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Author Topic:   Evolution as an Algorithm
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 8 of 74 (345113)
08-30-2006 5:02 PM
Reply to: Message 1 by Woodsy
08-30-2006 7:48 AM


I am convinced
Hello Woodsy,
First of all, a welcome to EvC from me too.
To anybody else (Phat?) who reads this: I cannot recommend enough the book Woodsy mentioned. It's a wonderful read and in my opinion the best book about evolution by a non-biologist.
The idea of evolution as an algorithm is a very powerful tool in thinking about evolution. I have mentioned it often here on EvC that the principle mechanism of evolution has been demonstrated very convincingly in the form of evolutionary algorithms.
Being a programmer, I have tried it myself, and seen with my own eyes that the simple repeated application of random variation with selection does indeed result in evolution of whatever is being subjected to this procedure.
For me, what you suggest has been demonstrated. Having written an evolutionary algorithm myself, I know that I have accurately implemented random variation with selection. I have seen evolution to be the result. I am totally convinced.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 1 by Woodsy, posted 08-30-2006 7:48 AM Woodsy has not replied

Replies to this message:
 Message 9 by ramoss, posted 08-30-2006 5:24 PM Parasomnium has replied
 Message 10 by Hyroglyphx, posted 08-30-2006 5:48 PM Parasomnium has replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 11 of 74 (345132)
08-30-2006 5:58 PM
Reply to: Message 6 by Hyroglyphx
08-30-2006 3:39 PM


Re: Algorithms
nemesis_juggernaut writes:
models tend to be grossly oversimplified to the point that it cannot be cited as a proof in defense of the theory.
This is not at all true. The beauty of the mechanism of evolution is that it can be implemented quite accurately on a computer. There is no need to simplify, let alone oversimplify, the principle of random variation. If you have data in the memory of a computer and you write a subroutine that makes copies of those data while randomly changing parts of it, then you have implemented reproduction with random variation very exactly.
Next, if you make a function that determines the fitness of the data copies and filter out the less fit for the next round of reproduction, you have implemented selection very exactly.
That's all there is to it: implement reproduction with random variation, implement selection, and let it run for a while, i.e. let the procedure repeat itself for a significant number of generations, and you'll see the data evolve.
I must also stipulate that a built-in goal or direction of any kind does not figure anywhere in the programme. It is not necessary, evolution will take place regardless.
As well, computer simulations of an evolutionary process seem to imply that the development which is being measured over so many generations is independent of development of other structures which are necessary for basic function. This, of course, is what IC "Irreducible Complexity" is all about.
Evolutionary algorithms do not just imply this independence, they actually prove it. And thus they also falsify 'irreducible complexity'.
the changes observed from the simulation are dependent on the original data input which could clearly be construed as biased reserch or leading the research in the direction of the programer desires.
It could perhaps be so construed, but that doesn't mean it's true. The only way to find out is to do it yourself. Which is what I have done, and which is what you should do. I guarantee you that the experiment I have outlined above is repeatable. If you program it yourself you can be absolutely sure that your programme works the way you intended. (If you're a good programmer, that is.) And if you have faithfully implemented reproduction with random variation and selection, and nothing more than that, then I guarantee you that you'll see evolution happening before your very own eyes.
When the theory is still lacking evidential credibility, why abandon the field and the lab and grind out abstract theorems or abstruse computer simulations?
OK, don't trust other programmers. There can be nothing abstract about it, or abstruse, if you try it yourself.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 6 by Hyroglyphx, posted 08-30-2006 3:39 PM Hyroglyphx has not replied

Replies to this message:
 Message 56 by Ben!, posted 09-01-2006 3:27 AM Parasomnium has not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 12 of 74 (345138)
08-30-2006 6:07 PM
Reply to: Message 9 by ramoss
08-30-2006 5:24 PM


Re: I am convinced
ramoss writes:
You are also drawing upon the vast amounts of evidence from the real world for your conviction though.
Of course I am. I never suggested that I was convinced of the truth of evolution by the evidence of evolutionary algorithms alone. But they are a very convincing argument about the principle mechanism of evolution though.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 9 by ramoss, posted 08-30-2006 5:24 PM ramoss has not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 13 of 74 (345141)
08-30-2006 6:11 PM
Reply to: Message 10 by Hyroglyphx
08-30-2006 5:48 PM


Re: I am convinced
The way it makes it happen, there are no catastrophic variables that would throw these readings in a tizzy. But as we should all know quite well, nothing in life is free, and things don't organize themselves by chance innumerable times.
I'm sorry, I don't quite get what you mean by that first sentence. Could you please explain?
things don't organize themselves by chance innumerable times
You are making an oft repeated mistake: you leave out selection. Evolution is not just a jumble a random events. It's the non-random selection that produces the interesting results.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 10 by Hyroglyphx, posted 08-30-2006 5:48 PM Hyroglyphx has replied

