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Wednesday, May 24, 2006

Dismembering Evolution 8: Avida

In this world of technology no theory would be complete without computer models being used to demonstrate the feasibility of the theory. In other words, program in the parameters of the theory and see what you get. If the simulation supports the theory you are good.

There is one problem though with any computer simulation. It simulates the parameters that are plugged in whether they happened in real life or not. When these parameters are based on massive amounts of assumptions that are not supported by laboratory experiments the program is running entirely off guesses. Even complete fabrications can be programmed into a simulation as any video game proves.

One example of just such a flawed computer program was one Richard Dawkins ran to show that random mutation in the early world could have resulted in the swift changes that are observed in the Cambrian. He selected a verse from Shakespeare, programmed in 27 variables, the alphabet plus a space, and had the simulation randomly change each slot. By randomly I mean random slots and random result. In just forty five generations the selected verse was completed to 100% accuracy. Subsequent runs showed an 80% likelihood of achieving the same result within forty five generations. Pretty spectacular huh?

There is just one teeny-tiny, huge, massive, glaring, fatal flaw to this program.

He programmed it to lock in the letters when the right one fell into place.

That’s right. Once a desired mutation was achieved he removed an essential variable, the possibility of losing the mutation. As both scientists and lay persons here have stated often, evolution is not a one way process. All is capable of being changed in such a way as to advance, or to regress. But don’t take my word for it, just the comments and links left in the discussion of previous articles in this series.

According to evolutionary theory there is no such thing as a locked in change. What is beneficial one generation may be fatal the next due to environmental changes. A mutation may or may not be passed on to future generations. A mutation may or not be repaired by the DNA as it happens, or the mutated cell may simply be attacked and destroyed by the organism’s immune system. What’s more, is the mutation even possible to pass on? Most are not transferable to future generations because the germ cells are not the cells that are mutated. This, of course, does not apply to binary fission such as in bacteria, or to viruses. So Richard Dawkins programmed a fatally flawed simulation to prove a point he could not make honestly. Bad scientists! Bad! No treat for you!

A much more important, and also much newer computer simulation is called Avida. This computer program is truly fascinating.

It has gone through several revisions until it is now the most exciting bit of research simulation for studying evolution there is. Initially, with the parameters being exactly what evolutionary theory states it had the problem of actually wiping out biological diversity. Then I was altered to reward any change whatsoever, and that solved the problem of destroying diversity, resulting in a rich environment of simulated organisms, but also not achieving this result in the time allowed by geologic history.

This problem demonstrates a weakness in evolutionary theory every time someone says that evolution is not random, but sequential. In sequential evolution the number of generation the simulation needed to produce a diversity resembling the Cambrian too until past the modern day. True to Darwinist fashion, rather than looking at evolution for the problem, the programmer looked at the program’s parameters. After much tweaking he decided to bombard the earliest simulated life forms with incredible doses of simulated radiation. This produced a random mutation rate sufficient to produce the appropriate diversity of life in the appropriate time.

Amazing huh?

But there are a few problems.

First, such a high radiation level is shown to prevent abiogenesis by the destruction of amino acids and proteins. Second, it is shown not to mutate cells, but to kill them. Third, eve if something were to evade the death trap of light it would be shielded form the mutating effects of the radiation. Third, assuming something survived completely unshielded and was randomly mutated, and successive generations continued the trend for a hundred million years or so, this destroys the notion that evolution is not random. It actually reduces the soft definition of evolution that is becoming fashionable, “The change in the frequency of alleles” to bull-spit because evolution absolutely required massive random mutation to do anything to begin with. It takes early evolution completely out of the soft definitions, and even takes it out of the idea of natural selection in the classical sense because extreme mutation is not compatible with that theory.

Scientists studying evolution are going nuts, absolutely raving about Avida. Never mind that the parameters it requires to operate according to evolutionary theory are actually in conflict with evolutionary theory. Never mind that the source of the conflict is the generally acknowledged problem of UV radiation of the kind required in this simulation is simply lethal to life rather than mutating it into many forms. It is the first computer program to successfully produce a model of evolution based entirely on random changes supported by a reward (a simulated environmental factor, actually, it is more food).

