real world, mutations cause cancer and hereditary diseases. Mutations, which are oxidation processes, cannot produce mutation repair systems, which consist of a multitude of interconnected chemical reduction processes, by which the decay of information is recovered using the redundancy of information in the DNA by pairs of chromosomes, pairs of chromatids and pairs of DNA-strands.

You need evidence demonstrating that mutations can not produce beneficial increases in fitness, and that mutations can’t procuce proteins that bind to DNA and change DNA.

[AMWolfe (Andrew M. Wolfe)]

@T_aquaticus

[ENCODE’s] definition of functional includes junk DNA. They even consider introns to be functional, for crying out loud. If a stretch of DNA is transcribed into just one copy RNA in one cell type they consider that DNA to be functional, which is a joke. We would absolutely expect junk DNA to be transcribed into RNA at low levels, so they have not shown that 80% of the human genome has sequence specific function. There is also the fact that 90% of the human genome appears to be accumulating mutations at a rate consistent with neutral drift. If that DNA is functional then we should see evidence of sequence conservation, but no such evidence is there.

Thanks for this. As a non-specialist, I had never read a detailed critique of the ENCODE findings, and the pop science journalist summaries were particularly unhelpful in this case. Appreciate the debunking!

[T_aquaticus]

@AMWolfe

Thanks for this. As a non-specialist, I had never read a detailed critique of the ENCODE findings, and the pop science journalist summaries were particularly unhelpful in this case. Appreciate the debunking!

If you want a more technical (and quite funny at times) takedown of the ENCODE claims, check out this paper:

On the Immortality of Television Sets: “Function” in the Human Genome...

A funny excerpt from the peer reviewed paper:
“The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.”

The basic mistake that ENCODE made was that they didn’t distinguish between “does something” and “functional”. ENCODE considered DNA functional if it simply did something, which is called the “causal role” definition of functional. If we use the causal role definition when we look at the heart then we would conclude that its functions include making sound, adding 300 g to our body weight, and preventing the pericardium from collapsing simply because those are things the heart does.

[WilliamDJ (William DeJong)]

@Jonathan_Burke

If your arguments were based on empirical science, you would be following the scientific method. You would have hypotheses, experiments, and evidence based conclusions.

You are wrong. Conclusions 1, 2, 3, 4, and 5 at the end of my post on 7 April are based on empirical evidence, a peer-reviewed article, a letter of the Class for Chemistry of the Royal Swedish Academy of Sciences, natural laws and laws of logic.

@gbrooks9

But if it takes 10 billion years for the sun to fall apart, that’s more than enough time for 5 billion years of evolution on Earth.

You are wrong. Oxidation cannot produce reduction, not in one year and not in 100 billion years. See further conclusion 1, 2, 3, 4, 5 at the end of my post on 7 April.

@glipsnort

When a nonscientist tells the world’s scientists that they don’t know how to do science, he’s not defending empirical science.

You are wrong in thinking that science is a closed system of knowledge. Scientific results and theories stay open for discussion and even falsification. The claim of Miller that his experiment shows that natural processes can produce and ever growing amount of amino acids is fake. His experiment proves that the production of an ever growing amount of amino acids requires the building and running of a factory. You have been fooled by your evolution teachers. See further conclusions 6 and 7 at the end of my post on 7 April.

@BoltzmannBrain

Mutations cause changes in the DNA sequence, which will cause changes in protein sequences, which will in turn carry the new function. There are lots of enzymes which catalyze reduction processes, so the reason why you think that the emergence of an enzyme which catalyzes the reduction of DNA is impossible is beyond me.

You are trapped in circular reasoning. In every cell (a completely automated chemical nano-factory) reduction processes are present. But you cannot use the presence of these cellular reduction processes as a proof that mutation/decay/rusting/oxidation of the DNA can produce the repair/recovery of information/de-rusting/reduction of the DNA. See further: conclusion 5 at the end of my post on 7 April.

@T_aquaticus

You haven’t shown that factories are required.

You are wrong. I proved that factories are required by the method of ‘proof by contradiction’, which is a common method in science. See the lasts sentence of conclusion 6 at the end of my post on 7 April (“If not, energy would become available for free”).

@T_aquaticus

You have already agreed that the beneficial adaptations in both the chimp and human lineages are due to the genetic differences between them.

