Can mutations produce mutation repair systems?


(William DeJong) #1

Hi folks,

In 2015 the Nobel Prize Chemistry was awarded for the discovery of the mutation repair systems that prevent the DNA in every cell to turn into complete chaos within a lifetime. http://bit.ly/1LhCGGC

My question: Can mutations produce mutation repair systems?

dr. William DeJong
(Evoskepsis)


(Jon) #2

You’ve had this conversation before, here.

I expect “The idea of evolution is based on medieval alchemy” to make an appearance soon.


(George Brooks) #3

@WilliamDJ,

If genetics support the eventual superstructure of an emerging mutation repair system, doesn’t it seem inevitable that flaws in the replication of the genetic support would lead to mutations where the mutation repair system makes itself felt… and with inevitable improvements to follow.

Remember, this is not an Atheist site that discusses Evolution. God guides evolution for many of us here. And this would be the expected course of action for any divinely led chain of genetic modifications… where genetic repair has a baseline level of activity, but is still not a perfect tool.


(Lynn Munter) #4

Yes. Because each mutation occurs before the mutation repair system is improved, and the repair system doesn’t act on older mutations.


(George Brooks) #5

@Lynn_Munter

He is “gonna” say that if there is already a mutation repair system, then how can there be any un-repaired mutations that would affect the mutation repair system?

When someone then counters by saying: some mutations don’t get repaired… he has nothing to say. He ignores the point completely… despite the fact we all know that mutations continue to present themselves, which by definition means there are mutations that don’t get repaired.


#6

Mutations can produce new proteins that bind to and alter DNA, so yes, they can.


(Lynn Munter) #7

If I put some waterproofing on my tent, how can there be water inside the tent? Impossible! It must have been magic! Nothing else could possibly ever account for this!!


(William DeJong) #8

Dear Jonathan,

  1. Current evolutionary theory is grounded in the claim that (organic) molecules have a spontaneous self-organizing ability by which simple molecules join together in increasingly complex structures with an increasingly higher energy level. This pre-Victorian alchemist belief has been refuted long ago by empirical science. Molecules have a spontaneously disintegrating capacity. Natural physical processes are decay processes. In order to run processes in the opposite direction, factories are needed. See further: https://www.evoskepsis.nl/docs/The%20faultless%20intelligence%20of%20the%20naturalist.pdf
  2. We are not discussing this pre-Victorian alchemist faith now, but the theory of Naturalists and Darwinists that mutations can produce mutation repair systems. Looks pretty magical to me: mutations that can repair themselves. Never observed a mutation in my computer files and programs, house, car, shoe or shirt to start repairing itself. Did you?

Dear George,

  1. Scientific theories must be refutable and therefore must be testable. As a consequence, Gods, devils or spaghetti monsters, cannot play a role in scientific theories, because gods, devils or spaghetti monsters cannot be dragged into a laboratory to test their creative powers. As Stephen Jay Gould has pointed out before, the domain of religion (including divinely led processes) and the domain of science must stay separated; also at this forum ‘Scientific evidence’.
  2. You are right that mutation repair is not perfect and sometimes fails, resulting in cancer and hereditary diseases. But we are not discussing the effectiveness of mutation repair, but the theory of Naturalists and Darwinists that mutations can produce mutation repair systems.

Dear Lynn,

  1. Please read the awarding letter that accompanies the Nobel Prize Chemistry 2015, at http://bit.ly/1LhCGGC . You will learn many new scientific facts, for instance that the DNA is an extremely vulnerable molecule, and would turn into complete chaos within a life time, without the mutation repair systems in every cell. Mutations are not a friend of the DNA (as you are made to believe), but the enemy (as science, and in particular the Nobel Prize Chemistry 2015 proves).
  2. You are wrong by claiming that the mutation repair systems do not act on older mutations. Mutation repair is continuously in action. Mutations that happened in subsequent generations are repaired, for instance, during the production of sex cells. http://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf.

Dear T Aquaticus,
Indeed, mutations alter the DNA. As a consequence, the correct proteins cannot be formed, which causes cancer and hereditary diseases. Based on wishful thinking, you claim that these incorrect proteins start to form mutation repair systems that restore the DNA in its original form! Such magic can only happen in the fantasy world of Naturalists and Darwinists. In the real world, a phenomenon P that produces a change process M cannot simultaneously produce a change process Reverse-M. Such a thing is logically impossible. In addition, the mutation of the DNA largely consists of oxidative deamination (see the awarding letter that accompanies the Nobel Prize Chemistry 2015, at http://bit.ly/1LhCGGC ). This ‘rusting’ of the DNA erases its information content in the same way as the information on a tag disappears, when the ink on it blurs by oxidation. The reverse change process requires a chemical reduction process and the restoration of the original information content, using back-up information. Only in your fantasy world such a restoration process can be driven by the oxidation process itself. Not in the real world because, according to the laws of chemistry, oxidation cannot produce reduction.

