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Thread: The role of the environment on the diversity of species in natural evolution; is it essential?

  1. #1 The role of the environment on the diversity of species in natural evolution; is it essential? 
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    First off, I just recently started to really research this topic (suggested readings would be great), so some comments might not be correct.

    In artificial evolution the problem of convergence towards equilibrium states (just one specie surviving after x generations) to me seems unsolved as of yet (as far as I know). Even though I found a lot of research on this subject in the different subfields of artificial evolution and related topics, they all seem to try to reduce this convergence by adding extra functions that offer greater survival chances for new (divergent) genes/species, but these are only able to reduce the rate of the convergence. I was wondering what the main causes of this discrepancy with nature are.

    I myself thought that it probably lies in the high amount of abstraction that an artificial environment has and the fixing of lots of parameters that this implies. One of the highly simplified factors is the world in which artificial evolution is allowed to function. Our real world, for example, is constantly changing, promoting the adaptation of species, thus “guiding” evolution. Also, our world gives the inhabitants lots of space to coevolve, species don’t have to be able to fight a certain, they can also hide in a different environment unsuited for the predator for example.

    How essential, and in what way, do you think that the environment is to the divergence of species that evolve in it? Does it need to constantly change?
    Or to put it in another way:
    In nature all species originated from one specie, turning in to the vast amount of species we now have. Do you think that this could also happen inside a laboratory if we where to place this first life form in an environment that does not change? I myself doubt this, but I can’t really determine why exactly.


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    Quote Originally Posted by huub8 View Post
    First off, I just recently started to really research this topic (suggested readings would be great), so some comments might not be correct.

    In artificial evolution the problem of convergence towards equilibrium states (just one specie surviving after x generations) to me seems unsolved as of yet (as far as I know). Even though I found a lot of research on this subject in the different subfields of artificial evolution and related topics, they all seem to try to reduce this convergence by adding extra functions that offer greater survival chances for new (divergent) genes/species, but these are only able to reduce the rate of the convergence. I was wondering what the main causes of this discrepancy with nature are.

    I myself thought that it probably lies in the high amount of abstraction that an artificial environment has and the fixing of lots of parameters that this implies. One of the highly simplified factors is the world in which artificial evolution is allowed to function. Our real world, for example, is constantly changing, promoting the adaptation of species, thus “guiding” evolution. Also, our world gives the inhabitants lots of space to coevolve, species don’t have to be able to fight a certain, they can also hide in a different environment unsuited for the predator for example.

    How essential, and in what way, do you think that the environment is to the divergence of species that evolve in it? Does it need to constantly change?
    Or to put it in another way:
    In nature all species originated from one specie, turning in to the vast amount of species we now have. Do you think that this could also happen inside a laboratory if we where to place this first life form in an environment that does not change? I myself doubt this, but I can’t really determine why exactly.
    At one level the answer seems trivially obvious: since natural selection is the engine of evolution, there needs to be something in the environment that favours one trait over another, or there is no evolutionary pressure. Hence, one would expect a complex and changing environment to create more evolutionary pressures - and more evolutionary responses - than a simple and static one.

    But I suppose it also depends what is meant by the "environment". From the point of view of one species, other species that (for example) try to eat it are part of its "environment" (it is suggested that shells evolved in the pre-Cambrian following the development of the mouth), whereas to a scientist studying an entire ecosystem, one might regard the "environment" as being the background habitat, i.e. separate from the organisms inhabiting it.


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    Can you provide a link or two to articles discussing what you call artificial evolution. I am not clear if you are talking about, for example the breeding of particular forms of dog, or vegetable, or experiments on bacteria, or ...... I need therefore to grasp your point about convergence to an equilibrium state - which seems to me the same thing that happens in natural evolution - and your assertion that it leads to one surviving species. You seem to be talking about a sub-set of scenarios unfamiliar to me.
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    With environment I mean background habitat.
    My question therefor is whether just the changing fellow inhabitants are enough to start and maintain an evolutionary process leading to a diverse set of species, or does the background habitat itself need to change as well to stop it from converging?

