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Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,05:52   

Cryptoguru:

Quote
I never said they were, I was equivocating the process of evolution in both organisms


That word... I do not think it means what you think it means.

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

    
Cubist



Posts: 501
Joined: Oct. 2007

(Permalink) Posted: Jan. 18 2015,06:18   

Quote (cryptoguru @ 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.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,06:21   

And my post here still stands as an accurate summation of things. Avida meets the requirements of Cryptoguru's "challenge" and Cryptoguru's further dismissals have been distributed between the irrelevant and the erroneous.

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

    
cryptoguru



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Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,06:26   

Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them. Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function. The genome is mutated at the nucleotide (symbol) level.

AGREE?

AVIDA is providing 26 elemental functional components (commands) as the building blocks to optimise compound functionality. This is the same as providing 26 proteins and performing stochastic optimisation to find compound functionality. AVIDA only selects BETWEEN these components, it doesn't allow mutation of them at the symbol level (the code that defines these components). Therefore the integrity of those component commands is never affected by the mutation process in AVIDA, and new components commands cannot emerge, there will always be 26 commands.

THIS IS NOT EQUIVALENT!

Pleas explain how any of my assertions here are wrong.

It could be argued that AVIDA is modelling the selection of combination of entire genes to create new functionality and adaptation of an organism to its environment ... I would not dispute that happens in real organisms ... but the elemental functionality never extends, so limits the functionality of the organism.

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,06:26   

Cubist:

Quote
Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"?


In my experience, antievolutionists do this because they think that evolution is supposed to replace de novo creation, so they require that it should look just like de novo creation. They don't want to hear about co-opting function, duplication and divergence, and all the other ways that evolutionary processes actually do things that haven't been done before. Because evolution doesn't do "poof!", they think that they have identified a problem. The fact that nobody else sees this as a problem is very frustrating to them.

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

    
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,06:28   

Quote
That word... I do not think it means what you think it means.


you're right ... it was late when I wrote it ;-)

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,07:00   

I am not "missing the point", I am rebutting erroneous claims.

Cryptoguru:

 
Quote
Pleas explain how any of my assertions here are wrong.


Already done for a bunch of stuff. Pardon me if I simply review where we are at.

The assertion that biological organisms created new chemical elements was wrong.

The assertion that Avida selected at something lower than the Avidian level was wrong.

The assertion that Avida composing functions out of instruction sequences is not analogous to biological organisms composing proteins out of amino acids is wrong.

The assertion that nobody besides Cryptoguru had read Lenski et al. 2003 was wrong.

Cryptoguru wanted an analogy between critters and computers. He's just unhappy that this exists. Avida provides an instruction set. The sequences of instructions form programs. A computer's instruction set is fixed; changing code sequences does not change the instruction set. Likewise, Avida's instruction set is fixed. Cryptoguru has invoked Turing machines, and the analogous piece there is the tape, and nothing on the tape changes the reader. Biological organisms aren't, in the common course of things, changing either the set of DNA nucleotides or the set of amino acids they use. If Cryptoguru doesn't like the way Avida gets to the functions it rewards, the problem isn't with Avida; the problem is with Cryptoguru's analogy/equivalence between biology and computation. The elements of Cryptoguru's stated "challenge" have been met. He seems intent to change the "challenge" post hoc to exclude things that meet it.

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

    
JonF



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Joined: Feb. 2005

(Permalink) Posted: Jan. 18 2015,08:10   

Quote (cryptoguru @ Jan. 17 2015,19:28)
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.

Lenski identified the mutations that led to citrate utilization, a new and novel function.  Are you alleging that there is some currently unknown information storage and processing mechanism in the cell that pre-programmed those mutations?

If so, interesting theory.  Got any evidence for it?

  
NoName



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Joined: Mar. 2013

(Permalink) Posted: Jan. 18 2015,08:14   

Quote (cryptoguru @ Jan. 18 2015,07:26)
Okay let me explain this in another way ... you seem to keep missing the point.

