Johnies Zaoudis

MSc Student, University

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Are we sure that DNA is making errors?

When David and biologist in generally say that DNA is making errors i think they see it only from the "copying" perspective. Could it be that this is in purpose or is there a proved theory that it happens due to failure? Is DNA trying to support the proliferation of the tolerant or some kind of evolution in species?

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    May 4 2011: DNA is not purposeful. But it's properties are tuned by feedback loops in the system of evolution.

    One parameter of sexual reproduction is the degree of randomness introduced by the copying of DNA. If copying were perfect, randomness would be zero, and all diversity would be introduced by the recombination of parent's DNA. If copying were 100% random, no "ideas" would be preserved from one generation to the next. Somewhere between these poles is an optimum degree of randomness. In these intermediate states, random errors introduce some additional novelty into a species genome--most of which is detrimental, and disappears, but occasionally a mutation is beneficial.

    "Optimal" is judged by how effectively species maintain their fitness with respect to the environment. This suggests that in the history of evolution, nature may have tried different degrees of randomness--the ecologies with more and less randomness have been less successful, so the current error rate is what we see. This view is supported by the error correction mechanisms in the copying process--the chemical reactions of copying would introduce more than the ideal degree of randomness, so correction mechanisms evolved to reduce it.

    This suggests an interesting implication for other evolving systems, like capitalism: if the pace of change accelerates, then we'd expect to see more experimentation and a higher failure rate--which we are.

    A quantitative theory of how the parameters of evolution are tuned by feedback is laid out in Stuart Kauffman's Origins of Order (technical) and At Home In The Universe (general).

    One question for this discussion: does anyone know if all species have the same incidence of random mutation? It would seem that those living in the slowest changing-niches should have less, and vice versa.
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      May 5 2011: Another question (perhaps you know Christopher):

      Have mutations been identified by analyzing human parents' and their child's DNA?

      And, has the mutation incidence rate been identified in humans? Is so, how?

      Thanks.
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        May 6 2011: @ Colgan... "has the mutation incidence rate been identified in humans? Is so, how?"

        The error rate within the Nucleus of a human cell is around 1 per 100,000 pairs of nucleotides. But i think that is the error rate prior to proofreading. not exactly sure what the ratio of mutations that become reproductive is and i'm sure its highly variable. and if your asking what percent of mutations successfully get proliferated into the gene pool, I have no idea.

        There are many different types of mutations, cancer for instance, are mutated cells that reproduce uncontrollably within the body. And I hope we all know that caner rates are highly variable and dependent on an individuals exposure to mutagens.
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      May 6 2011: @ Meyer..."One question for this discussion: does anyone know if all species have the same incidence of random mutation? It would seem that those living in the slowest changing-niches should have less, and vice versa." ...
      on the individual cellular level, different species certainly have different rates of mutation. Some species have much more efficient "proofreading" mechanisms than others for fixing errors in the nucleus such as mismatched or added nucleotides.

      As well, an individual genome's regions have different rates of mutations; the evolutionary process has selected for high rates of efficiency for "active" or functional sections because the organisms survival and procreation depends on these regions, whereas other regions may be less critical for survival and proliferation and so the process may have developed sloppier proofreading or fixes for those parts because errors in certain regions are less damaging to functionality than others.

      At the species level, the rate of proliferating mutations into the gene pool is also highly variable. Darwin proposed a model of evolution that was slow and gradual, but Gould (I may be wrong about the origin of this theory) proposed a punctuated model in which adaptation trends more towards peaks and valleys. Probably both concepts are valid, but the punctuated model has a more obvious effect such as bottlenecking gene pools, but then again ring species seem to display a slow and gradual process. so yes, rates of change are different depending on circumstance.
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    May 1 2011: Nothing that DNA does is purposeful. This is the big confusion that evolutionary theory tends to leave in people's mind, no doubt because biologists use words that imply that a species controls its future. The word "error" for example is a bad word choice. it suggests that DNA tries to copy itself exactly. Strictly speaking, DNA does or does not make an accurate copy, there is no try. In the same way, a comet does not try to fall into an orbit; dripping water does not try to form an icicle; uranium does not try to radiate. In the same way, no species purposefully adapts to its environment. The environment is inhospitable to those it is inhospitable to and those things die more quickly than others.
    The tolerance an environment has for a phenomenon is equal to the phenomenon's ability to continue.

    That said, a genome which does not mutate cannot survive in a changing environment. So, mutation serves survival in that way.
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    May 27 2011: I think they are only talking about that "copying" prespective. DNA has always and will always make errors. We, ourselves, as a specie, are a product of an error: due to an error on the replication of DNA or a mutation that occurred during a meiosis (process that "creates" gametes) we have diverged away from these primates and our specie. I think that they say this now because the "errors" that naturaly occur are now being seen through a different perspective, this is, even though they have always existed, they are know being more recognized, due to developement of genetic screening technologies and because we are living more than what we used to 100 years ago.