    I couldn't post links yet (new member). But what I mean is an evolutionary algorithm. Wikipedia has an explanation on this if you search “evolutionary algorithm”.
    So for example: you create a simulation where you have a grid for the species to move in.

    For a specific example search for Polyworld.

    I would, at some point, like to create something similar. But with as little fixed parameters as possible, so for example the mutation rate, the way of exchaning "dna", if and when to mate and even when to die etc would all be part of the evolution instead of a fixed program. I got some rough scetches on how to implement this, but I don't know yet what the role of the environment (and what is would need to hold/do) would be in terms of how dynamic it has to be.
    Last edited by huub8; September 9th, 2014 at 12:02 PM.
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    Quote Originally Posted by huub8 View Post
    With environment I mean background habitat.
    My question therefor is whether just the changing fellow inhabitants are enough to start and maintain an evolutionary process leading to a diverse set of species, or does the background habitat itself need to change as well to stop it from converging?

    I couldn't post links yet (new member). But what I mean is an evolutionary algorithm. Wikipedia has an explanation on this if you search “evolutionary algorithm”.
    You cannot post direct links, but you can type out the url, inserting a space or two so the software does not recognise it.

    I consider the other flora and fauna a vital part of the environment. There is a wealth of research on "arms races" between predator and prey, where both evolve in response to the evolution of the other.
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    Yes, but is this relationship between two competing species enough to maintain diversity (so not just a few competing species, but a lot) in a static world?

    Because in the simulations I saw, only a few species survived because they outperformed the others by so much that they effectively killed them off. I would like to create a simulation where more than just a few species coexist, like in our world.
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    Quote Originally Posted by huub8 View Post
    Yes, but is this relationship between two competing species enough to maintain diversity (so not just a few competing species, but a lot) in a static world?

    Because in the simulations I saw, only a few species survived because they outperformed the others by so much that they effectively killed them off. I would like to create a simulation where more than just a few species coexist, like in our world.
    Could you specify in more exact terms what model you are aiming at. From what I have read there are two base models. One classical evolution and the other simple adaptation via allele concentrations.


    “Techniques from evolutionary algorithms applied to the modeling of biological evolution are generally limited to explorations of microevolutionary processes and planning models based upon cellular processes. The computer simulations Tierra and Avida attempt to model macroevolutionary dynamics.” https://en.wikipedia.org/wiki/Evolutionary_algorithm



    One model is Mendelian (generational) the other seems classical Neo-darwinian (long time frame, slow change).
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    Quote Originally Posted by huub8 View Post

    How essential, and in what way, do you think that the environment is to the divergence of species that evolve in it? Does it need to constantly change?
    Or to put it in another way:
    In nature all species originated from one specie, turning in to the vast amount of species we now have. Do you think that this could also happen inside a laboratory if we where to place this first life form in an environment that does not change? I myself doubt this, but I can’t really determine why exactly.
    Enviromental pressure is very important in evolution of species. It is because of that adaptation to the environment that we have aquatic, terrestrial and flying living beings.
    Also, there are many other evolution theories that take in account other evolutionary agents, such as migrations, random genetic drift. They are all important.

    So the diversity of species is the consequence of those different selection pressures, in different times of history which are likely not to repeat again.
    So I also would say that is impossible to have such a diversity in a non changing environment.

    bye!
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    Enviromental pressure is very important in evolution of species. It is because of that adaptation to the environment that we have aquatic, terrestrial and flying living beings.



    I have a question about selective pressure causing anything but allele concentrations in hybridized organisms. I can cite the e. coli experiments and the adapted function of metabolizing citrate in anaerobic environments as strictly adaptation.


    The fossil record is harsh on the viewpoint of any macroevolution of organisms, I believe there is only a handful of candidates illustrating common decent between species and I believe they can all be explained.


