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Cubist



Posts: 514
Joined: Oct. 2007

(Permalink) Posted: Jan. 16 2015,18:57   

Quote (Doc Bill @ Jan. 16 2015,10:55)
Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

 
Quote
I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,19:14   

yeah I thought this would happen ... too many people with different points to address, and not enough time.
(and you guys accuse creationists of Gish Gallop)

Let me address some key ones ....
RE: living cell IS a Turing machine, therefore is computer
Quote

Prove it.  Don't assert it, prove it.
You can't because there simply are no significant respects in which it is true.
The entire realms of thermodynamic effects and of self-assembly, with constrained errors, and self-repair, with constrained errors, simply have no equivalent in computers.  At all.


Thermodynamic effects, self-assembly and self-repair are all things that a digital computer can do. We use thermodynamic effects in random noise generators, we can build computers using robots that are run by the same computers. Self-repair of the operating system, programs and data is one of the most common things implemented by computer hardware and software.
What do you mean by constrained errors?
So no ... why is it important to you to contradict this simple definition of how DNA in a cell works?

Here is the definition of a turing machine
Turing machine formal definition
The way DNA is processed in a living cell satisfies this definition as agreed with by the evolutionary biologist in the Nature Journal entry I linked to earlier.

Here is the definition of a computer
"A computer is a general purpose device that can be programmed to carry out a set of arithmetic or logical operations automatically. Since a sequence of operations can be readily changed, the computer can solve more than one kind of problem."

DNA as it is transcribed and translated satisfies this definition. We know for example that DNA is functionally non-linear and controls the expression of other parts of the DNA (eg HOX genes and other regulator genes) ... these are complex flow and boolean logic operations. The expression of multiple reading frames (6 we know of ... and potentially others in 3 dimensional space when DNA is folded) in DNA is an example of complex logical operations, which is controlled by boolean logic.

A computer is a Turing machine and vice versa.
DNA is a functional code ... it is processed as a code in the living cell, the functions in the code are used to efficiently describe how to build highly complex structures and to be able to replicate and differentiate its function as it progresses. This is more complicated, robust and versatile than any computer we've ever built or could probably conceive of building.
So my point is DNA is a code that runs in the computer of the living cell, it is more complex than any computer we know .... so how can corruption (mutation) to the operating system code and the program code result in better function? This contradicts our experience, and I claim has still not been demonstrated to happen.

Quote
I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.


Haha amazing ... how did he get removed from the gene pool? A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard ... He gets removed from the "Gene pool" (population) by dying ... he dies before reproducing (for whatever reason), so his genes aren't passed on. Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.
You're picking a fight over something we agree on here. I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition. Yes it IS competition, but only competition that results in something dying and other things not. Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)


Quote
in detail why AVIDA does not do what the writers of the software say it does

No detail needed ... it's simple. AVIDA defines the entity by prescribing a set of 26 functions that can be randomly selected in random combinations. Then evaluation functions are used to test how fit an organism is. Both these things are inaccurate and create a trivial subset of the proposed evolution theory. As I explained before, selected from existing functions is not the same as mutating the code that defines those functions. Biological function is determined on the protein level, proteins are equivalent to AVIDA's 26 functions, and a complex combination of proteins to create higher level function in an organism is equivalent to the combination of functions that AVIDA is "mutating" between. i.e. AVIDA is shuffling protein orders to get different high level functions, and only using 26 proteins. This is NOT the same as mutating the code that defines how the proteins are built .... the equivalence of this in AVIDA would be mutating the code that defines the 26 functions. This is a VERY different problem ... no-one has done that ... mainly because they know it will result in junk.
The problem of trying 26 functions in different combinations to optimise a specific trait is NOT the same as what you are proposing happens in biological evolution.

Quote
Can you say 'begging the question'?  You appear to be arguing that cells/organisms are programmed by asserting as one of your premises that cells/organisms are programmed.

No, not begging the question, I'm merely pointing out that Lenski's results don't show anything either way ... you can claim it's evolution, but I can claim that what he observes is part of its original programming, as the bacteria is still E. Coli ... it may have adapted and changed to resist death, because we know that is part of the inherent functionality of bacteria, they swap genetic code with other bacteria. Like a computer virus, the code is mostly concerned with reproduction and not any complex functionality. We embed all sorts of randomisation algorithms into computer viruses to make them harder to identify by the host and harder to stop ... this is engineered resistance. I'm claiming that all the research so far does not contradict that explanation. And in fact, if anything the experiment has proved that nothing has changed in millions of years of evolution. If evolution is so easy and happens everywhere to every organism world-wide to some degree, why are they still E. Coli and not Bananas or Dolphins or Pygmy Elephants? (that one's for Kevin)
This is why I ask for a simple model, that models the core features of the proposed theory of evolution. So far no-one has shown me one.
If you have a biological experiment showing one kind of animal naturally changing into another or developing completely new complex features then show me .... but so far all I've seen from experiments is no different to dog breeding and showing that a Poodle looks wildly different to a Great Dane or a Finch has a bigger beak. This is not evolution, this is artificially breeding out features and standard Mendelian genetics, and certainly isn't anything to do with mutations.

