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Author Topic:   Evolution as an Algorithm
Parasomnium
Member (Idle past 1106 days)
Posts: 2191
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 responded

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

  
Woodsy
Member (Idle past 1783 days)
Posts: 301
From: Burlington, Canada
Joined: 08-30-2006


Message 17 of 74 (345236)
08-30-2006 8:36 PM
Reply to: Message 14 by nwr
08-30-2006 6:19 PM


Re: Not an algorithm
nwr, thanks for your response. It would be pretty dull if everyone just said "of course". I would like to ask you to expand on a couple of your comments. I had looked at some definitions of algorithms and they seemed to me to fit; what might I have missed? Also, I don't see how evolution being an algorithm validates the "prescribed" hypothesis. I admit to having had only a brief look at that. Please fill me in.
I rather liked the book, although I found it a bit unfocussed and Dennett's constant posing of questions without much follow-up is irritating. I was quite struck with the algorithm idea and also the idea of a genomic space and paths in it.

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Woodsy
Member (Idle past 1783 days)
Posts: 301
From: Burlington, Canada
Joined: 08-30-2006


Message 18 of 74 (345239)
08-30-2006 8:46 PM
Reply to: Message 15 by Hyroglyphx
08-30-2006 6:28 PM


Re: I am convinced
Interesting posts. I would ask about two things. What is this "brick wall" that I see mentioned here and there. Also, I don't see why infinite (!!) variability should be needed. The chemistry would rule that out, if nothing else, but a good deal of variability might go a long way.

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nwr
Member
Posts: 5592
From: Geneva, Illinois
Joined: 08-08-2005


Message 19 of 74 (345250)
08-30-2006 9:29 PM
Reply to: Message 17 by Woodsy
08-30-2006 8:36 PM


Re: Not an algorithm
I would like to ask you to expand on a couple of your comments.

The technical definition of an algorithm is in terms of a Turing machine. You place the data on the TM tape. The TM operates, and the answer is what remains on the tape. If you are not familiar with the Turing machine, we can describe it in terms of a computer. You enter data at the keyboard. Then the algorithm operates on that data. Finally the result is displayed.

One significant point here is that an algorithm, by definition, is non-interactive. You may interact with the computer by providing data, but that's before the algorithm begins to operate. You may interact again, reading the answer, but that is after the algorithm has completed. There is no interaction during the algorithm.

Now consider the windows computer. You move your mouse just a little. The computer applies an algorithm and changes what appears on the screen. That's algorithmic, again with no interaction from the time the algorithm starts to the time that it completes (by updating the screen). So the windows computer uses algorithms. But if we look at it overall, then the computer is reacting to your mouse movements and updating the screen. But you watching the screen and your mouse movements are your reaction to what you see changing on the screen. This overall activity is highly interactive, with the computer reacting to you and you reacting to the computer. Since it is interactive, it is not algorithmic (even though it uses algorithms).

Biological systems are far more interactive than that. Evolution involves all sorts of interactions. So it, too, is not algorithmic.

For me, this mutual interaction is an essential part of evolution (and of a computer operating system). So it is not just a quibble that I claim it is not an algorithm.

Also, I don't see how evolution being an algorithm validates the "prescribed" hypothesis.

An algorithm is deterministic, so it leads directly to the kind of determinism that JAD assumes in his hypothesis. Interaction is not obviously deterministic, although it could admittedly be (as some argue) non-obviously deterministic. My point is that if you assume evolution is an algorithm, then you are pretty much assuming some sort of determinism.

Incidently, at least part of the arguement between Dawkins and Gould has to do with determinism. Dawkins is a biological determinist, and Gould takes the opposing view. All biologists will admit that both biology and environment play some role in behavior. But a biological determinist such as Dawkins tends to emphasize the biology and genetics, while Gould looks for other possible influence. For example, if there is a discussion about altruism, Dawkins will tend to seek an explanation in genetics, while Gould would have looked for an explanation in the choices of the individuals that have altruistic behavior.

I rather liked the book, although ...

Dennett is a pretty good writer. I do enjoy reading his work, even when I disagree with it. But, in the case of DDI, I was a bit turned off by his emphasis on biological determinism and his attack on Gould.