Let's see if we can agree on this point:-
The genome is a code comprised of symbols (G, A, C, T) stored in nucleotides (the same as computer code characters can be stored in bytes).
This code defines how to build proteins from amino acids arrange them and fold them.[/quote]
Strictly false.  The code is comprised of more than just the symbols.  Their specific arrangement and adjacencies matter critically.  This is entirely unlike computer code.
Secondly, the code emphatically does not define how proteins fold.  Physics and chemistry do, and they do so based on the local environment in which the genetic material and its products exist, as well as the local environment excluding the genetic material and its products.
Quote
Proteins are an elemental functional component. The genome also defines how to assemble the proteins into complex structures, with complex function.

Again, strictly false.  There is no one-to-one mapping between genes and the resulting structures of the life-form.
Quote
The genome is mutated at the nucleotide (symbol) level.

AGREE?

With the tiny bit you got correct, yes.  With the gross misunderstandings that are sufficient to warrant dismissal of all your claims, of course not.
Quote
...
Pleas explain how any of my assertions here are wrong.

Done and done.

I'll also note that you are ignoring the fact that your original challenge, as yet lacking any explicit modification or discussion by you, has been met in multiples ways by multiple posters.  That you ignore this suggests strongly that you see a single path of argument that reaches the conclusion you desire, that you are arguing from what amounts to a script that hangs off that particular singular path, and that you are unwilling and/or unable to deviate from that  script when others don't play along.  It also indicates strongly that  you are unwilling and/or unable to acknowledge that your challenge has been met, because that doesn't match the results you get by your singular preferred argument.  The rest of the world understands what it means when one 'preferred' argument out of many appears to succeed, but the facts show it to be incorrect, regardless of how appealing or apparently sound it is.  You appear not to understand this.
Your challenge has been met.
Revise it into a different challenge and admit defeat on this front.  Of course, that means admitting that you have no basis other than faith and a generalized distaste for rejecting evolutionary theory.
I thank 'The whole truth' for pointing out my careless wording that failed to make the distinction between evolution the fact and 'evolutionary theory'.  He's absolutely correct, and my post needs that correction.

I'll also note that it is strictly false to assert that the cell is a Turing machine.  The cell does not operate on a strictly clocked mechanism, does not have infinite storage, does not operate by singular read/write operations on singular 'memory cells', etc.  That the cell can be modeled by a Turing machine does not make the cell a Turing machine.
That the entirety of the living processes, all essential to the existence of a cell, can be modeled by a single Turing machine is a laughable claim.  At the very least, it requires proof, and said proof would be notable and prize-worthy.
Whole-cell modeling is still a very difficult enterprise and does not have a general solution.  I've worked in the field, I know this to be true.

And I'll note that you conspicuously fail to understand the point of thermodynamics as a problematic for cells that does not apply to computers.  The analogous problem for computers is high-energy gamma radiation randomly flipping bits in memory cells.  That phenomenon is rare enough that it did not become problematic 'in the field' until the late 90's, when ECC memory began to be required.  Do you understand why this is so?  Do you understand the analogy, and its limits?

Finally, I see no point in going back and addressing your response to my post from near the top of the previous page.  You give every evidence of being one of those "I've got my mind made up, don't confuse me with facts" people.  That a computer can use the various things noted, or can demonstrate them, is irrelevant to the argument, and it is tragic that you do not see that.

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,08:25   

Cryptoguru:

   
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.


Avida's instruction set is Turing-complete. Avidian genomes are sequences of instructions. Any computable function is possible to encode with Avida instructions. The notion that Avida is not capable of doing what computers and Turing machines do is wrong. This is not arguable.

It is possible that Cryptoguru has confused himself. Selection is an effect of the organism interacting with its environment, either in biology or Avida. That there are only certain things that are set up for selection in an Avida experimental environment is analogous to the limits of particular natural environments. Cave-dwelling fish, for instance, aren't in a position to evolve flight in air, either. As it turns out, there are some 60+ logic functions that stock Avida can evaluate in its environmental setup, only nine of which were activated in the Lenski et al. 2003 paper. And as I noted, Avida instruction set programs can encode any computable function. Faulting Avida for not having every computable function set up for reward in every experimental environment is quite ludicrous, and also quite beside the point of the original "challenge", which was that new functions arise from the model genome changes, not that every possible function must arise thereby.

If Cryptoguru means by his objections that Avida cannot be an analogy for biology because of the limits of computation, he has also refuted his own insistence that biology is computation.

