Can mutations produce mutation repair systems?


(Jon) #51

Actually it does, and gives two examples, one of which is the SIGen article.

In April 2009, the Open Chemical Physics Journal published an article advocating 9/11 conspiracy theories without anyone bothering to inform the journal’s editor, who promptly resigned.[5]

This aroused the interest of the curious, and Bentham was busted in 2009 accepting a paper for the Open Information Science Journal consisting of random sentences computer-generated with SCIgen, whose imaginary authors both worked at the Center for Research in Applied Phrenology (CRAP).[6][7] The editor of said journal also quit when he found out what the publisher had done.[8] Bentham’s director of publication claimed they merely sent a fake acceptance to flush out the hoaxer,[4] but no-one believes him.

I really enjoyed this find of yours.

DeJong & Degens (2011) conclude from the properties of digital codes that ‘nucleotide codes’ should have similar mutation protection. I argue that digital codes and ‘nucleotide codes’ are not sufficiently similar to draw conclusions about mutation protection and evolution. A ‘mutation protection paradox’ does therefore not exist in biology.

So that article has one single citation after 7 years (!), and it’s from someone debunking it.


(Andrew M. Wolfe) #52

My bad. Guess I didn’t read your link very carefully! But yes… exactly. Rather shows the opposite of what he was intending to show…


(Stephen Matheson) #53

These are great questions. If I read you right, you are pointing to one potential “use” for “junk DNA,” which is to provide fodder for further adaptation. If so, then while it might be valuable to an individual organism, on the spot, to have a lot less repetitive DNA to carry around, it would be problematic over long time-spans due to the loss of evolutionary opportunity. And in fact, studies of “proto-genes” in current genomes are a new thing. We know of genes that clearly used to be “junk,” so therefore we can surmise that those genes (and any associated adaptations) wouldn’t exist without “junk.”

At first glance, we might therefore conclude that junk DNA is not only valuable but utterly necessary for evolution, at least in animals and plants with genomes composed largely of repetitive elements. I think the main challenge to that reasoning is that we don’t really know the evolutionary cost-benefit matrix. We know that there is a cost to copying and maintaining a genome. We know that there are risks inherent in maintaining a complex genome, and especially in maintaining a genome with a lot of repetitive elements. On the other hand, we know of various benefits and “functions” of what looks like junk DNA. (Two examples we might discuss further: genome size is related to cell size, and junk-like introns can be used to control speed of gene expression.) We really don’t know how much “junk” would suffice to provide evolutionary opportunity, and we may reasonably wonder whether it is much, much less than the amount we are saddled with.


(Mervin Bitikofer) #54

Thanks for your clarification – and affirmation that I’m not totally bonkers. Indeed you stated my intent better than I had managed to with this observation:

…which captures exactly where I was trying to go (or to try restating again for myself): Perhaps there is a long-term evolutionary benefit to all the stuff being carried even when it has no immediate benefit to the individual organism that carries it.

Indeed. The first article you linked brought more of that quandary into focus for me.

It seems to offend our engineering sensibilities (for some Christians anyway) that a designer should be so profligately wasteful. They want 100% or 0%; but it also seems to me that we (Christians) ignore what I think I’ve heard referred to as a “principle of plenitude” which probably is a time-honored concept from well before modern science. God regularly delights in overabundance (in some things, and in some places, for some people – with all due respect to those who rightly may wonder where all this abundance is in wealth or food resources). But acknowledging such hardship, I’m still focusing more on the scientific observations we make: that 99.9…% of our sunlight shines off “uselessly” into the cold of space. Or that 99.? % of water shuffles about in the water cycle without directly servicing a thirsty organism in any given season. I don’t doubt these examples could be and have been multiplied.

It seems that when engineers among us get our creationist (or anti-creationist) dander up about “efficiency”, God just laughs. Our solar system could have been “exquisitely designed” with some mechanism to contain all our sun’s energy and release only a tight laser beam of it to illumine the earth (and perhaps a few more tight beams so that the other planets would be lit up to grace our night skies – it is “all about us”, after all, right?) And in fictitious “beam universe” the engineer swells up with pride and pleasure at the vastly increased efficiency of our star’s energy use. And yet we now see all the potential problems too. Should the earth’s orbit vary by just a bit, we might drift away from that carefully tracking laser, always needing to stay on that knife edge path – iceball death threatening from every side. But lo and behold, our fictitious “problem” gets its lethal blow from the reality of our sun casting its plentiful energy in all directions. Our poverty-enforced efficiencies that oblige human engineers to minimize waste (in the context of economies and systems we have set up for ourselves) do not exist for God. I indulge myself in the speculative possibility that DNA may also follow a similar principle in a wider context of evolutionary time scales. How unfortunate that so many of us Christians have shut down the consideration that would open up this possible dimension of God’s activity to our full appreciation. At least that’s my religiously-motivated take on it.

But I will cease from this digression on an otherwise scientific thread. Carry on that we all may learn more!