I'm a mathematician and programmer, last time I looked at the laws of logic you can't get information without a sender, matter does not contain the properties of information in itself, as information is outside of matter, it is the arrangement of matter that is information ... so if you're contesting that information can come out of matter by itself simply because of the environment it's in I want you to show me algorithmically how this is possible. Hence the request for a model.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 16 2015,19:19   

Quote (Cubist @ Jan. 16 2015,18:57)
Quote (Doc Bill @ Jan. 16 2015,10:55)
Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

   
Quote
I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.

Is that text an actual quote from cryptoguru, or is it a concise summary of cryptoguru's ideas which doesn't actually use their specific phrasing? I ask because I tried googling that quote, and I couldn't find a source.

It's over at Smilodon's Retreat under the "DNA is not like a computer" thread.  Near the bottom of about 4 pages of comments.

Yeah, it's a direct quote.  Think Quest/FL/JoeG/a mule/two thick planks/bag of doorknobs - and you'll get the general sense of this guy.

Back to my popcorn!

  
QED



Posts: 41
Joined: July 2008

(Permalink) Posted: Jan. 16 2015,19:30   

In that case, I'm guessing it's not a Gaulin clone at all.

I'm betting on the pidgeon/chess gambit: "wah wah wah - you're being mean to me, so jesus doesn't love you and besides you're wrong - I'm outta here..."

  
Wesley R. Elsberry



Posts: 4935
Joined: May 2002

(Permalink) Posted: Jan. 16 2015,19:34   

Cryptoguru:

   
Quote

Evolution is:
1) take an organism and let it replicate
2) random mutations should be introduced to the offspring DNA.
3) a selective pressure is applied to the environment the organisms live in
4) less fit organisms will die before replicating due to the pressure
5) most fit organisms will continue to replicate and mutate
6) eventually new functions and traits will emerge

Biological Evolution is presented as a scientific law, it is simple to define, so should be simple to model

My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

caveats:
- Mutation can't simply combine functions in different arrangements. Mutation must occur on the code that defines the functions themselves, and affect the ability of the organism to build itself, to function and to replicate.
- the selective process can't include measuring properties of the organism to remove them from the population, the selective process must rely on organisms dying off due to the environmental factors. (e.g. energy)



Avida does everything specified there except "model this process", given that Avida's model doesn't include misconceptions.

It is certainly possible to find points of disanalogy between Avida and biological evolution, since Avida's purpose is to establish a "computational chemistry" rather than to be an exact simulation of biological evolution via DNA. However, none of those points of disanalogy appear to have any bearing on the specific "challenge" quoted above. So any dismissals of Avida on grounds other than those stated in the "challenge" above are irrelevant. And, looking back at the discussion on OgreMkV's blog, I'm not seeing any accurate objection made concerning Avida that falls within the parameters of the "challenge".

One such invalid response is the one that equivocates about "functions". In Avida, the functions that can possibly accrue merit are logic operations, none of which are themselves singular codes in an Avidian's genome. Referring to those codes as "functions" in the sense of the quoted "challenge" is a mistake.

It's easy enough to modify "challenges" to be unfulfilled on some point or another. The point isn't to satisfy those with unreasonable doubt; it is to satisfy those who don't have inflexible precommitments.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 16 2015,19:45   

Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.


Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote
Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

  
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,20:08   

Quote (cryptoguru @ Jan. 16 2015,19:14)
Quote
I'd like to add that natural selection is not always a death.

It can be an effective removal of the gene pool. For example, the strongest, fittest, most efficient lion ever born might have a problem reproducing. Which means that he is removed from the gene pool. He can't pass his genes on to the next generation, so he's out of contention.


Haha amazing ... how did he get removed from the gene pool?

[/QUOTE]Wrong. Because he couldn't reproduce.

This is an example of you having a basic misunderstanding and I'm trying to correct it.

An organism that cannot reproduce, no matter how fit it is in every other particular cannot pass his genes on. He could live for decades longer (some research seems to indicate that being a eunuch means a male could add 25% to his lifespan... at the cost of not passing those genes on).

It doesn't have to be dead. It usually is, but it doesn't have to be. [/QUOTE]

A Gene pool isn't actually like a swimming pool you know, genes don't get thrown out for breaking the rules by the life-guard

[/quote]
Yes, you are correct, I should say, "the breeding population". I'm sorry, I will no longer use analogies in conversation with you.