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

    
OgreMkV



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Joined: Oct. 2009

(Permalink) Posted: Jan. 18 2015,08:38   

Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)
Cryptoguru:

     
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

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

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

   
Texas Teach



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Joined: April 2007

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

Quote (OgreMkV @ Jan. 18 2015,08:38)
Quote (Wesley R. Elsberry @ Jan. 18 2015,08:25)
Cryptoguru:

     
Quote

e.g. a robot that is built to support commands to go forward, backwards, left and right on the ground cannot learn to fly by combining those commands in an optimal order. You cannot select what isn't there to select. This is the level that AVIDA is working on, not the symbol or code level.

This is also interesting in that cryptoguru has previously rejected my statements that evolution can only build on previously existing DNA.

In fact, cryptoguru appears to be using evolutionary science as evidence that evolution can't work.

Truly a strawman of epic proportions.

He's also trying the old creationist trick of dividing mutation and selection to claim that each is insufficient for evolution.  Here we have the "natural selection can't do anything new since all the DNA sequences are the same" variant.  Others prefer the "mutations can't randomly assemble all the DNA pieces, tornado in a junkyard, blah, blah, blah" variant.

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"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 18 2015,10:08   

Quote (cryptoguru @ Jan. 18 2015,01:46)
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).

"... I was equivocating the process of evolution in both organisms."

I know.

"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."

Where do you get the idea that every biological entity* evolves by exactly the same amount from one generation to the next?


*I would have said life form instead of biological entity but I'm including viruses, and not everyone thinks that viruses are life forms.

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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

   
Jim_Wynne



Posts: 1205
Joined: June 2006

(Permalink) Posted: Jan. 18 2015,10:35   

Cryptoguru, condensed:

1.  All of biology and most of science is wrong.
2.  Frontloading.
3.  No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

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Evolution is not about laws but about randomness on happanchance.--Robert Byers, at PT

  
Texas Teach



Posts: 1634
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,10:41   

Quote (Jim_Wynne @ Jan. 18 2015,10:35)
Cryptoguru, condensed:

1.  All of biology and most of science is wrong.
2.  Frontloading.
3.  No evidence, no mechanisms.

I'll put the over/under on this thread at six pages.

Gaulin has no more than that, and his thread is at 429 pages.  Never underestimate the needs of TARD-addicts.

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
The whole truth



Posts: 1554
Joined: Jan. 2012

(Permalink) Posted: Jan. 18 2015,10:46   

NoName, thanks for taking what I said so graciously. :)

--------------
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

   
N.Wells



Posts: 1823
Joined: Oct. 2005

(Permalink) Posted: Jan. 18 2015,11:53   

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? 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.

My two cents on this earlier comment: Natural selection is not solely and only about death.  It's differential reproductive success, which may or may not be attributable to dying early.  

A long-term study of reproductive successes of 142 female sparrowhawks from 1971 to 1984 showed that 23 had no fledglings, 70 had only 1 to 4 fledglings, and 3 had more than 20 fledgelings (21, 22, & 23).  Obviously, the genes of the last three become much more widely represented in subsequent generations.  Some of the mothers died early, but others simply weren't successful at parenting.  This can involve a whole host of reasons other than dying.

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,12:32   

Cryptoguru:

Quote

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.


Here's another way Avida differs from Cryptoguru selection. Avidians get CPU time according to merit. It is perfectly possible for an Avidian to replicate while other Avidians have greater merit. The other Avidians, though, replicate themselves more often and thus the population comes to have more Avidians like those with more merit, and fewer Avidians like those with less.

This, by the way, is not a way in which Avida is distinguished from natural selection.

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

    
cryptoguru



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(Permalink) Posted: Jan. 18 2015,14:18   

Wesley R. Elsberry:

Again you've missed the point ... I'm not saying AVIDA should model every possible function, I'm saying that it doesn't model the proposed form of evolution. Real evolution is supposed to mutate the base code ... so you should be mutating the under-the-hood program code that defines the NAND, SWAP, DEC, IO, SUB etc. in AVIDA as this is what happens in a real genome.

I'm not doubting that AVIDA is excellent at solving generic optimisation problems, but it is misleading to pretend it is modelling biological evolution, because the core feature of biological evolution is random mutation of nucleotides (point, insertion, deletion). The variability of that problem is orders of magnitude greater than the simple optimisation problems you're solving with AVIDA.