(William DeJong) #55

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#56

Enzymes couple thermodinamically favorable reactions in order to compensate to the unfavorable ones, one example I can give is the plasma membrane Ca2+ ATPases, they pump Ca2+ from a very low, negative-inside membrane to a external media containing huge amounts of Ca2+, which at first glance seems completely against the laws of thermodynamics, however, they hydrolyze one molecule of ATP to ADP in the process, which ultimately makes the global reaction favorable. There is absolutely no fantasy on that.


(William DeJong) #59

Your are right! Miller built a (simple) amino acid factory, but he spread the fake news that natural processes can produce and every growing amount of amino acids. See further, conclusion 6 of my post on 7 April.


(William DeJong) #61

Your are fighting the progress of science. Any program or recipe (for instance for the production of an apple pie or a human being) consists of a relatively small part that describes WHAT will be processed, and another part that describes HOW and WHEN.


(William DeJong) #62

Dear Boltzmann Brain,
Indeed, enzymes are interesting molecules. But only in the fantasy world of Naturalists, Darwinists and Alchemists, enzymes are capable of organizing molecules into ever growing structures with an ever growing energy content. In the real world this is impossible, because if enzymes would possess this magical property, energy would become available for free (‘proof by contradiction’). See further conclusion 6 and 7 of my post on 7 April.


(William DeJong) #63
  1. The peer-reviewed article of DeJong and Degens (2011) mentions the basic scientific facts on how the DNA changes. See further conclusions 1 and 2 of my post on 7 April.
  2. A colleague has opposed to the article by claiming that there is no mutation protection paradox, but did not provide any argument.

(William DeJong) #65

To save followers of this discussion the trouble of scrolling back, a reprint below of the conclusions drawn in my post on 7 April:

SUMMARY OF CONCLUSIONS ON “CAN MUTATIONS PRODUCE MUTATION REPAIR SYSTEMS?”

  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 (‘Proof by contradiction’).
  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)


#66

Just one last rabbit trail, since I do enjoy this topic.

For complex eukaryotes, replication time really isn’t a problem. For prokaryotes, however, replication time is often very important which is why you see such compact genomes in bacteria.

As to energy budget, I highly doubt that a 100 million v. 3 billion base genome really makes that much difference relative to the total energy used. I haven’t done the math, but I would suspect that the lifetime savings in energy would equate to running a mile just once a year. The amount of ATP used for muscle contractions, keeping our bodies at 98.6F, RNA transcription, protein translation, etc. would seem to be way higher than DNA replication, at least in my estimation. In the case of the bladderwort there is a shortage of phosphates which would limit the source for nucleotides, not necessarily the energy needed to replicate DNA.


#67

The only stupid questions are the ones not asked. :wink:

There are some people who argue for junk DNA filling the function of a nucleoskeleton, sort of a rough framework that fills out the nucleus and frames the functional bits of the genome. Of course, this would not be sequence specific function which is the type of function that most biologists are looking for. However, the requirement for a bulky genome is still in the early phases of testing, but it is being considered.

This is why the bladderwort genome is so interesting to me. The human genome is 3 billion bases. The onion genome is 16 billion bases. The bladderwort genome is just 0.083 billion bases, a mere fraction of the human and onion genomes, but it still has about the same gene content as both of those genomes. Apparently, the experiment you are describing may have already been done by nature with the bladderwort genome.


#68

And yet mutations are responsible for the phenotypic adaptations that we see in species, such as the phenotypic differences between humans and chimps. Also, it is a fact that mutations occur.

The differences between chimps and humans is not due to a different mix of the same alleles. Humans and chimps have different alleles, and those differences are due to mutations.

And yet everyone is born with 50 to 100 mutations. This is just a fact.

DNA repair mechanisms are not causing the mutations, so they are not producing M and Opposite-M.

Was it magic when less complex molecules combined to create more complex molecules in the Miller-Urey experiment?

Can you please explain why mutations can not produce a protein that binds to DNA and changes DNA?


(William DeJong) #69

Irreparable mutations produce proteins that cause the selective disadvantage of cancer and hereditary diseases. According to Darwin, organisms that suffer from cancer and hereditary diseases will become extinct in short time. As a consequence, their offspring cannot develop mutation repair systems that recover information that is lost by the ‘rusting away’ of the DNA or by damaging radiation and chemicals, using the redundancy of information in pairs of chromosomes, chromatids and DNA-strands. See further conclusion 2 and 5 at the end of my post nr. 61 on 17 April.


#70

Not all mutations will cause cancer or hereditary diseases, but yeah, most of the time mutations will have neutral or deleterious effects. But once in a while a mutation can end up confering an advantage which will be selected, and that is not just theory, we can see that happening in experiments with bacteria.

That one was not selected on purpose, but it is a good example of that:


(Jon) #71

It was “peer-reviewed” in an extremely low impact journal published by a predatory publishing house with extremely low academic standards. The article has not received any academic recognition whatsoever, because it makes claims without evidence.

No, they demonstrated (with evidence), that your “mutation protection paradox” does not exist. To date you have not responded to this.


#72

I am not seeing an explanation as to how mutations could not produce a protein that binds to and alters DNA. Want to try again?


(George Brooks) #73

It has been 8 days since @WilliamDJ has last posted. Dare we awaken his slumber?


(system) #74

This topic was automatically closed 6 days after the last reply. New replies are no longer allowed.


Human Chimp Genome Similarity