Quote

... He gets removed from the "Gene pool" (population) by dying ...
he dies before reproducing (for whatever reason), so his genes aren't passed on.

And yet, I just gave you an example of a method, by which an individual could NOT ever contribute their genetics into the population and yet, still be alive.

What you are saying here, is that every woman who has a hysterectomy has died. Every male that has his tubes tied has died. Every cat and dog that's been neutered or spayed has died.

This is trivially wrong.

Quote

Natural Selection is not looking at his Genes and saying "hey this guy isn't fit enough ... throw him out" ... Natural Selection is just a name given to the fact we have lions that are still reproducing, and that lion isn't because he was less fit so simply dies.


No, selection is a process by which the organism is tested against the environment (including other organisms). Those are more fit TEND to reproduce more and those that are less fit TEND to reproduce less.

Again, less fit doesn't imply death. Indeed, you apparently have not read the AVIDA paper (or the part I quoted for you) showing that not only do less fit organisms sometimes reproduce. Those less fit organisms sometimes end up being the most fit.

This has been done with actual biological entities as well. Darwinian Evolution on a Chip by G. Joyce. Same thing as AVIDA. Some mutations resulted in lowered fitness, but they still reproduced and resulted in organisms with much greater fitness.

A simplistic view of life that is wrong.

Quote

You're picking a fight over something we agree on here.


No, because I don't agree with you. Scientists don't agree with you. Reality doesn't agree with you. Lab experiments don't agree with you. Observations of population genetics doesn't agree with you.

Quote

I'm demystifying the explanation of how Natural Selection works, it is death ... it is not just general competition.


No it's not. No matter how many times you say it, doesn't make it true.

Quote

Yes it IS competition, but only competition that results in something dying and other things not.


WHAT is competition? Competition for resources can often result in death. Competition for mates rarely does. But there are numerous cases of less fit organisms that discover a few tricks and reproduce anyway.

Quote

Remember "Natural Selection is a Blind, Mindless and Unguided Watchmaker" (Dawkins)

I love when you guys take Dawkins out of context. It's so telling. Tell me crypto, which book is that from? What page?

What does "unguided" mean to you? That's a critical definition.

For example, to most creationists (well, all that I have met so far), unguided means "random". While "guided" means shaped by an intelligence.

That's a false dichotomy. Guided doesn't mean an intelligence was involved. Fractals are guided by their equations. There are limits to them, but no intelligence has decided and enforced those limits.

When Dawkins speaks of unguided, he means that there is no purpose to life. No guiding hand. The only concern of this generation is to live long enough to reproduce. What happens before or after is not important to them.

The surviving offspring are in the same boat. None of them prepares for the future. None of them think, "Well, it's getting colder, we better let all the long furred ones mate." And yes, this have driven species to extinction... and will again.

I know you creationists don't like this because you feel that God is your guiding hand and things happen because they should. This tends to happen a lot with creationist engineers, programmers, and mathematicians.

I would encourage you to stop that thinking. It's not correct.

Why don't we ask Wesley, he was at a talk given by Dawkins about this? here's a link to his report of the talk. http://pandasthumb.org/archive....-2.html

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
OgreMkV



Posts: 3668
Joined: Oct. 2009

(Permalink) Posted: Jan. 16 2015,20:09   

Quote (cryptoguru @ Jan. 16 2015,19:45)
Quote

Greetings, NotGuru, we meet again!

Perhaps a full disclosure of your real purpose is in order.  I present to you NotGuru's Agenda:

Quote

I paint evolution (non-science) as faith ... because it is.
It's an absurd unsupported set of stories, based on the premise that there is no possibility of non-material causation. It satisfies a huge amount of self-centred god-haters, who've wanted nothing more than a decent excuse to pretend that there are no eternal consequences for their actions.

You still don't address any of the gaping black holes that I've pointed out.


I'm thinking this one is a Gary Gaulin clone, but super tard charged.  If you don't mind I'll duck out and get some popcorn.


Oh it's that angry Bilbo baggins character who just swears and says I know nothing ... and here he is quoting me out of context.

it was in response to this post from Bilbo, probably one of his least offensive ones

Quote
Typical useless god bot. Argument from incredulity. Has to paint science as a faith because of a narrow, restricted, dogmatic worldview. Forest full of straw men, drenched in tard and burning with the fire of the willfully ignorant. Sucks to be you, NotGuru. Enjoy howling in the darkness.


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

The problem is that you can't discuss science because your view of it so biased by your religion.

You're so obsessed with the way it should be, that you can't see the way it actually is.

--------------
Ignored by those who can't provide evidence for their claims.

http://skepticink.com/smilodo....retreat

   
midwifetoad



Posts: 4003
Joined: Mar. 2008

(Permalink) Posted: Jan. 16 2015,21:14   

All the verbiage about information is fascinating,  but why not cut to the chase? What specific physical phenomenon described by Darwin or his successors cannot happen? What specific point in the chain of descent is unreachable via the process described by Lenski, Thornton,  et al?

