In my opinion, jack did not sufficiently explain why evolutionary algorithms cannot be said to be analogous to biological evolution (which was the claim I was speaking to in my response to you). But on reading his post it does not seem that that was his point, anyway. His argument is suitable against the creationist strawman of "can x/y/z be created by random processes", when they are trying to cast doubt on biological evolution. But that does not speak to my response to you.

Both biological evolution and evolutionary algorithms in general both operate in an analogous fashion. Both incorporate random mutation and decidedly non-random selection. It would be silly to say that evolutionary algorithms prove biological evolution, but I do not think it is any less silly to say they are not analogues. And I have not seen any convincing arguments otherwise in this thread. And I say that wholly agreeing with jack's points. At most, his post states that biological evolution is a much more intricate model -- but that was not what I was protesting.

It's misleading to point to the results of EAs and say to our creationist friends, "See, randomness can produce complex and interesting things!" It's not the randomness that does it. To suggest this is to buy into their flawed logic...

Exactly, jack, exactly. I think you hit the nail on the head here. Interestingly, since he mentioned me, when I tried to even begin to suggest this to our friend OMGF, it all went over his head, and instead of discuss it intelligently, he just preferred to accuse me of "believing the lies of the creationists" even though I pre-stated I was not an evolution denier, then disingenuously chop a single sentence out a substantial discussion to accompany an immature ad hominem remark. Here's a little more context surrounding the sentence of mine that he farmed out of the other thread, which suggests a different story:

You seem to have misunderstood the relevance of Haeckel's embryos, as whether or not they were faked doesn't affect my point at all. Further, Claim CC216.2 directly supports my point, so I'm left to wonder why you'd reference that, and to wonder if maybe you're making knee-jerk responses here. These are even further supported by the fact that even after I explicitly told you I am not an evolution denier, you merely handwaved my claims and proceeded to gas on about how I've accepted the lies of the anti-evolution movement. I believe in LUCA for cryin' out loud, don't you read?!?!? And why on Earth would you assume I've never spent any time scouring the TalkOrigins archive and attempt to handwave me to an authority I'm quite familiar with? Your strategy here lends well to the idea that you can't formulate your own intelligent responses to my points, and that you'd wave me to a reference that supports one of them lends well to the idea that you haven't even understood them. (cl to OMGF)

This is sad, because we see how an irrational reaction obscures knowledge, meaning that instead of thinking and considering whether my points had validity, OMGF simply flanks me. Maybe he'll accept your well-reasoned criticisms? To accept my statements in the thread OMGF conveniently failed to cite or jack's statements here does not in any way entail that one is questioning or denying evolution, or attempting to make some lame, backhanded argument for creationism. As you said,

..this in no way casts doubt on the reality of biological evolution, nor does it imply that, for biological evolution to work as well as it does, it must have been set up by an intelligent designer.

The only reason I made my remark at all was to provide a more well-rounded treatment of the subject than was presented in the original posts. Sure, Ebon covered many of the positives of EA's just fine, but leaves important anomalous evidence out, or interpretations that challenge his point-of-view. People might like to know a little more about the subject.

Paul,

If you still have any questions jack didn't answer, let me know.

It's misleading to point to the results of EAs and say to our creationist friends, "See, randomness can produce complex and interesting things!" It's not the randomness that does it. To suggest this is to buy into their flawed logic, rather like trying to answer the question, "Have you stopped beating your wife?"

Evolution, natural or in computer simulation, is better described as stochastic, rather than random. It has randomness in it, and that randomness is essential, but it also has a highly nonrandom component: selection. Whenever a creationist asks me, "Do you really believe X could have arisen purely by chance?", where X is some example of beauty, complexity, order and function in biology, I just answer, "No, of course not. That could never have arisen by chance. But that is not what Darwin's theory of evolution says." I then go on to explain the highly nonrandom effects of natural selection. Of course I seldom succeed in changing their minds, but that's a separate issue.

Getting back to our computer simulations of evolution, some comments alluded to the role of the programmer as designer, in choosing how to represent the problem, deciding what attributes should be mutable, deciding how large a perturbation should be made with each mutation, etc. This is all true. These are thorny problems for anyone who sets out to solve a really hard, complex problem using EAs. But this in no way casts doubt on the reality of biological evolution, nor does it imply that, for biological evolution to work as well as it does, it must have been set up by an intelligent designer. Some of these thorny problems can be solved by evolution itself. A good example is the adjustment of the size of the perturbation used in mutation by indirect selection pressure, what practitioners call self-adaptive mutation rates. The correlation of mutations across multiple dimensions can also be handled in this way. The details are a bit too arcane for this comment, but can be found in books like this one.

Biological evolution works as well as it does in part because the details of the representation -- for example the mapping of the triplet codons onto amino acids in such a way that small errors in the genetic code tend to lead to small changes in the chemical nature of the amino acids -- are themselves the result of a long process of evolution that preceded the emergence of one dominant solution, the one that was the progenitor of all extant life. Similarly, mutation rates differ greatly in different organisms, being higher in simpler organisms with small genomes, HIV being near one extreme. In more complex organisms, these mutation rates are controlled by DNA repair enzymes, and the error rates are almost certainly fine-tuned by indirect selection pressure.

Using Avida to support biological evolution is about as scrupulous as using Haeckel's embryos or those damned horse diagrams.

Perhaps you can explain how the geno/pheno-type distinction represents selection pressures that cannot be properly emulated by an Evolutionary Algorithm? Or how the fitness function used by an Evolutionary Algorithm fundamentally differs from that which would have driven biological evolution (aside from the fact that the algorithm designers generally have a specific goal in mind, whereas unthinking nature would not)?

The next time an ignorant creationist insists that evolution can never produce anything complex, functional and useful, point him to the evidence of evolutionary algorithms.

By no means am I defending the "bedrock claims" of creationism you rebut, but in all fairness, what do you suggest we do the next time an ignorant atheist implies the conflation that EA's are analogous to biological evolution and can successfully account for the geno / pheno- type distinction?

Erigami's comments were also relevant.

Not sure what you mean by "junk DNA". If you are referring to mike's post where the Genetic Algorithm is developing a standalone computer program, it would seem possible to excise "junk DNA" (e.g. inaccessible/unexecuted code) by enforcing a selective pressure based on a minimum functionality you desire to be maintained as well as one on the overall code length. If your population size is large enough it's possible that such selective pressures will tend to weed out excess code without killing off the entire population. It's really just a matter of what selection pressures are exerted.

I don't think what you're pondering regarding EAs and NP-hard problems would be a meaningful distinction. I didn't get a PhD in Computational Complexity or anything, but NP-hard does not mean you cannot come up with a relatively efficient algorithm to approximate an answer. And that is really all you could get with an EA. You can find what seems to be very good local maxima, but that is not the same as "solving" the problem -- and being able to do so would still not necessarily tell you anything meaningful about Computational Complexity of the issue at hand.

Hey, I just like everyone to get along, all right?"

Don't make me post the code of the sith!

On topic, is there anyway to purge the junk dna that accumulates in the solutions?

Thanks for bringing this totally unknown material into my awareness. I am ever delighted with the scope of things you think about.

So we have evolved to a place where we use evolution as a tool, while there are yet those who deny evolution. How quaint (yet tragic)!

@Petrucio: Hmm, I wonder what the math involving EAs and NP-hard problems is like. Perhaps EAs could serve as a basis for defining a new class of computational complexity?