    Do you have any examples of supposed macro evolution?
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    In an unchanging, generally comfortable environment, the range of what is "Normal" for the species will become broader. Un expressed mutations will accumulate in the species. This is essentially what is happening to humans now. Humans can survive everywhere on our planet and can go where they want. There are still evolutionary pressures but they are relatively slight. Our environment is too favorable to present a problem for us.
    Evolution is driven by death. "Selection" is the key word.
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    Quote Originally Posted by GTCethos View Post
    I have a question about selective pressure causing anything but allele concentrations in hybridized organisms. I can cite the e. coli experiments and the adapted function of metabolizing citrate in anaerobic environments as strictly adaptation.

    The fossil record is harsh on the viewpoint of any macroevolution of organisms, I believe there is only a handful of candidates illustrating common decent between species and I believe they can all be explained.


    Do you have any examples of supposed macro evolution?
    How many times does it have to be explained to you what macroevolution is and is not?
    For how long will you keep insisting that adaptation is something other than an important aspect of evolution?
    Now you are saying that shifting allele frequencies is not evolution either, not realising that this is one of the most often used simple definitions of evolution out there.

    It's stuns me that you keep reinventing the most basic of terminology to suit your own agenda. You've redefined what evolution is in such a bogus manner that it's hardly surprising that you have doubts about it.

    You seem to (it's my guess) want to see a cat give birth to a flying fish-horse or witness a brand new protein evolve with a function that is unrelated to anything seen before, and do so from genetic material that appeared spontaneously from the vacuum.
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    Quote Originally Posted by GTCethos View Post
    I believe there is only a handful of candidates illustrating common decent between species and I believe they can all be explained.
    I believe there are 1000's of candidates illustrating common decent between species.
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    Quote Originally Posted by GTCethos View Post
    .... I believe there is only a handful of candidates illustrating common decent between species and I believe they can all be explained. ...
    Yes they can be explained, naturally. No need for the Great God Mud-dub to interfere at all.
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    Quote Originally Posted by huub8 View Post
    Yes, but is this relationship between two competing species enough to maintain diversity (so not just a few competing species, but a lot) in a static world?

    Because in the simulations I saw, only a few species survived because they outperformed the others by so much that they effectively killed them off. I would like to create a simulation where more than just a few species coexist, like in our world.
    So now I understand that you are speaking about computer simulations, not laboratory or field experiments. Is that correct?

    Recognise that these are simplifications designed to develop basic concepts. I am old enough to remember the first attempts at computer graphics. I can picture a Scientific American article from the 60s in which there were incredible illustrations of very rough frames in the shape of a jug. Life simulations are not much more advanced than that. We have not yet captured the complexity of the real world. That's just a matter of time.
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    Quote Originally Posted by GTCethos View Post
    I have a question about selective pressure causing anything but allele concentrations in hybridized organisms. I can cite the e. coli experiments and the adapted function of metabolizing citrate in anaerobic environments as strictly adaptation.
    Adaptation on long time scales = evolution. We are, after all, single cell organisms with a few adaptations.
    Do you have any examples of supposed macro evolution?
    Land animals to whales. More long term adaptation.
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    “Now you are saying that shifting allele frequencies is not evolution either, not realising that this is one of the most often used simple definitions of evolution out there.”


    Most often used definition but not observed.

    Because such allele shifts are reversible one way or another. What evolution has hoped for is an organism to experience a "classical selective sweep" of heterozygous distributions of those alleles (a change in genotype). Not ever seen in any experiments or observation (as far as I know).
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    Quote Originally Posted by GTCethos View Post
    “Now you are saying that shifting allele frequencies is not evolution either, not realising that this is one of the most often used simple definitions of evolution out there.”


    Most often used definition but not observed.

    Because such allele shifts are reversible one way or another. What evolution has hoped for is an organism to experience a "classical selective sweep" of heterozygous distributions of those alleles (a change in genotype). Not ever seen in any experiments or observation (as far as I know).
    And your reference for this assertion is what specifically?
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    Quote Originally Posted by Paleoichneum View Post
    Quote Originally Posted by GTCethos View Post
    “Now you are saying that shifting allele frequencies is not evolution either, not realising that this is one of the most often used simple definitions of evolution out there.”


    Most often used definition but not observed.