CONCLUSION
Mutations cannot produce mutation repair systems. This theory of Naturalists and Darwinists is contradicted by the laws of logic and the laws of chemistry. According to the playing rules of empirical science, this theory must be removed from the domain of science and transported to the domain of ‘Dark Ages illogical beliefs’.

Dear Jonathan, George, Lynn and T Aquaticus, please accept and respect the laws of logic and chemistry in the responses you are going to post.


(Jon) #9

Well this went exactly according to script.

That is nonsense.

The modern evolutionary synthesis is not based on anything like “pre-Victorian alchemist belief”. It is based on empirical science. If you were interested in empirical science, you would make an argument from empirical science.

In other words, your objection to it is not based on empirical science but on a personal feeling you have.

No, and I don’t expect to. These examples are not analogous to the biological systems explained by the modern evolutionary synthesis. You are making a false analogy.

I do. That’s why I don’t make spurious arguments based on mis-characterization of modern evolutionary theory, based on personal feelings.


(George Brooks) #10

@WilliamDJ,

You are mistaken if you think mutations and natural selection (along with God’s guidance if necessary) are not adequate to produce a mutation repair system. The repair system could have started in just one corner of cellular metabolism, and slowly increased to current states of scope.

Is it your understanding that mutation repair systems across plants and animals, and all sub-groups thereof, are identical in what they repair?


#11

I have personally run thousands of PCR runs, and I can confirm that simple nucleotides are strung together into longer molecules through natural processes. It isn’t a myth.

What about all of the mutations that differentiate us from chimps and are responsible for our physical human form? Are our larger brains and bipedal gait diseases or cancers?

DNA repair systems can only change DNA if there is a base pair mismatch between complementary strands of DNA or a gap in the sequence. It can’t look back in history at ancestral genomes and change modern DNA so that it matches that of its ancestors.

There is no such thing as the “correct protein” or the “correct DNA sequence”. There is just the protein and DNA sequence that exists. If, as you claim, DNA sequences can’t be changed at all without causing cancer and disease then there would only be one living species, and all the members of that species would have identical genomes. Obviously, this isn’t the case. You are just flatly wrong. Every species on Earth is proof that mutations can and do result in adaptations and viable variation.


(William DeJong) #12

Dear Jon,
You assure us that you accept and respect the laws of logic and chemistry. These laws, however, contradict your theory that mutations can produce mutation repair systems, as proven in my post on March 15 above. You cannot have it both ways: respecting empirical science and logic, and claiming that mutations can produce mutation repair systems.

Only in the fantasy word of Naturalists and Darwinists, molecules start to order themselves spontaneously by natural processes into mutation repair systems, and into ever more complex structures with an ever higher energy content. This pre-Victorian Alchemist faith is contradicted by the laws of chemistry and the laws of logic. See my post on 15 March above.

Multiplication of DNA requires the building of a DNA-multiplication-factory, which can only work if energy is supplied to it. If multiplication of DNA could happen without building a chemical factory and without building an energy supply, ever growing quantities of highly complex molecules with a high energy content would become available for free! Selling these costless high energy molecules would make you a very rich man. Unfortunately, such miracles only happen in the fantasy world of Alchemists.

Living nature continuously adapts to changing circumstances by gene regulation and by recombination of gene-variants (‘alleles’) and selection. Not by mutations! See for instance the evolution of the beaks of Darwin finches. It is unbelievable and a shame that you do not know the basic scientific facts on how living nature continuously adapts to changing circumstances. Please educate yourself and spend 20 minutes to read the peer-reviewed article (4 pages): “The evolutionary dynamics of digital and nucleotide codes” at http://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf.

You are wrong. During the production of sex cells (‘gametes’), code expanding mutations that have occurred in ancestral genomes are eliminated by comparing the alleles of the father with that of the mother; if they are not exactly of the same length, the cross-over fails and the production of gametes is aborted. See page 2 of “The evolutionary dynamics of digital and nucleotide codes” at http://benthamopen.com/contents/pdf/TOEVOLJ/TOEVOLJ-5-1.pdf.