What about it’s failures? What about its failure to punish the occasional change with a reduction in food, reduced viability, or even death? What about the lethality of the early parameters? What about the way it actually decimates the concept of evolution NOT being random? What about the conditions of early evolution being completely destructive to abiogenist as well? None of this matters because it provides a computer model that works.

More importantly to the skeptic, what about the parameters of the program in the first place?

This program follows a lot of assumptions, just like evolutionary theory itself. And just like evolutionary theory, this program has its serious flaws when compared to reality. To my way of thinking, the vital change that was needed to the early environment, which is generally considered to be a reasonably accurate simulation of the early Earth, and is also a set of conditions that would wipe out all life and pre-life, actually provides AGAINST evolution and abiogenesis. Without abiogenesis evolution cannot happen. If early life is destroyed by radiation the evolution cannot happen. Current laboratory experiments show that the radiation levels that are simulated absolutely destroy all life and pre-life. Lesser radiation does not provide the required mutation levels to form the diversity of life in the required geologic time. These basic incompatibilities only seem to bother skeptics, like myself, and not the highly educated scientists who should be able to look at this and see the exact same issues.

So, what do I think about computer simulations? I think they are proven to be a powerful tool for demonstrating what will happen within a given set of parameters. I think that if the parameters are demonstrably good then the tool is good. I think that if the set of parameters is questionable then the tool is not much good at all, and only shows an unrealistic simulation of what the programmer wishes were true.

And, no, there is no computer simulation to date that provides a working model of evolution under realistic circumstances.

7 Comments:

  • Daniel: In this world of technology no theory would be complete without computer models being used to demonstrate the feasibility of the theory. In other words, program in the parameters of the theory and see what you get. If the simulation supports the theory you are good.

    Are you saying that you honestly think there is a computer model that actually simulates the entire theory of evolution?

    Daniel: That’s right. Once a desired mutation was achieved he removed an essential variable, the possibility of losing the mutation. As both scientists and lay persons here have stated often, evolution is not a one way process. All is capable of being changed in such a way as to advance, or to regress. But don’t take my word for it, just the comments and links left in the discussion of previous articles in this series.

    You mean those discussions where you swore black and blue that if an organism regresses to a previous state, it isn’t evolution? Have you now changed your tune on this? Are you now saying that you were wrong in your opinion?

    Of course Dawkins retains the successful mutations. Only successful mutations survive. The organisms in the world that have survived are the result of occasions where the mutations are not fatal and have conferred a competitive advantage to the organism. A mutation that helps an organism survive is not suddenly lost from a population for no apparent reason.

    Daniel: A mutation may or may not be passed on to future generations. Blah, blah, blah…

    Irrelevant. It’s the mutations that are passed on to future generations that are one of the basic mechanisms of evolution. Are you now trying to say that this never happens?

    Daniel: A much more important, and also much newer computer simulation is called Avida. This computer program is truly fascinating.

    Before we go any further on this, please tell us what you think is the purpose and application of Avida. Then we can explore whether your criticisms of it are applicable to your argument or you are just being misleading.

    Daniel: Scientists studying evolution are going nuts, absolutely raving about Avida. Never mind that the parameters it requires to operate according to evolutionary theory are actually in conflict with evolutionary theory.

    You seem to be implying that Avida is a computer model of the entire theory of evolution. Is this what you would have us believe?

    Daniel: This program follows a lot of assumptions, just like evolutionary theory itself. And just like evolutionary theory, this program has its serious flaws when compared to reality.

    And, no, there is no computer simulation to date that provides a working model of evolution under realistic circumstances.


    You say the model has flaws when compared to reality. What do you mean by reality? The only thing you can compare it to validly is the theory of evolution. So are you saying evolution is reality? You see, you are saying the model is flawed because it doesn’t fit with the theory of evolution, but the theory of evolution is flawed because it doesn’t fit with the model. You can’t have it both ways. That’s just stupid.

    By Anonymous cjb, at 4:46 AM  

  • CJB,

    "Are you saying that you honestly think there is a computer model that actually simulates the entire theory of evolution?"