--------------
Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Acartia_Bogart



Posts: 1975
Joined: Sep. 2014

(Permalink) Posted: Jan. 16 2015,23:38   

Quote


I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.


If by "so popular" you mean a minority opinion in the US, then I guess it is popular.

What you are referring to is its general acceptance by scientists, the people who have actually conducted research on this. As opposed to religious fanatics who approach the subject with their "minds" already made up.

  
Cubist



Posts: 514
Joined: Oct. 2007

(Permalink) Posted: Jan. 17 2015,01:08   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

Yes, this is a verbatim re-post. Perhaps cryptoguru will deign to respond to it this time. Perhaps they won't. We shall see.

  
Quack



Posts: 1961
Joined: May 2007

(Permalink) Posted: Jan. 17 2015,05:14   

Maybe I am an oddball; Everywhere I look I observe objects and may extract information from them. The info just sits there ready for detection and observation without any external or supernatural operator having put it there. It sticks to the object like some red dye in a glass of water.

--------------
Rocks have no biology.
              Robert Byers.

  
JonF



Posts: 633
Joined: Feb. 2005

(Permalink) Posted: Jan. 17 2015,07:04   

Quote (cryptoguru @ Jan. 16 2015,11:06)

JonF: "adding information" - new and novel functions that didn't exist before that solve a problem that wasn't solved previously.

Such as evolving EQU in Avida or evolving the ability to digest citrate in Lenski's experiments?  Why are those not new and novel?

  
NoName



Posts: 2721
Joined: Mar. 2013

(Permalink) Posted: Jan. 17 2015,09:50   

Quote (cryptoguru @ Jan. 16 2015,20:45)
...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your  beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise.  As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God.  Generally, ideas as such are neither hated nor adored.  But more importantly, the idea of God is one that may or may not be true.  The nature of said God is asserted to be all sorts of things, all over the map.  We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'?  Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow.  I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly:  what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution?  Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena?  Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith.  How is that justified?
Show your work.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Jan. 17 2015,12:32   

Quote (cryptoguru @ Jan. 16 2015,19:14)
No, not begging the question, I'm merely pointing out that Lenski's results don't show anything either way ... you can claim it's evolution, but I can claim that what he observes is part of its original programming, as the bacteria is still E. Coli ... it may have adapted and changed to resist death, because we know that is part of the inherent functionality of bacteria, they swap genetic code with other bacteria. Like a computer virus, the code is mostly concerned with reproduction and not any complex functionality. We embed all sorts of randomisation algorithms into computer viruses to make them harder to identify by the host and harder to stop ... this is engineered resistance. I'm claiming that all the research so far does not contradict that explanation. And in fact, if anything the experiment has proved that nothing has changed in millions of years of evolution. If evolution is so easy and happens everywhere to every organism world-wide to some degree, why are they still E. Coli and not Bananas or Dolphins or Pygmy Elephants? (that one's for Kevin)
This is why I ask for a simple model, that models the core features of the proposed theory of evolution.

Actually, what you asked for was this:
 
Quote
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome.

You didn't ask for a model that shows E. coli turning into bananas or dolphins. You asked for a model that shows new functions and information being added, and you've been given multiple examples. If what you really want is a model that turns E. coli into bananas, then you're right. We're not currently capable of modeling evolution on that scale. But as others have pointed out, not being able to model something on a computer is not strong evidence that it doesn't happen.

Also, I'm curious. Were you just being mocking, or do you really understand so little about evolution that you think it means bacteria should turn into bananas (or any complex multicellular organism) over a few decades? Because if it's the former, then it suggests you're not interested in honest discussion. And if it's the latter, then your understanding of evolution is so poor that rational discussion is probably impossible. Of course, the two aren't mutually exclusive.

But hey, it's possible that I'm wrong on both counts. I'm a scientist; I believe in empirical evidence. So show me some evidence that you understand what evolution actually claims, and that you're willing to discuss the validity of those claims honestly.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 17 2015,15:11   

Re. faith:

DocBilbo has tried to smuggle in a discussion from another board, which I didn't want to even have there about faith. That is not the point of this subject thread and is an attempt to derail the discussion so it gets into an endless circle of atheists claiming creation-based belief is not science.
Let's leave this subject as it is really a philosophical argument and not something I'm wanting to get sidetracked with here.