CONCLUSIONS

Dear Jonathan, George and T-Aquaticus,

1. Please respect and accept the law of logic that a phenomenon cannot produce both M and Reverse-M at the same time. (For example: Apples cannot fall downwards and fall upwards at the same time).
2. Please respect and accept the law of chemistry that ‘oxidation’ cannot produce ‘reduction’ (For example: the rusting of an iron nail cannot transform the rust into iron).
3. Mutations cannot produce mutation repair systems, because the laws of logic and chemistry contradict this theory. According to the playing rules of empirical science, this theory must be removed from the domain of science and transported to the domain of ‘Dark Ages illogical beliefs’.


(George Brooks) #13

@WilliamDJ

There is no known law of logic, chemistry, biology or physics that makes it impossible for mutations to produce mutation repair systems.

In fact, unless you want to suggest that the very first cell was already equipped with mutation repair systems, the only way for such a system to emerge is via mutations. It’s an irony. It’s not an impossibility.


#14

ATP isn’t a fantasy. Taq polymerase isn’t a fantasy.

Do you really think PCR is alchemy?

Then how do you explain the physical differences between humans and chimps? Is it or is it not due to the DNA sequence differences between the species?

And yet every person is born with 50 to 100 substitution mutations as well as indels and recombination mutations. This is an empirical fact. How do you explain this?

What are you talking about? Oxidation and reduction are in constant equilibrium and there are reverse and forward reactions happening all of the time in any reaction, even if it is at very low levels. You need to get yourself to a chemistry class.


(Jon) #15

No they don’t. You didn’t prove anything. You’re writing theological apologetic, not science. If you were doing science you would follow the scientific method.

  1. Observation.
  2. Hypothesis.
  3. Attempt at falsification through testing.
  4. Conclusion.
  5. Peer review.
  6. Revision.

Let me know when you’ve done that.


(William DeJong) #16

Dear George,
You are wrong. Apples cannot fall downwards and fall upwards at the same time; and mutations cannot produce the opposite of mutations: mutation repair. In addition, the rusting of an iron nail cannot transform rust into iron; and oxidation (which causes most of the mutations of the DNA) cannot produce reduction (which is needed for mutation repair) . Please start to think independently and critically again!

PCR (= a technique to multiply DNA) gets shape in a (small) chemical factory built by engineers, maintained by specialists, operated by people like you, and driven by electricity from the grid. This combined and orchestrated effort of technology, skills, knowledge and energy to multiply DNA, refutes the pre-Victorian alchemist belief of Naturalists that molecules possess a spontaneous self-organizing ability to form increasingly complex structures with an increasingly higher energy level. Instead, molecules have a spontaneously disintegrating capacity. Natural physical processes are decay processes. In order to run processes in the opposite direction, factories like a PCR-factory are needed.

  1. We are discussing the question “Can mutations produce mutation repair systems?”, not the differences and similarities between humans and chimps, or between humans and mice, or between humans and tulips.
  2. Mutations are the enemy of the DNA, not its friend. You will not put your genitals under an X-ray machine to bless your posterity with improved DNA.
  1. DNA is a very vulnerable molecule, that would ‘rust away’ in a life time without the continuous effort of mutation repair systems. When rusting away, the information that it records is lost, like the information recorded on a page of inkjet-print is lost when the ink fades by oxidation.
  2. Mutation repair is based on the redundancy of information in pairs of chromosomes, pairs of chromatids, and pairs of DNA strands. The repair is not 100% effective, as you can see in COSMIC, the Catalogue of Somatic Mutations in Cancer, at http://cancer.sanger.ac.uk/cosmic . Ultimately, the information that is recorded by the DNA will turn into complete chaos.

In Chemistry, oxidation and reduction are well defined, opposed processes. They can be in equilibrium (for instance during the continuous battle on any sea ship against rust), but oxidation can never produce reduction. Such a thing is only possible in the fantasy world of Naturalists and Darwinists. Opposed processes cannot produce each other. George, please start thinking critically and independently again!

In your fantasy world , a phenomenon can produce both M and Reverse-M at the same time; as a consequence, in your fantasy world apples can fall downwards and fall upwards at the same time. In your fantasy world oxidation can produce reduction; as a consequence, in your fantasy world the rusting of an iron nail can transform the rust into iron. No scientific research program is needed to see that these things cannot happen in the real world, where the laws of logic and the laws of chemistry apply.