    Because such allele shifts are reversible one way or another. What evolution has hoped for is an organism to experience a "classical selective sweep" of heterozygous distributions of those alleles (a change in genotype). Not ever seen in any experiments or observation (as far as I know).
    And your reference for this assertion is what specifically?
    There is a great deal of circular reasoning about “classic selective sweeps”. The evolutionist looks at the different species of fruit fly genome (this case in particular) and say look at the selective sweeps that have occurred between them over time. The only problem is there is no evidence that these so called sweeps occurred at all.


    How do I know this, you might ask? Because after 80 years of fruit fly research there has not been one directly observed beneficial sweep in the genome of any fruit fly species. On the contrary, there has been damage observed to the genome of fruit flies that have seriously reduced the fitness of that population.


    Evolutionists are not proud of the findings….


    Here is a direct study in our species… The conclusion is as follows:


    “These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.” http://www.bioportfolio.com/resources/pmarticle/147396/Classic-Selective-Sweeps-Were-Rare-In-Recent-Human-Evolution.html



    “A new computational analysis based on data for nearly 200 human genomes assessed through the 1000 Genomes Project pilot effort suggests classic selective sweeps have occurred less often than expected in the human lineage.”http://www.genomeweb.com/sequencing/1000-genomes-pilot-data-suggests-recent-selective-sweeps-rare-human-lineage



    This 250,000 years might be extended back to Homo Habilis and Homo erectus maybe back 1.6 million years. Since we have not changed much since Turkana boy.


    This in spite of reproductive isolation of some humans and all selective pressure hard and soft.


    Here is a citation that directly supports the assertion above:


    the researchers tested the the classic selective sweep model, the predominant strategy used to look for evolutionary footprints for the last 35 years. But with a new, larger dataset, Hernandez and colleagues found little evidence for selective sweeps in the history of our species.http://sciencelife.uchospitals.edu/2011/02/21/sweeping-out-selective-sweeps/



    This paper discredits Selective sweeps in us and our ancestors.


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    Adaptation= something an individual does in response to a stressfull environment. Ie: When I lived in a fifth floor walk up apartment I developed an increased respiratory, cardiovascular and leg musculature such that I could run faster and longer.
    Evolution = something that happens to a whole population living in a stressful environment so that individuals within that population are born with greater capacity to deal with the stressor.
    Adaptation is what happens to individuals in their life time. Evolution is what happens to populations over generations.
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    Quote Originally Posted by GTCethos View Post
    Quote Originally Posted by Paleoichneum View Post
    Quote Originally Posted by GTCethos View Post
    “Now you are saying that shifting allele frequencies is not evolution either, not realising that this is one of the most often used simple definitions of evolution out there.”


    Most often used definition but not observed.

    Because such allele shifts are reversible one way or another. What evolution has hoped for is an organism to experience a "classical selective sweep" of heterozygous distributions of those alleles (a change in genotype). Not ever seen in any experiments or observation (as far as I know).
    And your reference for this assertion is what specifically?
    There is a great deal of circular reasoning about “classic selective sweeps”. The evolutionist looks at the different species of fruit fly genome (this case in particular) and say look at the selective sweeps that have occurred between them over time. The only problem is there is no evidence that these so called sweeps occurred at all.


    How do I know this, you might ask? Because after 80 years of fruit fly research there has not been one directly observed beneficial sweep in the genome of any fruit fly species. On the contrary, there has been damage observed to the genome of fruit flies that have seriously reduced the fitness of that population.


    Evolutionists are not proud of the findings….


    Here is a direct study in our species… The conclusion is as follows:


    “These findings indicate that classic sweeps were not a dominant mode of human adaptation over the past ~250,000 years.” http://www.bioportfolio.com/resources/pmarticle/147396/Classic-Selective-Sweeps-Were-Rare-In-Recent-Human-Evolution.html



    “A new computational analysis based on data for nearly 200 human genomes assessed through the 1000 Genomes Project pilot effort suggests classic selective sweeps have occurred less often than expected in the human lineage.”http://www.genomeweb.com/sequencing/1000-genomes-pilot-data-suggests-recent-selective-sweeps-rare-human-lineage



    This 250,000 years might be extended back to Homo Habilis and Homo erectus maybe back 1.6 million years. Since we have not changed much since Turkana boy.