Re. experiments:

the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ... creationists agree that variation within a kind is happening (e.g. viruses mutate, Finches change beak sizes etc) this is not proof of evolution. This can just as easily be explained as the normal function of the genome to vary. Epigenomic function allows for much variety within an organism on top of variation that already exists in DNA, where entire modules of DNA are regulated and switched on and off by other genes. This is not evolution ... it can happen in one generation, it is not as a result of mutation. So my point here is that these experiments do not demonstrate new features and traits being introduced to the genome, they can be explained as existing information and code being expressed in new ways that is controlled in how the genome responds to input from the environment. This is widely accepted ... hormone responses can switch on silenced genes and vice versa, allowing an organism to adapt to its environment.

Quote
do you really understand so little about evolution that you think it means bacteria should turn into bananas (or any complex multicellular organism) over a few decades?

Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time"  ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations. So evolution doesn't need time, it just needs lots of generations, which is what the E. Coli experiment has performed. Forgive me for being sceptical, but I'd expect more from 1 million years' worth of evolution than a change in metabolism, which could be attributed to the regulation of existing genes ... Behe explains this here Lenski article

SO ... this is why I'm asking for proof of the algorithm of evolution. Why is everyone being so sketchy about this? The evolutionary algorithm is simple ... randomly mutate the core code at the resolution of letters (not functions). Enforce selection by allowing organisms to compete for resources and allow them to die under natural conditions. AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising. It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?

  
midwifetoad



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(Permalink) Posted: Jan. 17 2015,15:13   

Quote
the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred


Surely you are not that stupid.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
rossum



Posts: 246
Joined: Dec. 2008

(Permalink) Posted: Jan. 17 2015,15:26   

Quote (cryptoguru @ Jan. 17 2015,15:11)
the point I'm making about experiments (e.g. Lenski's) is that all they have shown is that variation within a kind has occurred ...

Everyone agrees.  It is just that we disagree about where the boundaries between the different kinds lie.  For biologists, all evolution occurs within the "Life on Earth" kind.

If you think that Dr. Lenski's experiments show only evolution within the "Eubacteria kind", then we are already in reasonably close agreement.  That implies that you also accept evolution within the "Eukaryote kind", since Eubacteria and Eukaryotes are at the same level of classification.

If you want to split things below that level, then you are going to have to list the different kind boundaries, and show how you arrived at those particular boundaries.

rossum

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The ultimate truth is that there is no ultimate truth.

  
midwifetoad



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(Permalink) Posted: Jan. 17 2015,16:04   

That's not all the Lenski experiment shows.

The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

That is precisely what Behe said couldn't happen. And it is precisely what is necessary to move beyond local maxima.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
cryptoguru



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(Permalink) Posted: Jan. 17 2015,18:28   

Quote
Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?


Quote
If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote
The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

  
Cubist



Posts: 514
Joined: Oct. 2007

(Permalink) Posted: Jan. 17 2015,18:28   

Quote (cryptoguru @ Jan. 16 2015,09:09)
My challenge is this.
Show me a computer model that models this process and shows new functions and information being added to the genome. [emphasis added]

Whether or not you, yourself, are a Creationist, cryptoguru, this challenge of yours is (whether you realize it or not) the hoary old mutations can't create new information argument beloved of Creationists, just dressed up in computer terminology. So please, tell us if you will: What does "new information" look like? Given an arbitrary string of nucleotides, and a mutation which alters that string of nucleotides, how can you tell whether or not the post-mutation version of that string contains any "new" information?

cryptoguru did not respond to this the first two times I posted it; perhaps they merely overlooked it in the rush of responses. Maybe they'll notice it (and respond to it) if the text is larger?

  
midwifetoad



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Joined: Mar. 2008

(Permalink) Posted: Jan. 17 2015,20:13   

Will microbes may not be a good example for creationists to use,  but microbes account for the entirety of life for 6/7 of the time during which life existed. And microbes are still the dominant life form,  by any measure.

Nearly all genes were invented by microbial evolution. So stop posting shit. If you assert that mutation is not random with respect to selection, prove it.

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Any version of ID consistent with all the evidence is indistinguishable from evolution.

  
Wesley R. Elsberry



Posts: 4935
Joined: May 2002

(Permalink) Posted: Jan. 17 2015,20:17   

Cryptoguru:

   
Quote

AVIDA does NOT mutate on the nucleotide level, it mutates on the functional level, which is the same as choosing randomly from 26 functions and optimising.


That's still the erroneous equivocation that was already pointed out to be a mistake on Cryptoguru's part. None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome. The functions that accrue merit are built out of multiple codes in the genome, just as specified in Cryptoguru's "challenge" near the start of the thread.

 
Quote

It also calculates selection on a feature level, measuring properties ... that is NOT natural selection. This is what their paper says it does. Has anyone read AVIDA's paper here?


I'm not sure what the word salad above is supposed to convey other than dismissal. What's a "feature level" and "measuring properties"? If that's supposed to mean that Avida recognizes genomic patterns and rewards those, nothing could be further from the truth. It is the outcome of functional behavior that is the trigger for assigning merit to an Avidian.

