Could epigenetics be the guiding hand behind evolution?

Discussion in 'Biology & Genetics' started by notanumber, Sep 7, 2014.

  1. notanumber Registered Member

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    It's a thought I've had for ages, because I have a vague idea that evolution is directed by events, and not at all random. Is there any way that the expression of genes through epigenetics could be the main force guiding our genetic evolution as a species? - and by extension, the force behind the evolution of all life on earth? Feel free to take sides, this is an open question and might possibly be a dumb idea.
     
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  3. GeoffP Caput gerat lupinum Valued Senior Member

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    It's conceivable that epigenetic switches might force state or major quantitative changes in phenotype - but the switches themselves reset in the majority of cases at the succeeding meiosis. What might happen is that the switches get turned on again by persisting conditions. Mutations that then force the switches to stay on (or off) might promote micro- or macro-evolution. This might not be discernable from classical selection, however, particularly where the change is small.
     
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  5. river

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    Of course
     
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  7. wellwisher Banned Banned

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    If you look at neurons and memory, external potentials, inputting via the sensory systems, help mold and shape the connections between these neurons, from which specific memory will appear. This is an example of an epigenetic change, where potentials from the outside, can have an impact on the DNA and therefore the natural selection process; new behavior. In the next birth cycle, the DNA is reset and the neurons of the brain begin new.

    This process adds a wildcard to evolution, since although the epigenetic change (new behavior) can often be the cause of selection, it may not be reflected in the base DNA that we find. This can lead to a false positive based on the theory that the base DNA is always behind selection. A necessity in the environment, in conjunction with the brain, can lead to selection. This will not show up in the next generation, except by learning. But since this made the difference in terms of selection, other genes in the base DNA, that are not part of the selection, may get carried forward and lead to a false positive.

    As an analogy, say you see and find a gem stone while hiking in the woods, that is very expensive. You put it on a chain and when you wear it, there is awe among the crowd, which gives you the prestige of selection in the group and among the ladies. You get the prettiest wife and have children, but this bling effect will not be in their DNA at birth, since it was connected to an epigenetic change; behavior/prestige. It is an epigenetic bling but it gives you selection. Because of that being the reason for selection, your big nose will be carried forward via your base DNA. If we ignore the epigenetic change, one might infer that big noses was part of the selection process, since it allows more air intake to the muscles since one cannot see the epigenetic change that was behind the selection.

    Because the brain is moldable, allowing permanent changes in morphology beyond the base DNA, to allow unique memory, and since the brain and nervous system branches out and touches most of the cells of the body in some way, can the brain transfer its own epigenetic capacitance to other cells, by applying global and local potentials that reflect this change? For example, when an ovum is forming, can nervous input establish potentials in and around the ovum to impact the base DNA so change follows the bling. Only a small fraction of the DNA is used to code protein. The rest is more structural with packing and stacking equilibrium, impacting protein expression while maintaing the DNA.
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  8. GeoffP Caput gerat lupinum Valued Senior Member

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    It's conceivable also that if you have numerous descendants - say if you're r-selected, like a snail or a rat - they might also be more prone to stumble on this bling if they have the same enabling behaviour, creating persistent reproductive advantages.
     
  9. notanumber Registered Member

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    Wellwisher, tht is the kind of thing I have in mind: some, as yet undiscovered process, by which the DNA is altered by the epigenetic effects. It could be that the brain influences the ovum, or that epigenetic changes accumulate near the ovum and the testes, altering their processes. So the epiegentic change leads the way.

    The classical part of your example is simpler - your big nose may predispose you to taking woodland walks (more than sedentary people), while keeping your brain fully engaged with plenty of oxygen. And that, amongst other things, leads you to discovering the gem, which other woodland walkers are oblivious to.

    It could be some interplay of the two. (Hypothetically)
     
  10. notanumber Registered Member

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    GeoffP, I am having to look up the processes you mention, as my scientific knowledge of the subject is limited

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    I am taking in your points, and musing over them.
     
  11. GeoffP Caput gerat lupinum Valued Senior Member

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    Just this essentially: snail A possesses an allele that promotes increased roving, and finds some fancy bling in the forest because of it. He is much favoured by the ladies and has many progeny as a result: but the element that directly promotes his fitness (bling) is not heritable. However, a larger proportion of his progeny rove around and also find other bling - and they have greater fitness, despite no heredity for bling itself. It's sort of a very oblique parallel of the ideas behind epigenetics.
     