    I am saying the claim is that Avida does, and prominent evolutionary scientists are hailing it as such.

    "You mean those discussions where you swore black and blue that if an organism regresses to a previous state, it isn’t evolution?"

    You do have a remarkable ability to miss the obvious. In the simulation he ran there would have only been a 1 in 27 chance of regression to the previous state. Also, this model is mutation based, not one based on natural selection where only existing genes are used, which is what we were discussing before. Mutation is a radical change where something completely new is brought about in the genetic sequence. However, without bringing about a new species, even mutations are not evolution, although this particular point is open for genuine dispute due to th efact that mutations are generally quite radical.

    "Of course Dawkins retains the successful mutations. Only successful mutations survive."

    Not every time. Have you forgottenabout disease, starvation, predadtion, infant mortality, and the myriad of other ways an organism and it's offspring can die, even before reproductive age? Have you forgotten about localized populations that get wiped out by one calamity or another? Have you forgotten that this model was rearranging the entire sequence at once, only leaving the desired outcomes in place, which would assuredly be fatal in any livin organism. Have you forgotten that the living cell has a repair mechanism whereby almost all mutation are either repaired or wiped out by the organism itself? Have you forgotten that not all mutations are transmissible to offspring? Or are you just ignoring all of this inconvenient science because you want to support a faulty simulation?

    "A mutation that helps an organism survive is not suddenly lost from a population for no apparent reason."

    Name one such mutation that has been found in nature. And no, drug resistant bacteria don't count because they already have the appropriate gene sequence in their DNA and always have. That is a case for natural selection, not mutaion. It is only the high use of antibiotics that has increased the numbers of the drug resistant bacteria to the point where we took note of them.

    "Irrelevant. It’s the mutations that are passed on to future generations that are one of the basic mechanisms of evolution. Are you now trying to say that this never happens?"

    I am saying it fails to hapen plenty often enough to make any locked in sequnce in a simulation unrealistic. There must be a factor for the loss of the gene in the program or it is unrealistic. Therefore, this point is hardly irrelevant.

    "Before we go any further on this, please tell us what you think is the purpose and application of Avida."

    You do have the ability to be infuriatingly thick sometimes. Either you are pretending to be stupid, or you actually are. If you think Avida has anything to do with anything other than simulating abiogenesis followed by evolution based of what you have read here you must be mentally deficient.

    "You seem to be implying that Avida is a computer model of the entire theory of evolution. Is this what you would have us believe?"

    That is the claim that others are making.

    "You say the model has flaws when compared to reality. What do you mean by reality?"

    I mean when compared to what can actually be tested and proven, unlike almost all of evoluionary theory, which is based on broad guesses made from scant evidence. One such example is the assertion that Archeaopteryx is the ancestor to modern birds. A commonly held belief among Darwinists that is demonstarbly ridiculous when you compare the cladistic model it relies on to the actual geologic record. Darwinist are all too eager to jump to conclusions if they think they have something to support their pet theory.

    "So are you saying evolution is reality? You see, you are saying the model is flawed because it doesn’t fit with the theory of evolution, but the theory of evolution is flawed because it doesn’t fit with the model."

    Wrong on all counts. For some reality please see my criticism of the radiation factor in the program. Also, if evolution were reality (and it is not) the radiation factor would still be a HUGE poroblem. Also, if evolution were a reality (it is not) then the only thing that this program demonstrates is that when we cut the lethal radiation out evolution cannot have happened in the time frame we have available to us. So let's assume for a second that the scientists losing their mind about how wonderful and accurate Avida is are correct, the only thing Avida actually demonstrates is that evolution is wrong because it shows that for it to occur in the time it is supposed to happen in we must bombard early organisms with lethal doses of radiation, which, of course, would kill them, thereby wiping out all life and ending evolution on the spot.

    So either evolution is being weakened by the most accurate model of evoution to date, or Avida is just another innacurate simulation, and is therefore useless just like every other simulation of evolution to date.

    By Blogger Daniel Levesque, at 8:32 AM  

  • Great post!