But, yes, not only have I read that paper, I've also contributed to the Avida code base.

Lenski et al. 2003:

   
Quote

As in nature, selection in Avida depends on the phenotypic effects of a mutation in its genetic context and in relation to the organism’s environment; the researcher does not specify a distribution of selection coefficients.


This indicates that what Avida is doing is analogous to what occurs in natural selection. I think Cryptoguru needs more than cryptic dismissal to make his case.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
Wesley R. Elsberry



Posts: 4935
Joined: May 2002

(Permalink) Posted: Jan. 17 2015,20:35   

Not understanding how Avida works is seen in other antievolutionary argumentation, too.

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"You can't teach an old dogma new tricks." - Dorothy Parker

    
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 17 2015,21:34   

Quote (NoName @ Jan. 17 2015,07:50)
Quote (cryptoguru @ Jan. 16 2015,20:45)
...
I was trying to contest in the context of many faith-related insults that in my opinion evolution is not science, evolution is a belief and based on the religion of atheism ... and the reason it's so popular is that people hate the idea of God, mainly because they hate the idea of eternal consequences. So I don't see it as science vs religion ... I see it as religion vs religion and science vs science.
I didn't want to get into a faith discussion there and I'm not after one now ... I want to discuss the science.
This was me reacting, which I wish I hadn't ... in fact I should never have engaged with Bilbo at all.

On the one hand you put it all down to faith versus faith, or faith versus science, and on the other you insist you "didn't want to get into a faith discussion."
You really can't have it both ways.

You are entitled to your opinions, as opinions, even when they are loony [I'm not (yet) saying any particular one(s) of your  beliefs is/are loony].
But if you want to argue from a position that evolution is faith, not science, that it is based on a hatred for the idea of God, you have to establish the truth and accuracy of that premise.  As a presupposition, it is ludicrous and unsupportable, not least because so very many of the founders and developers of evolutionary theory were and are deeply religious.
To say nothing of how totally insane it is to assert that people hate 'the idea of' God.  Generally, ideas as such are neither hated nor adored.  But more importantly, the idea of God is one that may or may not be true.  The nature of said God is asserted to be all sorts of things, all over the map.  We know nothing useful about the nature of any particular deity, and before we can make recourse to the referent of the idea of God, we need to know in some detail and with some considerable precision [can you say 'operational definition'?  Do you know what it means?] what the nature and character of the referent actually is.
Otherwise the term is a magic word, swung about to fulfill any current rhetorical needs, which it can do solely because it is an idea unburdened with content.

Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails.

I'll get back to your lengthy, but largely pointless and obfuscatory response to portions of my earlier post later in the day or early tomorrow.  I actually lack the time to do the fishing it so richly deserves.

The core challenge to you has already been raised, repeatedly:  what facts on the table, specifically the known laws of chemistry, physics, and thermodynamics are alleged to be violated by evolution?  Where has it been shown that the laws of chemistry, physics, and thermodynamics do not suffice to explain biological phenomena?  Which phenomena, and how was it proven that they are not susceptible to natural explanations via chemistry, physics, and thermodynamics?

You find evolutionary theory distasteful, for reasons having nothing at all to do with science, so you attempt to shift out of the realm of science into faith.  How is that justified?
Show your work.

"Evolution is science because it fits all the criteria of science.  It is based on demonstrable facts, it makes predictions which can be falsified, it's theoretical structure is logically sound and provides a framework within which a broad variety of objective facts can be placed.  It has explanatory and predictive power, it has meaningful operational definitions for its key terms and concepts.  It suggests fruitful lines of inquiry and it has withstood the most concerted, and occasionally devious, attacks a host of small-minded ignoramuses, as well as highly intelligent knowledgable individuals have brought to bear.
It is not faith because it is susceptible to revision based on new insights and new facts, it operates in a consistent fashion such that it makes predictions which as a general rule turn out, and is capable of revision in light of those cases where the prediction fails."

No, evolution is none of those things. Evolutionary theory is.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 17 2015,22:17   

Quote (cryptoguru @ Jan. 17 2015,16:28)
Quote
Surely you are not that stupid.

Yes, I AM that stupid :-)
I'm making the point that nothing in the Lenski experiment proves evolution, it can just as easily be explained as programmed behaviour. Considering we're discovering more and more deterministic complexity in the genome, it is more than reasonable to assume that all the variation we see is specified complexity that already exists within the genome, and is not the result of random mutation. This has NOT been contradicted by any experiment yet, it is simply being asserted.

Therefore I again ask why there is no workable computer model of the theory of evolution in the form in which it is supposed to occur in the wild?


