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I'm somewhat irritated by "mutation" generally being described as a fully random factor in evolution: pure randomness does not seem like something that can survive in a long evolutionary process.

And some basic evolution in some long-lived organisms appears to happen in quite fewer generations than one would consider plausible considering just natural selection over an unbiasedly mutated genetic base.

So I'm wondering whether there have been attempts to view mutation itself as a process influenced by evolution. For example, couldn't "junk DNA" result in a susceptibility to certain mutations that is determined by environmental factors, like amount and constitution of nutrients, ambient temperatures and others.

The overall discussion of mutagenesis I can find focuses entirely on "damage", again basically assigning all mutations a negative or at least undirected character (like more mutations occuring under stress, with the "aim" being more likely to have more random mutations where one offspring might be more successful than the stressed parent by chance).

In a similar vein, I don't see not much of anything about evolution and competition of gametes: how different environmental factors influence which of an abundance of eggs mature and which of the (asexual) male gamete reproduction mutation in the testes will be favored over time or under environmental conditions.

Basically all of evolution and natural selection seems about how to survive into fertility and select a partner, and that's it as genes are constant apart from random cosmic radiation or toxic substances.

I think that this kind of viewing the message in the DNA as isolated from its medium just does not sound like something that would survive billions of years without something less random replacing the pure randomness.

So are there any major studies trying to figure out whether certain mutations leading to better adapted phenotypes occur in a non-random manner (namely not just affecting mutation rate but also direction) in response to environmental circumstances?

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closed as off-topic by Remi.b, rg255, AliceD, fileunderwater, WYSIWYG Aug 31 '15 at 5:33

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  • $\begingroup$ I'm a bit unclear what your question is. Are you asking what the general mutation rate is of genomic DNA, if anybody has looked at this, and if certain base pair changes are more common than others? $\endgroup$ – The Nightman Aug 30 '15 at 14:48
  • $\begingroup$ Welcome to Biology.SE. There is a mixture of different concepts in your post, most of them seem to be a little unclear to you. I recommend that you take some time to follow some introductory course to evolution. Understanding Evolution for example would be a good fit. $\endgroup$ – Remi.b Aug 30 '15 at 14:51
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    $\begingroup$ I am voting to close as the question reveals several misconceptions that cannot be fully addressed in a post (although I gave it a short try). $\endgroup$ – Remi.b Aug 30 '15 at 15:27
  • $\begingroup$ Biology SE is not the place to come and just throw out an opinion like this, if you have a proper biology question then please focus on that. The effect of a mutation is random - a species cannot will itself to produce a mutation with specific effect $\endgroup$ – rg255 Aug 30 '15 at 21:36
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    $\begingroup$ "pure randomness does not seem like something that can survive in a long evolutionary process." This is the "argument from incredulity". Just because it doesn't seem that way to you doesn't mean it isn't that way. $\endgroup$ – Chelonian Aug 30 '15 at 23:54
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pure randomness does not seem like something that can survive in a long evolutionary process.

I think this is because you don't quite understand (no offense) the interplay between mutations and natural selection. You should have a look at Understanding Evolution.

The overall discussion of mutagenesis I can find focuses entirely on "damage"

This is because the vast majority of mutations are deleterious (=damaging). But obviously, not all mutations are deleterious, otherwise no adaptation would be possible (only purifying selection would occur).

In a similar vein, I don't see not much of anything about evolution and [..]

I don't understand this paragraph.

Basically all of evolution and natural selection seems about how to survive into fertility and select a partner [..]

No! There is much more to evolution than that. Note that the semantic of evolution and natural selection is wrong as they are used in your sentence. Again, check out an introductory course.

I think that this kind of viewing the message in the DNA as isolated from its medium

No! The environment is a fundamental tenet in evolutionary biology. The association between genotypes to fitness is a function of the environment as well.

Are mutations random?