In DNA, mutations occur at the symbol level of the code that is used to build and assemble proteins, direct their sub-assembly (amino acids ... translational pausing etc) and further controls the protein assembly into complex functional parts. These themselves are part of the whole organism, where cells are differentiated in function and perform many complementary roles with other cells.

AVIDA is basically 26 assembly code instructions, which are mutated randomly under competition until something useful happens. This is not analogous to DNA mutation and selection.

I say it again, THIS is like mutating 26 proteins in DNA to make different complex structures and rewarding certain combinations that give known favourable complex structures. AVIDA is applying mutations on a much higher level than occurs in the Genome, so doesn't allow the possibility of code corruption, base functionality regression and crash, which a real genome does.

This effect is amplified by the fact that the instruction set is Turing-complete ... AVIDA is MOST likely to find useful combinations of the 26 functions ... this is a cumulative SEARCH (similar to WEASEL it has targets), and not like biological evolution. The human genome has billions of base pairs, even mutating 3 neighbouring nucleotides to any codon anywhere in the genome is less likely than winning the lottery twice in a row. Being able to mutate an AVIDA command to another functioning command is 100% likely. DO YOU GET IT YET??? (I doubt it)

Most of the responses I've had so far are so off-the-wall and lacking in fundamental logic that it's impossible to even address their stupidity.

If you guys can't see the difference between a process which mutates nucleotides in a huge code that has MANY layers of complexity, inter-dependency and non-linear function and a process which randomly mutates 26 assembly instructions in different ways, scores combinations that perform a simple function and allows them to compete ... then you're more wilfully ignorant than I had initially assumed.

It's wishful thinking of the highest degree to expect useful behaviour to come out corrupting a computer program. Comparing that to shuffling assembler instructions until you get a useful function is absolutely laughable. I suppose you have to come up with something like this though to keep the funding rolling in and slap the word "evolution" all over the papers so the similarly confused peer reviewers get all excited and happy that evolution is a FACT and we can all sleep soundly.

Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.

I'm going to go and do some actual work that isn't based on fairy tales now ...
... and leave you all to your mutual backslapping and peddling the nonsense postulation that random mutations plus a sprinkling of magic selection (which is the secret ingredient that we should never really define properly lest it became understandably deficient) will eventually mutate a Banana into Barack Obama. I do hope some of you get to use your brains for things that actually benefit people and this is just a hobby thing that you do in your sparetime.

Have fun folks.

Oh ... please DO let me know when Lenski suddenly finds a fish in his E. Coli. That will be a monumental day for all of us.

  
cryptoguru



Posts: 53
Joined: Jan. 2015

(Permalink) Posted: Jan. 18 2015,14:39   

final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

  
rossum



Posts: 243
Joined: Dec. 2008

(Permalink) Posted: Jan. 18 2015,15:00   

Quote (cryptoguru @ Jan. 18 2015,14:39)
Natural Selection is about death.

No, natural selection is about reproductive success, not death.  Death may be important, but only because of its impact on reproductive success.  Dying at 20, leaving two children is better than dying at 80, with no children.

The process of natural selection is a bit like compound interest.  As an example, take a stable population of 100 organisms; on average each organism has one descendant in the next generation.  Now let a beneficial mutation appear with a 1% advantage, so the mutated organism will have on average 1.01 descendants in the next generation.  For comparison I include a second mutated organism with a 1% disadvantage.  Start with a population of 1 deleterious, 98 neutral and 1 beneficial mutations.  See what happens if we let the population reproduce for one thousand generations:

Code Sample

Generation  Deleterious   Normal   Beneficial
----------  -----------   ------   ----------
    0         1.00       98.00          1.00
    1         0.99       98.00          1.01
   10         0.90       98.00          1.10
  100         0.37       98.00          2.70
  500         0.01       98.00        144.77
  700         0.00       98.00       1059.16
 1000         0.00       98.00      20959.16

(That should be monospaced, but I can't get it to work well.  Sorry.)

You can see how the small 1% advantage is amplified over the generations as the beneficial variant spreads through the population.  The deleterious mutation disappears.