CONCLUSIONS

_Dear George, T-Aquaticus and Jon,
_
Mutations cannot produce mutation repair systems, because the laws of logic and chemistry contradict this theory. According to the playing rules of empirical science, this theory must be removed from the domain of science and transported to the domain of ‘Dark Ages illogical beliefs’. Apparently, your faith in the doctrines of Naturalism and Alchemism is of greater value to you than the laws of logic and chemistry and the playing rules of empirical science. This attitude makes you an enemy of empirical science and revives the Dark Ages.


(Jon) #17

No. No one here is saying any such thing.

No one is making the claims you assert. The point here is that you keep making pseudo-scientific claims which are patently false, and you have failed to present any evidence for your specific position. You write pages of rhetoric, but you are not doing any science at all. In particular (and most tellingly), you are not following the scientific method.


#18

You called it alchemy which indicates that it was supernatural and couldn’t be produced through natural or artificial means.

All that needs to happen in order for atoms to form complex molecules is the input of energy. That’s it. The Miller-Urey experiment demonstrated that.

They are the same question. What do you think is responsible for the physical differences between chimps and humans? It is a simple question and you need to answer it.

The problems with this statement will be illuminated by you answer to the question of where the differences between humans and chimps comes from.

The vast majority of organisms on Earth only have one chromosome.

You can have both oxidation and reduction occurring in the same reaction, which is the point being made. You can have oxygen binding and then unbinding during the same reaction.


(George Brooks) #19

@WilliamDJ

You seem to think animal biology and genetics is some sort of electronic game, with yes or no answers, and bits that are zeros or one’s.

And you keep assuming that the kind of Evolution being discussed here is happening in the absence of God.

Many pro-Evolution participants here would agree with you on the point that nothing can happen without God’s leading the way in the natural order. So why do you keep saying “it can’t happen”? I think it’s because you keep forgetting which blog you are writing on.

This is the one where God makes all things happen…


(William DeJong) #20

Dear Jon,
You are wrong. Step 1 in the scientific method is to reject a theory immediately if it is in conflict with natural laws. This first step protects science spilling energy on nonsense. Your theory: “Mutations can produce mutation repair systems” is such nonsense, because oxidation cannot produce reduction.

You are wrong. The Miller-Urey experiments proves that a (simple) factory must be built to produce an ever growing amount of amino-acids. Before you make a reply, please read the following information and learn that you have been deceived by Miller, Urey and your teachers of evolution.

In 1953 PhD student Stanley Miller set out to prove that natural processes can transform basic organic substances into amino acids in an ever higher concentration. To this end, he took a glass flask with two inwardly projecting electrodes between which he could make sparks stagger and filled the flask with water, methane, ammonia and carbon dioxide. Indeed he found that the artificial lightning in his simulation of a primitive earth atmosphere could produce amino acids. But he also found that the concentration of building block in the flask did not increase ever further, because new sparks destroyed the building blocks that were initially formed; the larger the faster. Instead of reporting that natural processes are not able to produce an ever concentrated primordial soup, he attached a transport mechanism to the lightning flask, to transfer the building blocks that were produced to a second flask where they would be safe for destruction. In fact, Miller built a primitive amino acid factory, with which he succeeded to produce an ever more concentrated ‘primordial soup’. Miller claimed his adjusted test set proved that natural processes could have produced billions of tons of building blocks for life in the primordial oceans. Instead, Miller’s experiments prove that an ever more concentrated soup of amino acids cannot arise by natural processes, but demands the building of a factory. Based on the false claims of Miller and his supervisors, it is broadly believed today that organic molecules possess an intrinsic, hidden desire to organize themselves spontaneously into increasingly larger structures. This view on matter is a repetition of the Alchemist’s view, who believed that matter does not merely consist of four basic elements (water, fire, air and earth) but also contains a hidden force (the ‘quint essence’). Many people believe that if we search long enough, this hidden force will be discovered and after triggering it in the right way, it can be released, resulting into a natural process in which organic molecules will transform themselves into increasingly larger and more complex structures. As a consequence, energy would become available for free and the chemical industry would become useless.

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

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

  1. The chemical processes in every cell obey the laws of chemistry and logic.
  2. Theories that are in conflict with natural laws an logic, like “Mutations can produce mutation repair systems”, must be removed from the domain of science and be transported to the domain of ‘illogical Dark Ages beliefs’.

CONCLUSIONS

Dear George, T-aquaticus and Jonathan,

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. 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.
2. Your opinion that mutations can produce mutation repair systems is an illogical Dark Ages belief.

(Notice that the belief that DNA mutation repair systems are created by a transcendental creator, is a rational belief, because all repair systems we know, for instance of cars, houses, cloths, text files, health, and relationships, are created by a creator.)