The mutation rate varies dramatically among species and along genomes (roughly speaking from $10^{-2}$ to $10^{-10}$). For example microsatellites (repeated sequences) are highly mutable. Note also that the probability of a given nucleotide to mutate depends also on the exact nucleotides that are around it (Rob Ness; Personal communication). The mutation rate is also a plastic trait (and is therefore under selection) in some species (of plants typically). The environment affect the mutation rate and the environment can be chosen by some species (avoidance) or even constructed in some species (niche construction). In multicellular organisms, the age of the father correlates with the number of new transmitted mutations as well. However I have never heard of any studies showing such behaviours in order to affect the mutation rate. Epigenetic changes (does not concern all species) can also the mutation rate and even into what new nucleotide the old nucleotide will be mutated into (with a given probability). Mutations are more likely to be transitions than transversions. If a specific region is under environment-depend selection, then a mutation that would allow to drastically increase the mutation rate at this nucleotide whenever the organism has a low fitness (or even whenever the trait of the organism is unfit for the specific environment) could reach fixation. This process (and maybe others I am not aware of) are I think encapsulated within a hypothesis called (and it is a horrible name as it can yield to confusion) adaptive mutation hypothesis. But really don't start studying any field of science by jumping into an advanced subject (or even worst, a controversial subject). You should start with an introduction.

However, the impact on fitness (and on phenotype) of a new mutation is essentially random. An organism has absolutely no way to know what protein will be caused by a given new mutation. Selection then select upon the variance created by the mutations, the variance decreases and adaptation occurs. The impact of new mutations seem to follow more or less two weighted gamma distributions (added to which a bump of probability density for lethal mutations).

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  • $\begingroup$ The studies you cite seem focused on short-lived organisms with a high reproduction rate. I did explicitly mention longer-lived specimens. Some correlations like a higher male birth rate for older first parents are well-known and not attributed to destructive mutations. It's also established that the number of birth defects for old fathers is not explainable by mere random mutation but rather by higher competitiveness in replication of gametes with a certain defect inside of the testicle issue. But all of that is always focused on defects and not on correlation with desirable features. $\endgroup$ – user17586 Aug 30 '15 at 17:06
  • $\begingroup$ I don't actually cite any studies. Not all what I am talking about is specific to short lived vs long lived organisms. I don't fully understand why the short-lved vs long-lived distinction metters for your question but I guess I don't really understand the question. $\endgroup$ – Remi.b Aug 30 '15 at 17:33
  • $\begingroup$ I think I am also confused about the low level of understanding of evolutionary processes that your post shows and am even more confused now that I see that you actually have some knowledge...but in the same time things like number of birth defects for old fathers is not explainable by mere random mutation but rather by higher competitiveness in replication of gametes with a certain defect inside of the testicle issue really doesn't seem to be related to the question. Also I don't understand the use of the concept of "junk DNA" in your title. I guess I just don't understand the question. $\endgroup$ – Remi.b Aug 30 '15 at 17:33
  • $\begingroup$ junk DNA is an obvious contender for contributing to tertiary molecule structures and/or hydrogen bonds that make the neighboring non-junk DNA more or less susceptible to certain environmental influences. Those can be either direct influences of factors like acidity or other ion concentrations, temperature, viscosity, osmotic pressure or more specific organic substances potentially generated by the body itself in response to external stimuli. When people "turn grey with grief overnight" (no, hardly overnight) does the responsible change in body chemistry also affect gene mutation? $\endgroup$ – user17586 Aug 30 '15 at 17:46
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Did you hear about the historical Luria-Delbrück experiment where they demonstrated that in Escherichia coli mutations conferring resistance to antibiotics are essentially random?

Also, discussions and some references on the phenomenon of (directed) adaptive mutagenesis, which I think you are asking about, is mentioned in the Wikipedia article. But I don't know much about the debate.

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  • $\begingroup$ Most antibiotics are essentially "random" environmental factors since the substances in question don't as a rule occur in massive amounts in nature (penicillin being a notable exception). Escherichia coli also is not exactly a higher organism with slow reproduction and long life. $\endgroup$ – user17586 Aug 30 '15 at 17:08
  • $\begingroup$ As Rémi.b, I don't see why slow reproduction and long-life are relevant for your question. You seem to be surprised about mutations appearing quickly, but a mutation can and does actually appear in one generation because it appears in an offspring. What takes time then is just the "propagation" of the mutation to the population through successive new offsprings, but this has nothing to do with the complexity or life expectancy of the organism. $\endgroup$ – The Quark Aug 30 '15 at 23:40
  • $\begingroup$ Also, whether an environmental factor is "random" or predictable is independant from whether the mutations that occur in an organism experiencing those factors would be random or targeted, so I don't see the relevance here either. $\endgroup$ – The Quark Aug 30 '15 at 23:50
  • $\begingroup$ slow reproduction and long life are relevant for the question since there is not much of a necessity for adaptive genetic changes bypassing the selection process of phenotypes when phenotype selection already happens fast enough to follow typical environmental changes. $\endgroup$ – user17586 Aug 31 '15 at 7:24

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