    As we are living more than we used to, genetic errors are becoming more frequent. So that you can understand, there is a "error" correcting mecanism in cells (some genes are responsible for reading the DNA and correct any error that might occur). However, as we get older, this mechanism becomes less effective and the mutations that occur are not detected and therefore produce what you call of DNA error.
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    May 27 2011: I don't know much about DNA or evolution but I don't believe in a divine entity so I don't believe DNA was designed.
    I believe so called errors in DNA are the inescapable result of probability and bias as described by quantum theory.
    I don't think errors are the right word. I'd call them deviations. I don't think DNA and life could exist for any extended period of time (evolutionary time) if it did not have these deviations. Without them, life would never have evolved beyond the first few DNA strands.
    But that's just my view of it.
  • May 11 2011: One needs to understand the mathematical model behind the DNA map. More over, if such a mathematical is found, it needs to be mapped in terms of a Binary code...in order to understand the precise logic and direction. A binary logic based on multiple 'And' loops has no question of an error in it.

    But the point is...can 'Cognition' the defining logic of the human brain understand the source code of the DNA map which is not even 'Binary'. 'Relativity' is a concept which stems from the human mind.
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    May 6 2011: @Zaoudis...I think we can appropriately term mistakes in copying as errors because there are mechanisms in place to fix those errors when they occur, and the efficiency of those mechanisms has been honed by evolutions selective pressures.

    Evolutionary outcomes have no plan or purpose, the whole process is about what "works" or doesn't and by this I mean what survives and breeds succeeds, what doesn't dies off. Their is no goal or aim to the process and there is no progress either. Evolution is not working towards some goal such as intelligence or strength. if a species is smart and strong it is merely because within that species those were the survivors, if however say sexual selection favored slow fat stupid slobs over strong smart intelligent ones in a particular species the gene pool would be proliferated with those genes. Survival of the fittest really just means survival of those genes that get passed on at the highest frequencies into the gene pool.
  • May 2 2011: Hi, I am just a layman, but the way I see it, DNA must be sentient. When species evolve and mutate, they have to mutate not only for the benefit of their own species but for all species. The food chain is a good example of this. During these periods of mutation it's inevitable there will be some mistakes. This is the pattern throughout and within our history, from the beginning of life itself. It's only by the mistakes we make, will we ever progress. This also includes evolution.
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    May 1 2011: Nothing is perfect.

    Try this experiment.
    1. Take a sheet of paper and draw a straight line on it.
    2. Pass the paper to someone else and tell them to copy what they see on another paper.
    3. Repeat No. 2 with the latest copy. ( Don't tell them that it started with a straight line, just tell them to copy what they see )

    I saw this experiment done with 500 people. Go watch it on youtube - search for "evolution 500 lines" and click the first video.
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    May 1 2011: Great discussion, interesting question. I often wonder if some of the genes we are going to try to eliminate will help us fight a disease later. Mayhap there is a disease that has been dormant for sometime that had caused our DNA to change. So the changes hold it at bay but if we eliminate the gene then it can run rampant. This is one of my biggest hesitations about gene therapy and manipulation on a large scale. This may seem off track, but if DNA is going through a type of scientific process to adapt then it may also hold on to seemingly outdated genes.
  • Apr 30 2011: I would like to first point out that proteins, which are encoded by DNA, replicate DNA. DNA is not self replicating without the help of these expressed proteins.

    Now on to the original question:
    Let's assume that the goal of life is to pass one's DNA onto the next generation, regardless if it is the exact same sequence or not. Some life-forms, like infectious bacteria, will benefit from a somewhat rapidly changing genome. This is because they produce a lot of progeny and need adapt to the host's attack on them. On the other hand, humans have much less genomic change overtime. There is not as much of a benefit for new mutations to us as there is for an infectious microbe. However, humans do sometimes benefit from new mutations and we would be a very vulnerable species if we did not have genetic diversity.

    I am not certain a species could evolve to totally stop mutation. Theoretically, as it approached a completely perfect DNA replication and repair system, it would get harder and harder to get mutations to increase the systems accuracy.

    So, in conclusion, the amount of mutation is a balancing act for each species. Some species benefit from more mutation, others from less.
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    Apr 30 2011: I think you have found an interesting question.
    Let us say, that every effort, that enables a gene to replikate is a succsess and every effort, that prevents it from succeeding is failure. In this case a copying error would be failure from the false copyed genes poin of view. The other genes, of whom some regulate the copying procedure and the mechanisms which make shure, that no errors occure, might profit in there ability to be passed on, when there neighbours change from time to time.
  • Apr 30 2011: I think that it is simply errors. I say that because if it was not an error (ie: it was intentional) it would mean one of two things:

    1. DNA is sentient

    or

    2. DNA was designed
    • Apr 30 2011: And if it wasn't "an error" it would be perfect(i.e. no mutations).

      I don't think there is a proven theory per se, that there is isn't something in DNA that wants to mutate(failure to copy) I think that it is really just assumed because so many(the vast majority of) mutations are non-beneficial.