Replies to this message:
 Message 15 by Hyroglyphx, posted 08-30-2006 6:28 PM Parasomnium has replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 16 of 74 (345180)
08-30-2006 7:01 PM
Reply to: Message 15 by Hyroglyphx
08-30-2006 6:28 PM


Re: I am convinced
What I meant to say is that I doubt variables, such as catastrophes are not introduced as possible scenarios that would effect the outcome.
That's still a bit confusing because you're saying that you doubt that variables are not introduced et cetera. This sort of double negation makes it hard to follow. Fortunately, your next sentence provides the answer, I think:
In other words, it makes the presumption that life just kinda organizes itself beneficially without assistance.
I'll proceed from the assumption that you doubt that variables are introduced.
And it's funny you should say that, because a catastrophy is what I had to introduce to overcome the problem of so-called 'local minima'. This is a technical term which means that sometimes an evolutionary path leads to a solution that cannot be improved upon other than by an enormous change at once.*
But evolution only proceeds by small changes. Since any small change to a local minimum will most likely diminish its fitness, it is therefore less likely to be selected for. Only a catastrophy once in a while will make sure that the gene pool is "cleaned up" as it were, wiping out successful and less successfull solutions alike.
So, in short, your doubt is unfounded.
How did you determine that I leave out selection. There is only so far the genes can drift in a population before you hit a brick wall. The fallacy is that the genome of any given organism is basically infinite in its variability. That's obviously not the case.
But you're forgetting that it's the genome that determines the organism, not vice versa. Yes, for a given organism, it's obviously true that its genome cannot be endlessly varied upon, or it would cease to be that given organism.
But in evolution, the organism is not a given, it is a result. A sequence of DNA can be endlessly changed, partly duplicated, or maltreated in many other ways. It's what you get when you express it where it gets interesting. Along the way of all the variations on an initial sequence of DNA, you get all kinds of interesting resulting organisms, a lot of which are totally unlike each other, as long as there has been enough variation along the way.
_____
* For example, the human eye could be hugely improved upon by moving the retina to the other side of the nerve layer (like in an octopus eye), thus doing away with the problem of the blind spot and improving vastly on the possibilities for seeing colour in near total darkness. But that improvement is far away in genomic space and any mutation in that direction is probably a short term liability. That's why, starting from a human eye, it's virtually impossible to evolve an octopus eye.
You could say that the human eye is located on a mountain top in the genomic landscape while the octopus eye is on another mountain top, with a vally in between the two. In genomic space you cannot jump from one summit to another one in a single leap, you have to travel in small steps. In this case, the first part of your journey would take you down the slopes of your own mountain, and in genomic space that means that you become less and less fit. So the chances that you'll make it to the other summit are virtually zero.
Edited by Parasomnium, : spelling and adding eye example
Edited by Parasomnium, : more spelling and other augmentations
Edited by Parasomnium, : extending the eye example with more explanation
Edited by Parasomnium, : correcting an omission

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 15 by Hyroglyphx, posted 08-30-2006 6:28 PM Hyroglyphx has replied

Replies to this message:
 Message 35 by Hyroglyphx, posted 08-31-2006 11:56 AM Parasomnium has replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 25 of 74 (345377)
08-31-2006 9:00 AM
Reply to: Message 23 by ThingsChange
08-31-2006 8:22 AM


Re: There is always an escape clause
ThingsChange writes:
Even if you could replicate data for the many variables (don't forget environment) over a time period and predict a new species that actually exists, you would run into the following argument:
1. That is one explanation, but not the only possibility.
2. Another possibility, as written in __religious document__ is that God/Allah/etc. created it.
Woodsy's point is, if I understand it correctly, that if: 1) you can devise an algorithm that implements reproduction with random variation and selection, and 2) said algorithm results in evolution, and 3) you can prove that in nature things reproduce with random variation under selection, then confidence in the theory of evolution is justified.
What he is not suggesting is that the algorithm in question should be an exact, extensive model of reality, complete with all manner of interaction and interconnectedness et cetera, in order to see if, in the model, evolution is what follows.
The algorithm would simply implement the basics of the mechanism. If evolution ensues, that would be reason for more confidence. Or so Woodsy wants to know. To which question my answer is a resounding "yes".
Edited by Parasomnium, : adding last sentence

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 23 by ThingsChange, posted 08-31-2006 8:22 AM ThingsChange has not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 27 of 74 (345382)
08-31-2006 9:27 AM
Reply to: Message 26 by nwr
08-31-2006 9:18 AM


Re: Not an algorithm
nwr writes:
It would be better to say "evolutionary process" instead of "evolutionary algorithm".
Maybe the people who originally coined the term "evolutionary algorithm" didn't have the strict definition of the word 'algorithm' in mind.

"Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

This message is a reply to:
 Message 26 by nwr, posted 08-31-2006 9:18 AM nwr has seen this message but not replied

  
Parasomnium
Member
Posts: 2224
Joined: 07-15-2003


Message 45 of 74 (345458)
08-31-2006 1:56 PM
Reply to: Message 35 by Hyroglyphx
08-31-2006 11:56 AM


Re: I am convinced
nemesis_juggernaut writes:
I'm glad you added that element, because history is full of catastrophe's that surely would effect numerous populations and how and when they would evolve, supposing that would at all.
I only included it to allow the whole evolutionary process to get out of local minima. Without the catastrophies evolution still took place.
But you're forgetting that it's the genome that determines the organism, not vice versa. Yes, for a given organism, it's obviously true that its genome cannot be endlessly varied upon, or it would cease to be that given organism.
Well, this a chicken-egg argument I suppose.
I don't think so. The phenotype of an organism is for a large part the result of its genotype. The reverse isn't true.
But you make the distinction for me that if organisms were so prone to variabilty, we would not have the populations that we do. In fact, if evolution were true why wouldn't we see so much more variabilty than we do?
What do you mean? Isn't the variability in nature enough for you? There are about 3.500 different species of mosquitos alone. Based on that fact, can you imagine the total number of different species in the whole of nature? I know I can't.
Besides, how do you propose to calculate how much variability evolution should yield?
  • A ”trait’ can only be quantitative so that any move towards the objective can be selected for. Many biological traits are qualitative”it either works or it does not, so there is no step-wise means of getting from no function to the function.
  • To see why this is not true, please ask the nearest person with glasses whether they prefer their myopic eyes over no eyes at all.
  • A single trait is selected for, whereas any living thing is multidimensional. A "GA" (Genetic Algorithm) will not work with three or four different objectives, or I dare say even just two. A GA does not test for survival; it tests for only a single trait. Even with the simplest bacteria, which are not at all simple, hundreds of traits have to be present for it to be viable (survive); selection has to operate on all traits that affect survival.
  • Nothing stops a programmer from developing a more complex fitness function, or a set of them, all of which a candidate for survival has to pass.
  • Something always survives to carry on the process. There is no rule in evolution that says that some organism(s) in the evolving population will remain viable no matter what mutations occur. In fact, the GAs that I have looked at artificially preserve the best of the previous generation and protect it from mutations or recombination in case nothing better is produced in the next iteration. This has a ratchet effect that ensures that the GA will generate the desired outcome”any move in the right direction is protected.
  • This is a property of the evolutionary algorithms that you've looked at, but in no way a property that all of them must have of necessity.
    (And this objection could be applied to your introduction of the catastrophe. I agree that such variables should exist simply because they surely exist in actual nature, however, one cannot introduce a catastrophe simply because their algorithm is no longer producing viable organisms any longer).
    As I've stated above, I only included catastrophies to allow the evolutionary process to get out of local minima. I did not include them to in order to better model reality. Again, without them, evolution took place all the same.
    # Perfect selection (selection coefficient, s = 1.0) is often applied so that in each generation only the best survives to ”reproduce’ to produce the next generation. In the real world, selection coefficients of 0.01 or less are considered realistic, in which case it would take many generations for an information-adding mutation to permeate through a population. Putting it another way, the cost of substitution is ignored.
    Again, evolutionary algorithms are a proof of concept, not an accurate model of the whole of nature. It is of no consequence that some aspects of evolution are a bit different in reality than they are in an evolutionary algorithm, or that they are absent in them altogether. What matters is that the principle still holds, you can see evolution happening, by just implementing the basics of it's mechanism.

    "Ignorance more frequently begets confidence than does knowledge: it is those who know little, not those who know much, who so positively assert that this or that problem will never be solved by science." - Charles Darwin.
    Did you know that most of the time your computer is doing nothing? What if you could make it do something really useful? Like helping scientists understand diseases? Your computer could even be instrumental in finding a cure for HIV/AIDS. Wouldn't that be something? If you agree, then join World Community Grid now and download a simple, free tool that lets you and your computer do your share in helping humanity. After all, you are part of it, so why not take part in it?

    This message is a reply to:
     Message 35 by Hyroglyphx, posted 08-31-2006 11:56 AM Hyroglyphx has not replied

      
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