This is a very simple model, but it is enough to show the advantage a beneficial mutation has and how it can spread through a population.

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

  
N.Wells



Posts: 1823
Joined: Oct. 2005

(Permalink) Posted: Jan. 18 2015,15:06   

Quote (cryptoguru @ Jan. 18 2015,14:39)
final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

You are pervasively wrong here, because you are simplifying natural selection incorrectly.

Death, although important, is just one of many "selective agents", so differential reproductive success can be extremely different from "life versus death", and simplifying natural selection to "life versus death" has led to many misunderstandings about evolution, such as your misunderstandings.  Natural selection is usually much more subtle than just differential mortality rates.

An organism that fails to reproduce as successfully as the neighbors will have a smaller proportion of genes in the next generation.  That (with recombination and many generations) can indeed cause the genes to become very rare and eventually be lost from the population.  Because of recombination and multiple generations, lineages do not have to go extinct for genes to be lost.

   
Quote
Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that....
"Millions" is an overstatement, but polymorphic alleles are indeed very common, as are races, sister species, and overlapping ranges between competitors, all of which indicate that the world does not function as simply as you imply.

From http://www.biologyreference.com/Mo-Nu......on.html
Quote
A persistent misconception is that natural selection occurs mainly through differences between organisms in death rates, or differential mortality. Differential mortality can be selective but only to the degree that it creates differences between individuals in the number of reproductive offspring they produce. Reproductive rate, rather than death rate, drives natural selection. A cautious tomcat that seldom crosses busy streets might live to a ripe old age without leaving behind as many descendent kittens as another less staid tomcat killed on a highway at a much younger age. If the short-lived cat leaves more descendants, its genes will spread faster than those of the long-lived cat, and natural selection will favor a short life span. Unless living longer allows or results in higher reproductive success, long life is not favored by natural selection.

See also http://www.zo.utexas.edu/courses....on.html

Edited to add: Thanks for a more specific response, Rossum - you posted while I was writing offline, or I'd have mentioned it.

  
Cubist



Posts: 501
Joined: Oct. 2007

(Permalink) Posted: Jan. 18 2015,16:25   

Verbatim re-post. I fully realize that cryptoguru's schedule is full up with telling evolutionists how wrong they are, but perhaps they will find the time to explain what they mean when they say "new and novel genetic material", or even determine whether or not one specific concrete example of a mutated nucleotide sequence qualifies as "new or novel genetic material". Or perhaps they will continue to make noise about how wrong evolutionists are. I dunno.

 
Quote (cryptoguru @ 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.

"Never been observed", you say. Well, I say, show me a person who's never heard of a kinkajou, and I'll show you a person who wouldn't recognize a kinkajou if a rabid one was chewing on their face. And in my experience, it's awfully damned common for Creationists who claim that thus-and-such has never been observed, do not actually know what thus-and-such would look like, and therefore those Creationists don't actually have any valid grounds for asserting that thus-and-such "has never been observed". So I want to drill down on your verbiage here, cryptoguru, and see whether you actually do know what you're talking about.

You have a definition of "new information". Groovy. I note that your definition of "new information" is sufficiently imprecise that it doesn't provide any way to tell whether or not a given string of nucleotides qualifies as "new information" under your definition. So let's see if we can dispel the vagueness, shall we?

Your definition of "new information" includes a clause about "new and novel genetic material".  Why must the "genetic material" of "new information" be both "new" and "novel"? I ask because "new" and "novel" strike me as basically synonymous, hence, using both words is gratiutous redundancy. But perhaps you weren't being redundant; perhaps you actually are using distinct referents for "new" and "novel", such that the two words are not, in fact, gratuitously redundant. Please explain how "genetic material" which is "new" differs from "genetic material" which is "novel".  Is it possible for "genetic material" to be "new" without also being "novel"? Is it possible for "genetic material" to be "novel" without also being "new"?