Quote
If you want to split things below that level, then you are going to have to list the different kind boundaries

Rossum, I'm saying that the variation we see can be explained by deterministic behaviour in the genome and need not be explained by "mutation". A control gene that regulates another gene dependent on an environmental input may make it look like something is evolving, but that function could already exist in the genome.
In fact the more layers of complexity and non-linearity we observe in the genome and how it is processed makes it more difficult to explain how a mutation could ever be understood to be advantageous; with multiple reading frames a mutation to a nucleotide could be imagined to have a positive effect somehow on the expression of a protein, but what about the other types of protein that get expressed from the same code? They're now broken.

This is a multi-layered code, I have previously worked in Cryptography and compression algorithms for many years. The genome implements compression to represent data in an efficient way. Corrupting even one bit of compressed data usually has an effect on multiple parts of the data ... if that data is a program, you can expect the program to crash if enough bits are corrupted.

This makes sense for the genome too (and is observed through genetic diseases) ... that along with the fact that Lenski's experiments fails to show evolution from one kind of an organism (bacteria) to a different, more complex organism despite an equivalent of 1 Million human years of evolution suggests this process doesn't work; except that everyone is the field is saying it works. I'm a sceptic, I want to see actual scientific proof that doesn't just gloss over the facts and pretend that mutation could be the only reason for an increase in cell size or a change in metabolism.

A working and accurate computer model still wouldn't prove evolution is happening in the wild, but it at least would show that it is theoretically viable. Currently I don't see how it is even theoretically possible, from an algorithmic perspective.

Quote
The Lenski experiment shows that mutations that reduce reproductive success can survive in a population long enough to enable further mutations that leapfrog function for a given environment.

Bacteria is also a bad example because it seems to deliberately use fuzzy logic and implement randomness in its genome as part of the programming ... so although a change may look random, it may be deterministic in function.
This is exactly how we program computer viruses. We expect them to evolve in a deliberate way.
So I do think there is some application for evolution as a concept in the modelling of bacteria and viruses, but their function is still deterministic and constrained by the master code, they may reprogram themselves (and transfer/shuffle genes with other bacteria) for versatility, but they can never vary to become a frog. In the case of viruses and bacteria I expect randomness is being used like we use pseudo-random noise generators in computers. We generate random variables and use them in our code ... we are NOT varying the functional part of the code itself randomly.

I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them.

"I think therefore it is misleading to look at what happens in bacteria and extrapolate it to other organisms, when we don't see the same processes happening in them."

Since that's how you feel, you might want to reconsider making statements like this:

"Lenski's experiment has achieved 60,000 generations in April 2014.
You need to understand, the proposed theory of evolution is not about "time"  ... it is about how many generations. Lenski's E. Coli has run for the equivalent of 1 million years of human generations."

Bacteria are not "equivalent" to humans.

I'm looking forward to your response to Cubist.

--------------
Think not that I am come to send peace on earth: I came not to send peace, but a sword. - Jesus in Matthew 10:34

But those mine enemies, which would not that I should reign over them, bring hither, and slay them before me. -Jesus in Luke 19:27

   
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,03:46   

Quote
What does "new information" look like?


New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.



Quote
Nearly all genes were invented by microbial evolution.

begging the question! Demonstrate the process ... don't simply assert it happens.



Quote
Bacteria are not "equivalent" to humans.

Straw-man argument ... I never said they were, I was equivocating the process of evolution in both organisms. Bacteria can "evolve" quicker because their generation time is MUCH shorter (hence why Lenski chose E. Coli). So I can compare 26 years of E. Coli to 1 Million years of human evolution ... they are exactly the same amount of the same process. We would expect to see novel traits emerge in humans over 1 million years and be able to identify new genes that didn't exists previously that code for that new trait. We don't see this in Lenski's experiment.

Quote
None of the logic functions that obtain merit in Avida are due to singular codes in an Avidian's genome

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.
AVIDA is a very interesting modelling algorithm, great for solving some real-world competition problems. It does NOT model biological evolution.
I have clarified this point countless times, I don't see how I can simplify it any more for people to understand here.

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.
AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.

These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).

  
rossum



Posts: 246
Joined: Dec. 2008

(Permalink) Posted: Jan. 18 2015,04:10   

Quote (cryptoguru @ Jan. 18 2015,03:46)
New information is new and novel genetic material that codes for new function or traits in the organism i.e. not a point mutation in a control gene that switches other pre-existing functionality off/on or a trade/inheriting of genetic material between bacteria ...NEW genetic material that codes for new function; this has never been observed.

Yes it has.  Lenski's long term experiment showed bacteria developing a new function, the ability to digest citrate.  That function was not there previously, and that new function evolved during the experiment.

I can also point to the example of the  from Japan, "Nylon digesting bacteria" which happened naturally.

--------------
The ultimate truth is that there is no ultimate truth.