      You could get into a whole pHiliZoPHiGal argument about how the DNA might somehow "know" or "want" to mutate as to "consciously" build towards evolution but that argument won't go anywhere.

      ... But hey you have the Masters I'm just a lowly undergraduate ;)
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        Apr 30 2011: Actually that was what i had in mind too...
      • Apr 30 2011: DNA is a molecule and therefore subject to chemical reactions. Hydrogen Bonds, bond nucleotide chains together and therefore DNA structure is very susceptible to radicals(cation, and anionic compounds, polyatomic ions).

        It is pure physical law.
        Say I hold a stone over an open well. When I let go of the stone it will fall to the bottom of the well. We do not claim that the stone or the well are sentient, this is merely the effect of gravity on the stone.

        This is the same as with dipole-dipole interactions. Full charges from radicals overwhelm partial charges in the hydrogen bonds. I could get into a whole thing about acids and alkali's here but I don't think it is necessary.
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          May 6 2011: Hi Richard
          As always, amazed I am with your breadth and depth of knowledge , interest & analytical skill.

          Yes I agree all living beings are sentient though their basic designing materail DNA is not.

          Was just curiours whether you are particular about only plant and insect to be so.
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          May 1 2011: Hi Richard , good thoughts

          Considering nucleotide level of DNA , my thoughts favors randomness of mutation while going through replication in changed or even unchanged environment

          What do you think?

          Thought a bit so editing the post , what thoughts are there to be particular about insects & plants to be sentient Richard ?
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        • Apr 30 2011: Debra,
          The caterpillar adapted eyes in this way...
          At some time a caterpillar had little blotch pattern on its coat. This made the bird slightly less inclined to attack it, because of fear, after all why risk it for that caterpillar when other non-threatening caterpillars are everywhere. Then that caterpillar had offspring which may or may not have had the blotch, if they did maybe the blotch looked slightly more like an eye maybe it didn't, but eventually throughout the generations the caterpillars with the "eye blotch" were less and less likely to be eaten because the birds were afraid of them, therefore they more than the others who did not have the "eye blotch", survived long enough to procreate. The caterpillars without the "eye blotch" were then more likely to be eaten because if the bird is afraid of the "eye blotch" those "eye blotch" caterpillars have been taken off of the menu for the bird. Kind of like if I had 5 burgers 2 without and 3 with mustard, but you didn't like mustard, you would then be more likely to eat the 2 without.Insects procreate rather quickly and so you could see how incremental steps could get you from not having the "eye blotch" to having one that looks pretty precise, even though in the beginning it was just a blotch.
          I hope this isn't too confusing
          If you would like me to explain how the Sickle-cell adaption works I will in another post.
          Error and adaption are relative terms, if the mutation is beneficial we call it an adaption, if is not we call it an error but in essence all mutations are "errors."
          I think the intuition for this might be difficult because it is hard to strip the entire process of any purpose.
        • May 1 2011: I'm not sure what level of detail you want here or if you know what sickle cell actually is so I will try to describe this in some basic fashion.
          Sickle cell disease is caused by a mutation that affects one part of the protein complex that makes up hemoglobin. Specifically we are interested in Hemoglobin S,C,E and a- and B-thalassemia as well as a couple of other protein mutations related to blood.
          Sickle cell causes clots during states of oxygen deprivation, and people with sickle cell are then vulnerable to kidney failure.
          So how does this adaption both survive long enough to cause an almost immunity to malaria and yet at the same time kill the host?
          I am hoping you are familiar with the differences between recessive and dominant alleles.
          People who have one gene for Hemoglobin S etc. and one for say A, neither die from the recessive disorder or malaria because they are effectively able to produce both the "anti-malaria" Hemoglobin S and the normal A. Therefore they can fend of the malaria and yet are not overwhelmed with the Hemoglobin S, which cannot sufficiently carry oxygen throughout the body.
          Since the sickle cell gene is heritable we can bet that it is a germ-cell mutation, meaning a mutation of the sex cells that lead to embryo formation. Interestingly enough you'll find quite a bit of mutations of the germ cells, the thing is mutated sperm usually are not the fastest swimmers.
          So here we are again with the caterpillar. One person was born with a recessive gene for sickle cell and maybe it was dormant for them but eventually over long periods of time two people with the recessive gene had kids and that kid may have died of sickle cell. BUT since Afrika and SE Asia are so malaria ridden, people with only one gene, or a recessive gene were somewhat immune to the disease, and therefore had a greater chance of surviving long enough to procreate, and therefore the gene doesn't die out.
          So you are left with a bad thing that does a good thing.
        • May 1 2011: If you would like to understand how an inability for blood to transfer oxygen around the body is related to the malaria parasite...

          Get a textbook!(LOL)

          Or go to this quick article that is exactly what you are looking for.
          http://sickle.bwh.harvard.edu/malaria_sickle.html

          Just get over your natural inclination to look for intention in the process and it will make clear sense.