    This in spite of reproductive isolation of some humans and all selective pressure hard and soft.


    Here is a citation that directly supports the assertion above:


    the researchers tested the the classic selective sweep model, the predominant strategy used to look for evolutionary footprints for the last 35 years. But with a new, larger dataset, Hernandez and colleagues found little evidence for selective sweeps in the history of our species.http://sciencelife.uchospitals.edu/2011/02/21/sweeping-out-selective-sweeps/



    This paper discredits Selective sweeps in us and our ancestors.


    First of why are you yelling again, you were warned against that less then a week ago.

    You're arguing from the starting position that "selective sweeps" are the only mechanism that is proposed for evolution to occur. This idea has been shown to be false a number of times already. Why do you use it?

    Your assertion specifically was that selective sweeps have never been observed in evolution, the papers you link to specifically disprove that point by acknowledging they do occur, while stating that they may not have occurred in recent homonid evolution. This paper documents several specific sweeps and discusses them in context with human evolution http://mbe.oxfordjournals.org/content/31/5/1275.full

    Also stop using the derogatory term "evolutionist", its rude.
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    Moderator Comment: GTCethos, and others - (possibly including myself.) This is a thread about the role of environmental variability in generating species diversity. It is not a place for creationist claptrap. Cease the discussion on that now. If I have time this evening (GMT) I shall try to detach the relevant posts to a separate thread.

    Usual constraints on responding to this note apply.
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    I am indeed talking about a computer simulation (I should have made that more clear).

    I do not aim at making a simulation that completely simulates real natural evolution, that would be way out of reach (if it is even possibly given the limited computing resources). I do however want to create an environment that keeps evolving (diverging) for as long as possible, creating possibly interesting behaviour. The final goal is to alter this undirected evolution in directed evolution (but that’s of later concern).

    In the polyworld example, the world only consists of a few barriers and randomly spawning food basically. Now this would be to simple to really create diverse life I think. What kind of things do you think that a world should hold? What kind of patterns/events should occur in it, how would you present food/energy? Should it house different environments, and if so which?

    (do you know any usefull papers on this?)
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    First of why are you yelling again, you were warned against that less then a week ago.



    Actually I use the available font size provided by this forum, sometimes it is size 2, sometimes it is size 3. Most of my recent posts have been option 2. If it is forbidden why is it an option. The problem may be your selection of zoom in your text editor… Your problems are not my problems.
    It is not “yelling”.


    You’re arguing from the starting position that "selective sweeps" are the only mechanism that is proposed for evolution to occur. This idea has been shown to be false a number of times already. Why do you use it?



    I never said that…






    Your assertion specifically was that selective sweeps have never been observed in evolution, the papers you link to specifically disprove that point by acknowledging they do occur, while stating that they may not have occurred in recent homonid evolution. This paper documents several specific sweeps and discusses them in context with human evolution http://mbe.oxfordjournals.org/content/31/5/1275.full



    It is becoming apparent that “classical selective sweeps” have not been observed. Evolution paradigm is changing terms again.


    Also stop using the derogatory term "evolutionist", its rude.



    You are an evolutionist I presume. There is nothing wrong with the brand unless you are ashamed of the paradigm. Some people would ban the names of football teams and other such nonsense.


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    In the polyworld example, the world only consists of a few barriers and randomly spawning food basically. Now this would be to simple to really create diverse life I think. What kind of things do you think that a world should hold? What kind of patterns/events should occur in it, how would you present food/energy? Should it house different environments, and if so which?



    My friend this sounds like a doctoral dissertation. Maybe even way above that and above my pay grade. I respectfully bow out of this thread. Good luck… truly all the best.
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    Quote Originally Posted by huub8 View Post
    I am indeed talking about a computer simulation (I should have made that more clear).