What does "new and novel genetic material" look like? I'm going to provide some concrete data to work with. Here's an arbitrary nucleotide sequence, with a randomly-picked nucleotide—the thymine in the 4th codon—colored red:
gcc tac agg gat cgt ggg gac ctt acg aat ggc ctt ttt gac tat tct tcg aat cta agc tca gca tca ttc ccg tct acg gga agt ccc ttc cca ata cat atc ctc ggc acc gca ctt gca ggc tca cgc ttc gcg tca ttt agg tca
That sequence of codons yields the following sequence of amino acids, with the 4th amino acid colored red on account of it's the AA that's yielded by the codon with the red-colored nucleotide:
alanine, tyrosine, arginine, aspartic acid, arginine, glycine, aspartic acid, leucine, threonine, asparagine, glycine, leucine, phenylalanine, aspartic acid, tyrosine, serine, serine, asparagine, leucine, serine, serine, alanine, serine, phenylalanine, proline, serine, threonine, glycine, serine, proline, phenylalanine, proline, isoleucine, histidine, isoleucine, leucine, glycine, threonine, alanine, leucine, alanine, glycine, serine, arginine, phenylalanine, alanine, serine, phenylalanine, arginine, serine

One possible mutation of that sequence would be if the thymine in the 4th codon was deleted, like so (and the thereby-altered 4th codon is colored red here):
gcc tac agg gac gtg ggg acc tta cga atg gcc ttt ttg act att ctt cga atc taa gct cag cat cat tcc cgt cta cgg gaa gtc cct tcc caa tac ata tcc tcg gca ccg cac ttg cag gct cac gct tcg cgt cat tta ggt ca
Since a codon is three nucleotides in a row, deleting that one nucleotide from the 4th codon in the original sequence doesn't just change that 4th codon; it also has the effect of changing pretty much every codon after that altered 4th codon. This, in turn, yields a very different sequence of amino acids than the original, unmutated sequence. The red-colored AAs are ones which don't occur at all in the original, unmutated sequence:
alanine, tyrosine, arginine, aspartic acid, valine, glycine, threonine, leucine, arginine, methionine, alanine, phenylalanine, leucine, threonine, isoleucine, leucine, arginine, isoleucine, [end], alanine, glutamine, histidine, histidine, serine, arginine, leucine, arginine, glutamic acid, valine, proline, serine, glutamine, tyrosine, isoleucine, serine, serine, alanine, proline, histidine, leucine, glutamine, alanine, histidine, alanine, serine, arginine, histidine, leucine, glycine, [???]

Does the mutated nucleotide sequence qualify as "new and novel genetic material"? Does the mutated nucleotide sequence contain any "new and novel genetic material"?

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,16:49   

That was quick!  I don't think I've ever seen someone go through the Stages of a Creationist as quickly as CreeptoGuru.

1.  Disingenuous Introduction (Hi, everybody!  I've got some questions.  Hope you can help.  Feel free to correct any misconceptions I have!)

2.  Creationist boilerplate.

3.  Patient explanations by Saint Wes and others.  (Doc Bill heavily sedated with DramaTARD to prevent chronic mockery.)

4.  There is no evilution!  Lenski benski!  Whaaaaaa, you're mean to me!  Jesus!

5.  Flounce.

Thank you, Creepto, for providing us with this hilarious brick of TARD, although it probably won't make it into the Hall of Flame:

Quote
Also the minion-like responses I've had concerning Lenski's experiment on here are equally hilarious. Trying to deny that after he's performed 60,000 generational steps seeing a small metabolic change is not something to get excited about is utterly self-deceptive.

This is a dying theory indeed when models can't model it ... and experiments don't demonstrate it.
The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


In the future, Creepto, try to work in some flourish like "altar of Darwin" or "high priests of science."  That's a crowd pleaser!

  
Wesley R. Elsberry



Posts: 4928
Joined: May 2002

(Permalink) Posted: Jan. 18 2015,18:06   

Cryptoguru:

 
Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

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

    
OgreMkV



Posts: 3668
Joined: Oct. 2009

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

Quote (cryptoguru @ Jan. 18 2015,14:39)
final point to N. Wells


Natural Selection is about death. It doesn't matter what the reasons are for advantage, whether it's because some are stronger, or shorter, or bluer, or have better ovaries, or avoid nightclubs .. whatever. The selective agent is death. If an organism dies before it can reproduce it will be removed from the gene pool. Things that haven't died yet compete for resources, eventually a hereditary line will die off removing it from the competition (death again).

