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Suppose we have a population of about 1000 with an environment that does not change a lot (e.g. the atmosphere is more or less the same) and we leave this population to evolve. From what I understand some genes will be lost because they won't be suited enough to continue in the next generation. Also the generations can only reproduce within their generation (e.g. a male can only have reproduce with people from his generation).

My question is: won't some genes, combined with others have a better chance to make the individual "better" but they for example make it less fit right now. Or will the mutation of the genes actually promise that eventually we will hit that minimum of the function.

I want to point out that I'm a computer scientist and my biology is awful. I'm looking at this from evolutionary algorithms point of view in particular genetic algorithms.

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Can you clarify what you are asking? That second paragraph is very confusing. –  Amory Oct 15 '13 at 14:54
    
As in evolutionary algorithms (you might know from computer science), real evolution is random. It might hit a local minimum, but miss the global one. Different to evolutionary algorithms, evolution can even make things worse for a while, so there is a chance to have a "bad" mutation "surviving" long enough to be paired with another mutation that actually makes it "good". But it is random. –  skymninge Oct 15 '13 at 15:05
    
Indeed your second paragraph is confusing. What function are you talking about. It seems that in you example, two individuals with the same genotype in the exact same environment have different fitness. It is theoretically not possible. Does your question has to do with genetic interactions [en.wikipedia.org/wiki/Epistasis] or gene-environment interactions [en.wikipedia.org/wiki/Gene–environment_interaction]. What does your question has to do with game theory? Are you talking about newly arising mutations or only about alleles (gene variants)? –  Remi.b Oct 15 '13 at 22:52
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Your second paragraph starts with "My question is..." but does not actually contain a question. What are you asking? There is a well known mutation that makes individuals susceptible to sickle-cell anaemia but the same mutation also protects from malaria. Is that the kind of thing you're thinking about? –  terdon Oct 17 '13 at 15:00
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It sounds like you're asking about local minima that is, "dips" you can get stuck in though there might be a "valley" next to you? –  Oreotrephes Oct 17 '13 at 16:01
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What I think the question is "Why wouldn't an organism be more efficient from selection than the environment demands?" Please let me know if I'm hitting the mark here.

A scenario suggested by the question is this: If there is selection pressure on say an animal to resist a disease, and then it evolves two resistance systems to the disease. This could be an immune response and a taste for a certain plant containing compounds with remedial properties. If either system is adequate to resist the disease, hasn't selection gone above and beyond what is needed?

If so, the answer is either not recently, or all the time.

First, for 'not really' you have to consider the importance of competition. Reading about the Red Queen's Hypothesis is helpful here.. First there is a natural random mutation rate, which can cause one of the system to become less effective. Or if the disease is also changing to increase its efficiency, then either one or both of the defense mechanisms in this case would fail from time to time. Then having two systems would not be too much. There is a clear benefit to having redundant systems of resistance here. For both these broad categories of reasons, you have much redundancy and interdependence among the genes which create traits in living things (phenotypes). Because of the background mutation rate, traits which are not needed disappear relatively quickly; because of competition, those which convey an advantage, even if a small one, have a strong likelihood to stay in the gene pool.

now: "all the time" There are cases where traits are exhibited that are not efficient though. Evolution works over generations, typically selection influences traits on the order of 10s of generations and the population can show traits which are not helpful if the environment or the competition has changed drastically.

An example of this is the current obesity epidemic in the developing world. The sudden availability of cheap food has caused those people who have access to become obese. This is because they have a heavily reinforced trait to save up fat because humans experience famines regularly. Its going to take a long time before efficient energy storage in human beings is lost. In the meantime, people are not living to reproducing age at the same level of fitness they might have.

I want to add a note on genetic algorithms. The difference between genetic algorithms to achieve the same efficiencies as biological systems are worth thinking about:

  • As far as failing to find a global minimum, natural selection usually has many more samples. A typical selection experiment with flies or worms often have thousands or tens of thousands of individuals screened. GA models of reasonable complexity have usually a few score at most - am I right? A bacterial or yeast experiment can have 10^9 individuals.

    • The genetic system of the chromosome itself is tremendously complex. We can't even model itself and so the product of millions of generations of selection already will has a heretofore unmodelable response to selection.

    • The typical selection environment is equally undefinable, so a survey of living things in a complex environment has unpredictable effects. While most of us think as laboratory experiments as being less complex, its not completely true. I was at a talk recently that mentioned how E coli K12 seems to have diverged in various laboratory environments despite the fact that its mostly been in frozen stocks since being isolated in the mid 20th century.

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Re: Red Queen's, van Valen's original paper has perhaps the best acknowledgement ever: "I thank the National Science Foundation for regularly rejecting my (honest) grant applications for work on real organisms...thus forcing me into theoretical work." –  Oreotrephes Oct 17 '13 at 19:04
    
@Oreotrephes That's amazing. –  Amory Oct 17 '13 at 20:25
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@Oreotrephes Van Valen's paper is wonderful in all its weirdness, and provides useful perspectives on scholarly communication. –  fileunderwater Oct 18 '13 at 9:43
    
I'd not read this either - thanks @Oreotrephes! –  shigeta Oct 18 '13 at 14:11
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Im going to take a stab at this. I think he is saying that sometimes there will be mutations that will occur in a population that are beneficial, but only in certain environments. But he is asking, wont these mutations be eliminated often, since they may not be in an environment where their advantage is obvious?

First, there is something incorrect in your original post. You said "From what I understand some genes will be lost because they won't be suited enough to continue in the next generation". It is kind of unusual for a whole gene to be lost. Especially from a whole population! I think what you mean is 'allele'. And yes some alleles will be lost. But fitness is a gradient. Just because a mutation does not have an obvious advantage does not mean it will be lost. Most mutations are not really noticeable. In a recent post here, I think I quoted a website that says there are 70 or so de novo mutations every generation in humans. This means that both you and I have 70 new mutations that our parents did not. But we are both functioning just fine (I hope!).

And some of these mutations may be beneficial in certain environments, but dont do anything in others. Lets say that one of my de novo mutations was to make me sweat less. Not really noticeable, right? And it really wont give me fitness advantage or disadvantage, so natural selection wont really act on it. It's frequency should remain at about a constant level in the population . But now lets say something happens to the world climate and there is a drought that lasts for centuries over N. America. My mutation would now give me a fitness advantage since my body would lose less water.

So, to answer what I think your question was, natural selection will not always act on every mutation. It has to clearly give a fitness disadvantage to select against it, or an advantage to select for it. So if it gives no immediate advantage, it may not spread through the gene pool very quickly, if at all, but it will still be there. So when it is in an environment where it is advantageous, it will still be around, and then it will begin to spread through the population.

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