    I do not aim at making a simulation that completely simulates real natural evolution, that would be way out of reach (if it is even possibly given the limited computing resources). I do however want to create an environment that keeps evolving (diverging) for as long as possible, creating possibly interesting behaviour. The final goal is to alter this undirected evolution in directed evolution (but that’s of later concern).

    In the polyworld example, the world only consists of a few barriers and randomly spawning food basically. Now this would be to simple to really create diverse life I think. What kind of things do you think that a world should hold? What kind of patterns/events should occur in it, how would you present food/energy? Should it house different environments, and if so which?

    (do you know any usefull papers on this?)
    Then keep changing the environment (atmosphere gases, number of species, nutrients, fight for food, fight for space, climatic disasters, migrations) I don´t know... If you want something to keep diverging, I would change it continously...

    By the way, in this simulation, if the environment keeps changing, what are the parameters of interest you would measure while keep on changing the environment? Also, you would have to programme what would happen to environment if one of the parameters measured changes... For that you need information that if A interacts with B, would give C if it happens in D conditions... I don´t know... that´s way to complicate.... I can´t even imagine how to do it. But...... I have no idea of bioinformatics either... only how to search on NCBI and make alingments, hehe
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    Quote Originally Posted by huub8 View Post
    What kind of things do you think that a world should hold? What kind of patterns/events should occur in it, how would you present food/energy? Should it house different environments, and if so which?
    In real life, every parameter of that life is a trade off for success in some environmental situation. This is probably the problem with the simulations, there is too much overlap. You need enough limits on life so that it cannot overrun every part of the environment.

    The environment has wide ranges of parameters:
    Temperature ranges
    Amounts of sunlight
    Water available(underwater to desert)
    Salinity of water
    Local resource limitations (chemicals needed for life) Not just the main three for plants
    Granularity of these resources (eg. availability of bound nitrogen is high only where something just died)

    Nothing should be able to live in all of the combinations of the ranges of these environmental parameters.
    Life must adapt to enter more radical environments.

    Other limitations on life due to scale and biocompatibility (eg. poisonous as food or even in proximity) should ensure diversity.
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    Quote Originally Posted by huub8 View Post
    Does it [the environment] need to constantly change?
    It's perfectly possible to have evolution without the environment doing any filtering (natural selection). Drift and gene flow will continue to reshape genomes - in fact, it can't be prevented. In addition, the environment itself does not need to change for organisms to open up an exploit new niches and resources within that environment.
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    Ok, so you guys seem to agree on two points:
    1. The environment should contain multiple areas that have specific characteristics that make sure that one specie can’t strive in all of them.
    2. There should be conditions that effect the performance of species that continually change.

    The species in my simulation will consist of a string of commands/statements, so this would be like there DNA, but unlike DNA this string will directly control their behavior (as it can be executed like a regular computer program).
    So for example the way they mate/reproduce would also be defined in this string (in a separate section), so they themselves could "decide" how many ofspring they want (in a certain situation). But also when to eat, or if something is near them whether to move towards or away from it.


    The world in which these creatures live will be a kind of grid, and they can see a certain amount of cells around them. So if they see another of there own species two cells to the left they could move towards it, and mate (assuming that the other "is in for it").

    The thing that I'm struggling with is how to judge whether someone is of your own species. Because the DNA string doesn't have to be exactly the same to be able to mate (that would stop evolutionary drift) so that's not a suitable way to check this. Do you have any suggestions?
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  30. #29  
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    Quote Originally Posted by huub8 View Post
    Because the DNA string doesn't have to be exactly the same to be able to mate (that would stop evolutionary drift) so that's not a suitable way to check this. Do you have any suggestions?
    So how large of a difference is acceptable before mating starts to produce infertile hybrids or fails entirely? Can such a parameter be set in your program?

    I am also a bit curious about if you might be able to include lethal mutations?
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    Well thats the question, how could one determine this?
    I can introduce any parameter I want, but I need to base this parameter on something.

    Lethal mutations won't be a problem, I don't mind it if the ofspring dies before reproducing. (I would like to set as little constraint as possible right now)
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  32. #31  
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    How does this system work in nature, what abstract principles does it use?
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