The whole premise of natural selection can be simplified to be death. Differential reproduction is a misleading concept, because the preservation of an advantageous trait can only occur when eventually all other competing hereditary lines are extinct. (death). Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that, so all other lines must become extinct to allow the favoured line to become the parent to the next stage. (I obviously think this is crackers ... I'm just explaining that the evolutionary concept of natural selection is very simple)

My point is that the evolutionary concept of natural selection is easy to model, you just set natural conditions and environments for the organisms to live and compete in and see which survive, you shouldn't be measuring the advantages and rewarding them ... nature does not do that, it just provides conditions for death, those who survive it are considered "selected".

I don't see what all the fuss is about ... just trying to demystify the Natural Selection deity.

Bye for now

The selective agent doesn't have to be death. Again, this is trivially untrue... unless you think that neutering a dog kills it.

The animal is alive, but totally unable to pass it's genes on to the next generation. This is an extreme example, but there are plenty in the real world. Especially among herd animals with a single dominant male. Either you are the dominant male or you don't contribute to the genetic population of the group.

"The whole premise of natural selection can be simplified to be death."

No. The whole premise of natural selection is what Darwin said. You might read what the people who came up with the idea actually said instead of attacking a strawman.

Quote
Otherwise you evolutionists would expect to see millions of intermediate evolutionary stages living now alongside the "favoured" one ... and you don't believe that,


I think that this is especially funny. Because biologists think that every single organism is transitional. You are transitional between your parents and your kids. You are transitional between your uncle's kids and your aunt's kids.

There are millions of intermediate evolutionary stages. We don't see all of them because a vast majority are dead and not everything fossilizes. But still, we see them.

We even see transitionals in the genes. In fact, that is one of the reasons that multi-species whole genome studies can work. I've provided you with a paper that shows the transitional nature of genes among closely related species.

So, again, you are attacking a strawman. You say that we believe one thing... which we don't. And then you attack it (incorrectly).

Natural selection is fairly simple. When will you ever understand what it actually is?

To model it, you have to understand it correctly... and you don't.

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

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

   
midwifetoad



Posts: 3992
Joined: Mar. 2008

(Permalink) Posted: Jan. 18 2015,18:22   

He does write better than GG.

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

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,18:29   

Quote (Wesley R. Elsberry @ Jan. 18 2015,18:06)
Cryptoguru:

 
Quote

The power behind this theory is you guys ... your zeal at flocking around any assailant and trying to neutralise any attacks on the precious, by employing as much ridicule, incredulity, slander and mock as you can muster whilst still attempting to sound scientific.


Anyone whose analogies require living organisms to create new chemical elements is eminently mockable on their own demerits.

And, by the way, what I engaged in was disagreeing with Cryptoguru, not "missing the point". Given the many exceedingly basic errors I pointed out in his commentary, one would think he'd be a bit less full of himself. Anybody reviewing the thread is likely to see what I see, that Cryptoguru made a bunch of erroneous claims, got told they were erroneous and why they were erroneous, and made his exit with exceedingly bad grace.

Unless, of course, he's one of those people who makes endless farewell tours, and he's just given his first farewell concert.

Saint Wes, an eternal fan of the Ungrateful Dead.

  
Woodbine



Posts: 1210
Joined: June 2007

(Permalink) Posted: Jan. 18 2015,19:07   

Quote (midwifetoad @ Jan. 19 2015,00:22)
He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

  
Doc Bill



Posts: 1039
Joined: April 2007

(Permalink) Posted: Jan. 18 2015,19:34   

Quote (Woodbine @ Jan. 18 2015,19:07)
Quote (midwifetoad @ Jan. 19 2015,00:22)
He does write better than GG.

The fish drowning in Lenski's e-coli writes better than Gary.

Well, this is the typical creationist's view of evolution, isn't it?

CreeptoGuru demanded "new" and "novel" thingies and what he was demanding was a New Ford Chromosome 2015 with triple exhausts and a 13 cylinder engine, or some such.

Going back to Pandas, the hedge was "fish with fins and birds with feathers" with no ancestors.

That's what CreeptoGuru is demanding.  Ironically, that's the definition of creationism.  The fact that CreeptoGuru claims it's never been observed means that creationism has never been observed and that is totally correct.  It hasn't!

Well done, CreeptoGuru, you just disproved creationism!  Drinks on me.

  
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