  12. notanumber Registered Member

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    Yes, exctly. But that roving may be genetic or epigenetic -? So the r-selection can favour either.

    But what if the roving is epigenetic, say, because the snail's mummy had a history of bad homes? - Then in classical genetics, snail A's babies revert to type, and don't do much roving. But if the epigenetic change causes a genetic change, his babies do more roving and find more bling.

    But say there is an interplay... say snail A's roving is epigenetic. His bling, and his status as a ladies man, cause another epigenetic change of his own, which dispose his babies to do yet more epigenetic roving (for different reasons). But that is as far as it goes. Unless there is some mechanism, perhaps over a longer time span, by which the endless epigenetic roving causes a genetic change. A process like that would have survival value.
     
  13. Aqueous Id flat Earth skeptic Valued Senior Member

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    Random events. Yes. Every sperm and egg cell is the result of the randomizing of meiosis, i.e. the process called crossover. Thus a random egg of randomized traits is fused with a random sperm of randomized traits. Additionally, random mutations can occur during meiosis, as well as chromosomal anomalies. Most fertilizations are selected through natural abortions. Thus every offspring is a living example of natural selection, as is every genetically damaged stillbirth.

    No. Gene expression itself isn't a cause for the change in the genotype, although it determines the phenotype and therefore the success or failure of the individual under pressures of natural selection, which introduces all kinds of randomization. But I think this is way off the point. You are asking how humans evolved from other simians. To get to the answer, consider this:


    A major argument supposedly supporting human evolution from a common ancestor with chimpanzees is the “chromosome 2 fusion model” in which ape chromosomes 2A and 2B purportedly fused end-to-end, forming human chromosome 2. This idea is postulated despite the fact that all known fusions in extant mammals involve satellite DNA and breaks at or near centromeres.


    (etc.) I won't cite any more of it, but this is enough to get you started. The source is creationist, which means that to get somewhere with the information, you need only reverse the explanation. (The fusion did occur, a fact which hardliners like the nut above are converting into propaganda.) Chromosomal anomalies like this are a toss of the dice. By far they produce non-viable embryos and a wide variety of genetic disorders. This random fusion happened to produce a new genus in the Homind family, Homo. The evolutionary stages between primitive and modern H. sapiens sapiens can be attributed to natural selection acting on randomized phenotypes.

    The evolution of sexual reproduction from asexual forms succeeded precisely because it increases the randomization of genetic mixtures. It can be attributed to the Cambrian "explosion" - the rapid diversity in forms normally associated with evolution.

    Not dumb at all. But there is no escape from the randomness of reproduction, esp. sexual reproduction, which enjoys success because it increases the randomization of alleles. A huge amount of energy is expended in the sexually reproducing species on behaviors (sexual displays, competition, selection) and all the trappings (physical processes like bills, plumage, tusks/antlers, coloration, etc.)

    There is also far too much random mutation and even random chromosmal anomalies to shy away from the importance of randomness in filling every niche as fast as available energy allows. Random mutation is so common that it is a subject of study unto itself.
     
  14. notanumber Registered Member

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    That is interesting, and obviously you know a lot about the subject. But I am still wondering if all that "randomness" is not actually random. There may be hidden, subtle processes which are directing it. The "black box" appearance of randomness may be due to science's limited understanding, so far; and when those "random" things are properly analysed, they may be found to contain a myriad of very non-random causes and effects. (Cavemen probably thought the weather was random).

    Is there any solid evidence to refute this idea?

    Also - I thought I read somewhere (perhaps I didn't) that the timescales are simply too short, for species' to develop as far as they have, if all mutations were random. The "selection of fitness by mates" has partly come to the rescue. My knowledge may be out of date here.
     
  15. Aqueous Id flat Earth skeptic Valued Senior Member

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    Random processes are basic to nature. A Gaussian process is also called the Normal distribution, because it's the most prevalent way randomness manifests itself.

    I think you misunderstand that Probability Theory is a well developed branch of applied mathematics, not at all a black box. It's foundational to all of science. Biology is not different. As soon as you take your first lab class you are confronted by the many random processes inherent to natural systems. A large amount of most every scientist's work involves characterizing randon processes. The entire premise of communications systems is to detect a signal in the presence of noise. The list of examples is endless.