  
Soapy Sam



Posts: 659
Joined: Jan. 2012

(Permalink) Posted: Jan. 18 2015,05:09   

Quote (cryptoguru @ Jan. 18 2015,09:46)
These are VERY simple concepts to grasp.
Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation


A model does not have to include everything. It would be a simple matter (in many GAs, at least) to permit 'core function' to be subject to mutation also. If it happened to be fatal when it occurred, the evolving population would remain unperturbed by these occurrences. Mutational change is not 'not evolution' simply because it is not 'core function' change.

   
Quote
and the selection process is working on the compound functional level (by rewarding compound functions).


The entirety of a genome can be considered a 'compound function'. The survival or otherwise of a genome is assessed at a compound level - whole-genome survival and replication. But there are multiple levels of selection when aggregated over many generations.

Edited by Soapy Sam on Jan. 18 2015,11:12

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SoapySam is a pathetic asswiper. Joe G

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Wesley R. Elsberry



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(Permalink) Posted: Jan. 18 2015,05:49   

Cryptoguru:

   
Quote

You're misunderstanding the point. The original 26 functions (commands) that AVIDA uses are not subject themselves to mutation. So finding new logical functions that are combinations of these elemental functions is trivial using an optimisation algorithm (which is what AVIDA is). You will only get functionality that is described by compounds of those functions.

This is equivalent to having a chemistry set with 26 elements, you combine them randomly and select combinations of chemicals that produce interesting reactions, you optimise over those. You will NEVER create a new chemical element from this process. The elemental level in AVIDA is the function (command), these should therefore be evolved, not prescribed.


No, I understand "the point" quite well. I've shown the error there before, and I can do it again.

Cryptoguru's analogy would require that he somehow believes biological organisms create new chemical elements. Cryptogurru is wrong. Biological organisms do create novel chemical compounds out of the plain, ordinary elements that are hanging around. Mostly, these are novel proteins, constructed out of a toolkit of 20 amino acids. Cryptoguru's "challenge" conditions are handily met by Avida, which mutates the "code that defines the functions themselves". (That's one leve of indirection, not multiple levels.) Avidian instruction sequences define the functions that accrue merit. Those instruction sequences are mutated, changing the functions. In biology, nucleotide sequences are mutated, resulting in changes in function. And it is not a matter of "optimization" alone: the seed Avidian program is composed of a series of NOP instructions and a section that handles self-replication; the only function performed by the initial Avidian is self-replication. (The self-replication code is also subject to mutation, and Avidians routinely die without progeny due to mutations there that do not preserve self-replication capability.) The logical functions that accrue merit all have to be constructed de novo, they are not performed at some low level and increased, as Cryptoguru erroneously asserts with the "optimising" comments. Cryptoguru wants to endlessly modify his "challenge" to avoid admitting that its conditions have been met. That leads to absurdities in his analogizing, like the one about creating new elements, and in his perversely clinging to error that has clearly been called out.

In biology, you only get codons that are three-tuple combinations of four DNA nucleotides, and you only get proteins that are n-tuple combinations of the fixed set of amino acids that organism uses. (There's a canonical set of twenty amino acids.) The situation in Avida is analogous to one level of indirection, though not two. Fortunately, Cryptoguru's "challenge" only requested one level of indirection. The complaint that functions are built out of combinations is a non-starter, since that is exactly how the biology works, too.

Cryptoguru:

   
Quote

Explain precisely where, in my description of AVIDA and the biological evolution algorithm I have got any of the details wrong.


There are too many misconceptions in Cryptoguru's discussion of biology to bother with. The notion that biology produces new chemical elements is just the absurd topping on a cake of error.

   
Quote

AGAIN (to explain this problem one last time)
1) evolution mutates DNA on a nucleotide level affecting function (gene level) and selects on the organism level.
2) AVIDA mutates "DNA" on the gene level affecting compound function and selects on the compound function level.


The first point is pretty sloppy, because most functionality in organisms is at the protein or higher levels.

As for point 2, Cryptoguru apparently has no clue how Avida works, because Avida as in the Lenski et al. 2003 paper doesn''t do anything but select at the Avidian level. There is no process in Avida that permits the propagation of the instruction sequences that define a logic function on its own. This is an own-goal on Cryptoguru's part.

   
Quote

These are VERY simple concepts to grasp.


Certainly. The problem being that Cryptoguru is completely wrong about point 2.

   
Quote

Please explain how AVIDA is possibly modelling biological evolution when the core functions (commands) cannot be corrupted under mutation and the selection process is working on the compound functional level (by rewarding compound functions).


I haven't claimed that Avida models "biological evolution". I have claimed that Avida is sufficient to meet the terms of the "challenge" as it was stated early in the thread.

The functions that are awarded merit in Avida can be lost via mutation (the paper Cryptoguru claims to have read discusses this at length), so that is another plain error on his part. And I have noted already the error in claiming that Avida selects at any level lower than that of the Avidian.

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
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