    By Blogger Philosopher, at 6:54 PM  

  • Daniel: I am saying the claim is that Avida does [simulate the entire theory of evolution], and prominent evolutionary scientists are hailing it as such.

    [Avida is a computer model of the entire theory of evolution.] That is the claim that others are making.


    Who claims this? Show us the examples you found that convinced you that “prominent evolutionary scientists” claim that Avida models the entire theory of evolution. Give us quotes from these scientists that show that they make this claim. I find it difficult to believe that any scientist would claim that the entire theory of evolution has been encapsulated in a computer model. I think this is a fabrication on your part.

    Daniel: Also, this model is mutation based, not one based on natural selection where only existing genes are used…

    And how do you think those existing genes came to be different in different individuals in the population if not through mutation? Remember, we were talking about single celled organisms that reproduce asexually.

    Daniel: Mutation is a radical change where something completely new is brought about in the genetic sequence. However, without bringing about a new species, even mutations are not evolution, although this particular point is open for genuine dispute due to th efact that mutations are generally quite radical.

    Where are you getting your information? What makes you think mutations are generally radical and that they aren’t part of evolution? This is just wrong.

    Daniel: Have you forgottenabout… blah, blah, blah…

    I have forgotten none of these. They are all red herrings. Learn a little more about evolution before continuing with this nonsense. The mutations that matter to evolution are the ones that are transferred vertically or horizontally. And you seem to be always concentrating on individuals or groups in your arguments rather than populations as a whole.

    Daniel: Name one such mutation that has been found in nature.

    Read the article I linked to above.

    Daniel: If you think Avida has anything to do with anything other than simulating abiogenesis followed by evolution based of what you have read here you must be mentally deficient.

    I suggest you read the ‘About’ page on the Avida website. Avida is a tool to aid in the study of elements of evolutionary theory, nothing more. How on Earth did you extrapolate that to being a computer model of the entire theory of evolution?

    Daniel: So either evolution is being weakened by the most accurate model of evoution to date, or Avida is just another innacurate simulation, and is therefore useless just like every other simulation of evolution to date.

    Unlike the computer models we have for the entire theory of creation. Here’s one I prepared earlier in perl.

    print “God did it!”;

    By Anonymous cjb, at 12:54 AM  

  • you guys love leaving long comments, huh?

    By Blogger Will, at 10:14 AM  

  • In regards to scientists and Avida, ones who are essentially calling it the crowning achievement of an evolutionary model are:

    Richard Lenski, who claims it even has "the smell of life", so much so that he was tempted to shut down his labe where he has been trying to induce evolution in E. Coli bacteria for 17 years and 35,000 generations, so far he has been unsuccessful in doin g anything beside breeding a bigger bug with no new species being derived, kind of like a dog breeder. In regards to Avida he says "In one hour I can gather more information than we have been able to gather in years (of real life experimentation) of working on bacteria. it just spits data at you."

    Dunsan Misevic is using Avida to try to explain the emergence of sexual reproduction in evolutionary terms.

    Heck, Avida has even been described in following manner: "Avida is not a simulation of evolution; it is an instance of it."

    Like I said. It is being billed as THE model of evolution. The fact is that all it proves it that the program parameters do what they were designed to do, and that create evolution in a simulated environment. The best this program can be billed as is an instance of intelligent design. Of course, had the program written itself from a bunch of random electonic data transmissions at random with no human aid I would be much more impressed regarding it as a moel of evolution.

    By Blogger Daniel Levesque, at 7:33 PM  

  • Daniel: "He programmed it to lock in the letters when the right one fell into place."

    I just ran across this blog post. There is no discussion of locking characters in Dawkins' "The Blind Watchmaker". But we don't need to quibble about inaccessible programs from 1986. One can easily code the "weasel" program without any "locking" and still have it perform just as well as what Dawkins described. In fact, the performance difference between "locking" non-weasel programs and proper weasel programs is minor at reasonable values of population size and mutation rate.

    See http://tinyurl.com/atbc-ec-thread for more information.

    Wesley R. Elsberry

    By Blogger Wesley, at 4:26 PM  

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