    It's the other way around. You begin with the proposition that rejects first principles of math and science as improperly done. But it lacks any basis in evidence. Are you interested in learning probability theory? Because that's the course you would have to take to understand what you are attempting to refute. We can discuss that in greater detail if you're interested in it.

    All mutations are probabilistic, but the nature of the processes which produce mutations can vary widely. Did you study the fruit fly in school? What does the typical fruit fly lab experiment teach?

    It's one of many randomized processes acting in tandem. It doesn't apply to all organisms, obviously, even after we exclude the asexual forms, the sessile (sedentary) forms (usually), and other organisms which did not exploit the gains from sexual selection during their evolutionary history.
     
  16. notanumber Registered Member

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    I think you misunderstand me. I know probability reasonably well. There are many thing which appear, superficially, to be random, producing various types of distribution at a macro level. But when you look more carefully at the detailed processes at work, they are not random. For instance, throwing a dice could be calculated with the mechanics of a bouncing cubic object; and the weather can be predicted with more and more accuracy by using more and more powerful computers, eg. to calculate smaller and smaller moving parcels of air; where, superficially, both of those things have the appearance of randomness. Throws of a dice will produce an even distribution, and the weather can be said to have a "chance" of rain, and so on.

    I think there are very few truly random processes. But there are plenty which seem too complicated to work out mechanistically, and look random from a distance. I am suggesting that - most likely (imo) - genetic mutations and combinations are like that - superficially random, but in fact very predictable, if only we knew the processes at work.
     
  17. Aqueous Id flat Earth skeptic Valued Senior Member

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    You sound like you have never worked with random processes in any real world application.

    I don't know what you mean. When you shuffle an ordered deck of cards, the information that was present in the ordering is lost. How is that only superficial?

    If that were true then every toss would be the same in controlled experiments. The processes at work are random processes -- otherwise we would be living in a deterministic world.

    I can guess, with narrowing margin of error, the consecutive deals at a game of blackjack, merely by counting the cards. That doesn't change the fact that the cards are shuffled (randomized).

    Loss of information can't properly be called superficial. It's either there or it's not.

    The distribution tells you the probability of rolling a given number. It does not tell you what the next roll will be with certainty. This is what we mean by "random".

    But there is uncertainty. Hence, we call it random.

    That would be a very challenging PhD dissertation to defend.

    The problem with looking at a distance is that you lose the scope of what nature is actually doing. Consider, for example, the difference in outcomes from rolling one die or rolling two. That difference has nothing to do with the mutual effects of air turbulence. It has to do with the nature of two die versus one. That nature has nothing to do with mechanics. In other words, there is more to Nature than mechanics. I will call this case "natural causes" although there is no causation here, merely the intrinsic nature of having two dice as opposed to one.

    I think you'll find that it's not distance from nature, but a proximity to it, which affords the best vantage point for deciding how things work.

    I think the processes at work are not that mysterious. Chemicals bond, but only probabilistically. At the tails of the distribution, no bonding occurs, or else the improbable bonding of the wrong nucleotide or amino acid occurs, and a mutation results. Crossover is more obviously random for reasons best described as systemic rather than chemical. Every crossover produces a new random assortment of alleles, whereas genetic mutations due to bonding errors are rare.

    Did you do the fruit fly experiment, or at least read about it? I think the process of random mutation is well enough understood to address your doubts. Are you familiar with the evolution of the peppered moth? Anthropogenic soot was the cause of the change in niche pressure (from light coloration to dark). But random mutation provides the cause for spontaneous variations; either that or the random re-emergence of the recessive gene causes it, probably through the randomizing effect of chromosome crossover during meiosis.

    Of course it was the pressure of predatory selection which caused the evolution to occur.

    There you have two simple examples of random causes of mutations, the second of which lead to a remarkable shift in the dominant phenotype.

    Incidentally, I think the best place to arrive at an understanding the stochastic nature of genetics is, well, genetics. If you aren't familiar with Mendel's pea plant experiments, it's the seminal work that explains randomization of the genes in crossover. You can't say with certainty what the color of the flower or pod will be, but control this by hybridizing, and you get a randomized result which follows the distributions Mendel discovered.

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  18. notanumber Registered Member

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    "I don't know what you mean. When you shuffle an ordered deck of cards, the information that was present in the ordering is lost. How is that only superficial?"

    Because the shuffling can be observed and the result can be known. If you can't see that, and insist on telling me I don't understand things, I have nothing more to add.
     
    Last edited: Sep 9, 2014

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