You twist my words: I told you that the differences in appearance between chimps and humans are caused by differences in their DNA. Subsequently, you apply circular reasoning to prove that these differences are produced by mutations. Please, acknowledge the scientific fact that mutations are not the friend of the DNA but its enemy. See further: conclusion 1 at the end of my post on 7 April.

@T_aquaticus

If a stretch of DNA is transcribed into just one copy RNA in one cell type they consider that DNA to be functional, which is a joke.

The ENCODE project is not a joke, but reflects the progress of science in understanding the functions of the parts of the DNA that do not code for proteins. Cutting edge science turns the fairy tale of Naturalists and Darwinists that 90% of the DNA is junk, into a joke. People who deliberately ignore the progress of science, are enemies of science. See further conclusion 7 at the end of my post on 7 April.

@T_aquaticus

You need evidence demonstrating that mutations can not produce beneficial increases in fitness

You provide that evidence yourself, dear T-Aquaticus: you will refuse furiously to put your genitals under an X-ray machine to bless your offspring with improved DNA. This empirical evidence falsifies your theory that mutations are the motor for improvement and innovation of the DNA. See further: conclusion 2 and 7 at the end of my post on 7 April.

[AMWolfe (Andrew M. Wolfe)]

@WilliamDJ

you will refuse furiously to put your genitals under an X-ray machine to bless your offspring with improved DNA.

On a forum for gracious, Christian dialogue, perhaps we’d best leave people’s genitalia out of the picture, shall we?

[T_aquaticus]

@WilliamDJ

You are wrong. I proved that factories are required by the method of ‘proof by contradiction’, which is a common method in science. See the lasts sentence of conclusion 6 at the end of my post on 7 April (“If not, energy would become available for free”).

You proved no such thing. If we found the same conditions in nature as we found in the reaction vial in Miller and Urey’s experiment, then the same complex chemicals would be made in those natural conditions. There isn’t something magical about a lab.

@WilliamDJ

I told you that the differences in appearance between chimps and humans are caused by differences in their DNA.

Yes, and those differences are mutations. A mutation is a difference in DNA sequence.

@WilliamDJ

Cutting edge science turns the fairy tale of Naturalists and Darwinists that 90% of the DNA is junk, into a joke.

90% of the human genome is still junk, and that is according to cutting edge science. All ENCODE did was try to scam the general public into thinking that “doing something” is the same as functional. Biologists didn’t fall for the scam.

On the Immortality of Television Sets: “Function” in the Human Genome...

Just because a stretch of DNA is transcribed into an RNA molecule does not automatically make that DNA functional. It never has. Junk DNA will be transcribed, and it is still junk. RNA transcription is not a valid indicator of function, contrary to the claims made by ENCODE.

@WilliamDJ

You provide that evidence yourself, dear T-Aquaticus: you will refuse furiously to put your genitals under an X-ray machine to bless your offspring with improved DNA. This empirical evidence falsifies your theory that mutations are the motor for improvement and innovation of the DNA. See further: conclusion 2 and 7 at the end of my post on 7 April.

All of your claims are debunked by the very existence of the beneficial mutations that separate the chimp and human genomes.

[glipsnort (Steve Schaffner)]

@T_aquaticus

90% of the human genome is still junk, and that is according to cutting edge science.

90% of the genome is junk according to cutting edge science, including ENCODE. They concluded that ~11% of the genome affected the well-being of humans.

[BoltzmannBrain]

Do you know what an enzyme is and how they are produced? I feel like that is where your misconceptions about DNA repair are coming from. I’d be glad to explain it to you if that is the case.

[BoltzmannBrain]

@T_aquaticus

Just because a stretch of DNA is transcribed into an RNA molecule does not automatically make that DNA functional. It never has. Junk DNA will be transcribed, and it is still junk. RNA transcription is not a valid indicator of function, contrary to the claims made by ENCODE.

Are you counting in non-coding RNAs with regulatory functions? I know some people which work with them in their labs and their results seem pretty convincing to me (more specifically with non-coding RNA Polycomb-mediated gene silencing). I don’t work directly on molecular biology (though every biologist need to know something about it in one way or the other), so that is an honest question/curiosity, not an attempt claim that you are wrong. Are their corresponding DNA sequences included on the 10-11% non-junk DNA?