This message is a reply to:
 Message 17 by Woodsy, posted 08-30-2006 8:36 PM Woodsy has responded

Replies to this message:
 Message 20 by Wounded King, posted 08-31-2006 5:17 AM nwr has responded
 Message 21 by Woodsy, posted 08-31-2006 7:05 AM nwr has responded
 Message 22 by JavaMan, posted 08-31-2006 8:00 AM nwr has responded
 Message 24 by ThingsChange, posted 08-31-2006 8:31 AM nwr has responded

  
Wounded King
Member (Idle past 2504 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 20 of 74 (345354)
08-31-2006 5:17 AM
Reply to: Message 19 by nwr
08-30-2006 9:29 PM


Re: Not an algorithm
For me, this mutual interaction is an essential part of evolution (and of a computer operating system). So it is not just a quibble that I claim it is not an algorithm.

Is it perhaps cybernetic then given the importance of mutual interaction, i.e. feedback (Is there a gaian in the house?).

An algorithm is deterministic, so it leads directly to the kind of determinism that JAD assumes in his hypothesis.

Is this neccessarily the case? Aren't there algorithms which accept inputs from random sources? Why could an evolutionary algorithm not be a probabilistic Turing machine?

TTFN,

WK

Edited by Wounded King, : No reason given.


This message is a reply to:
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Woodsy
Member (Idle past 1783 days)
Posts: 301
From: Burlington, Canada
Joined: 08-30-2006


Message 21 of 74 (345363)
08-31-2006 7:05 AM
Reply to: Message 19 by nwr
08-30-2006 9:29 PM


Re: Not an algorithm
Very nice and clear. I wonder if we could look at evolution as a sort of nested algorithm? That is, repeated cycles of reproduction-with-variation-plus-selection, with the output of one cycle feeding the next and change in the selection rule from time to time. Would this provide the interaction you desire? That way the system could track whatever it is that is governing the selection rule.
It just struck me that one could, and in biological systems probably would, have more than one selection rule operating at the same time. There seems to be lots of room for complexity here, even if the mechanism is relatively simple.

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Replies to this message:
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JavaMan
Member (Idle past 728 days)
Posts: 475
From: York, England
Joined: 08-05-2005


Message 22 of 74 (345372)
08-31-2006 8:00 AM
Reply to: Message 19 by nwr
08-30-2006 9:29 PM


Re: Not an algorithm
An algorithm is deterministic

In what sense is Parasomnium's genetic algorithm deterministic?


'I can't even fit all my wife's clothes into a suitcase for travelling. So you want me to believe we're going to put all of the planets and stars and everything into a sandwich bag?' - q3psycho on the Big Bang

This message is a reply to:
 Message 19 by nwr, posted 08-30-2006 9:29 PM nwr has responded

Replies to this message:
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ThingsChange
Member (Idle past 4335 days)
Posts: 315
From: Houston, Tejas (Mexican Colony)
Joined: 02-04-2004


Message 23 of 74 (345374)
08-31-2006 8:22 AM
Reply to: Message 1 by Woodsy
08-30-2006 7:48 AM


There is always an escape clause
Woodsy writes:

If one can show that the description of the evolution algorithm is correct and if one can show that biological systems do exhibit reproduction with variation, and that selection operates, surely one should then expect evolution to occur. If these requirements are satisfied, is that sufficient for confidence in the ToE?

For some yes, and others, no.
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.

The algorithm approach is similar to what I would call a pattern. I see a pattern of change in all aspects of life, not just biology (that's why I picked "ThingsChange"). For example, the pattern applies to business, culture, and religion, too. Hence, that gives me sufficient confidence without having to write a computer program (which uses languages that have evolved).


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ThingsChange
Member (Idle past 4335 days)
Posts: 315
From: Houston, Tejas (Mexican Colony)
Joined: 02-04-2004


Message 24 of 74 (345375)
08-31-2006 8:31 AM
Reply to: Message 19 by nwr
08-30-2006 9:29 PM


Re: Not an algorithm
nwr writes:

One significant point here is that an algorithm, by definition, is non-interactive. You may interact with the computer by providing data, but that's before the algorithm begins to operate. You may interact again, reading the answer, but that is after the algorithm has completed. There is no interaction during the algorithm.


In the classic definition, you are correct, but that is getting muddy these days, especially with machines receiving input from sensors and even other independent devices. The military has some very sophisticated networked devices and sensors that each have algorithms that determine the reaction to interactive input from many concurrent sources.
My point is that there can still be a high-level algorithm governing many small ones, and this concept fits the biological model, too.

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 Message 19 by nwr, posted 08-30-2006 9:29 PM nwr has responded

Replies to this message:
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Parasomnium
Member (Idle past 1106 days)
Posts: 2191
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 yet responded

  
nwr
Member
Posts: 5592
From: Geneva, Illinois
Joined: 08-08-2005


Message 26 of 74 (345381)
08-31-2006 9:18 AM
Reply to: Message 20 by Wounded King
08-31-2006 5:17 AM


Re: Not an algorithm
Is it perhaps cybernetic then given the importance of mutual interaction, i.e. feedback (Is there a gaian in the house?).

"Cybernetic" fits much better than "algorithmic".

Aren't there algorithms which accept inputs from random sources?

Sure. But the input is not the algorithm. The term "algorithm" applies to the sequence of well defined steps applied to the input.

Why could an evolutionary algorithm not be a probabilistic Turing machine?

Once you add a random number generator, it is no longer a Turing machine. It would be better to say "evolutionary process" instead of "evolutionary algorithm".

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Replies to this message:
 Message 27 by Parasomnium, posted 08-31-2006 9:27 AM nwr has acknowledged this reply

  
Parasomnium
Member (Idle past 1106 days)
Posts: 2191
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 acknowledged this reply

  
nwr
Member
Posts: 5592
From: Geneva, Illinois
Joined: 08-08-2005


Message 28 of 74 (345383)
08-31-2006 9:30 AM
Reply to: Message 21 by Woodsy
08-31-2006 7:05 AM


Re: Not an algorithm
I wonder if we could look at evolution as a sort of nested algorithm? That is, repeated cycles of reproduction-with-variation-plus-selection, with the output of one cycle feeding the next and change in the selection rule from time to time.

Yes, that woud be a better description.

There is another point that I didn't mention in my earlier posts. An algorithm makes its decisions based on a predetermined standard. When we use an algorithm in a computer, we describe it as using logic, and we describe the decisions as being made on the basis of truth or falsity. Evolution, on the other hand, works with pragmatic judgement - does an organism survive.

To redescribe that, an algorithm is a logic process that makes decisions by applying a predetermined standard. Evolution is more of a measuring process that samples reality to see what works as its way of making decisions.


This message is a reply to:
 Message 21 by Woodsy, posted 08-31-2006 7:05 AM Woodsy has not yet responded

  
nwr
Member
Posts: 5592
From: Geneva, Illinois
Joined: 08-08-2005


Message 29 of 74 (345384)
08-31-2006 9:33 AM
Reply to: Message 22 by JavaMan
08-31-2006 8:00 AM


Re: Not an algorithm
In what sense is Parasomnium's genetic algorithm deterministic?

Does the term "genetic algorithm" apply to the individual steps taken, which are algorithmic and deterministic? Or does it apply to the overall process which uses random input, and is thus neither algorithmic nor deterministic (unless a deterministic pseudo-random number generator is used)?

This message is a reply to:
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nwr
Member
Posts: 5592
From: Geneva, Illinois
Joined: 08-08-2005


Message 30 of 74 (345386)
08-31-2006 9:38 AM
Reply to: Message 24 by ThingsChange
08-31-2006 8:31 AM


Re: Not an algorithm
In the classic definition, you are correct, but that is getting muddy these days, especially with machines receiving input from sensors and even other independent devices.

The "receiving input from sensors" is not part of the algorithm. Rather, the algorithm is in the application of rule based procedures to the input that has been received.

This message is a reply to:
 Message 24 by ThingsChange, posted 08-31-2006 8:31 AM ThingsChange has not yet responded

  
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