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Author
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Topic: Dembski on functional subsystems in "Uncommon Dissent"
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RBH
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Member # 380
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posted 30. July 2003 19:20
Nelson Alonso chopped contiguous sentences into fragments, lopped off part of one of them, and reversed their order in a futile attempt to support his false claim. He parses my posting as quote:
In a previous post RBH wrote: quote:
The remainder of the two-input logic functions were not rewarded with reproductive resources; their reward functions were disabled.
This sentence was written directly after this one: quote:
NOT, a single-input function, and OR_N and AND_N, both two-input functions, as rewarded intermediates
However, it seems as though you are now saying that the two remaining functions were not rewarded, did not persist, and therefore, were not required.
The complete paragraph I wrote (26. July 2003 01:45) was: quote:
The run that evolved to perform the EQU mapping (as I said in the original posting above where I described it) used NOT, a single-input function, and OR_N and AND_N, both two-input functions, as rewarded intermediates. The remainder of the two-input logic functions were not rewarded with reproductive resources; their reward functions were disabled. Genotype length was rendered selectively neutral by awarding SIPs in proportion to length, as in the Lenski, et al., procedure. (Emphases added)
On the basis of his tortured parsing of my posting, Nelson Alonso claimed that quote:
You [RBH] stated that two functions persisted and yet were not rewarded,or are you saying that because they were part of the other three functions you listed, they were rewarded?
Does Nelson Alonso truly not know that a "two-input logic function" is a function that takes two inputs (e.g., A AND B, where "A" and "B" are the two inputs), and is not "two functions"? Doesn't he know that all of the logic functions listed in the fitness table (Table 1, p. 140) in the Lenski, et al., paper are two-input logic functions with the exception of NOT, a one-input function? I have the distinct feeling that I'm wasting my time here.
Nelson Alonso further wrote quote:
Well I have access to several networks that could possibly confirm your claim. But of course, you're claim cannot be independantly verified at the moment. In fact, due to the stochastic nature of the program, your confirm (sic) may indeed never be verified. I need to know exactly how many intermedaites were rewarded, and what the starting conditions were. As well as exactly how many instructions EQU used. If it was a very simple form of EQU, then I wouldn't be surprised that only 3 intermediates were required. If it was one of the complex forms of EQU, which Lenski report required way more than 3 intermediates, then I would need to look at the data, because I find it completely outlandish, that EQU would either be so plastic that 3 intermediates, along with many chance events, would evolve EQU (although that wouldn't really surprise me). However, if the instructions themselves exhibited complexity, but they still required only 3 intermediates, then I would think something was frontloaded.
I can only say that this is incoherent. The minimum numbers of instructions required to perform mappings corresponding to the various logic functions are available: Those will provide minimum estimates of the probabilities of chance formation. Calculate those and any evolved program that is more complex will be less probable.
The internal contradiction here is palpable: quote:
If it was one of the complex forms of EQU, which Lenski report required way more than 3 intermediates, then I would need to look at the data, because I find it completely outlandish, that EQU would either be so plastic that 3 intermediates, along with many chance events, would evolve EQU (although that wouldn't really surprise me). (Emphases added)
Outlandish things are not surprising to Nelson Alonso, it seems.
Nelson complains that he would have to know exactly how many intermediates were rewarded. I have repeated that information twice in this thread. Let him read for comprehension. Then he says "due to the stochastic nature of the program, your confirm (sic) may indeed never be verified." On the contrary, because it is a stochastic phenomenon, a sufficiently large sample of differently randomized runs will allow Nelson to come to a statistically reliable estimate of the proportion of evolutionary runs in which one can expect the EQU mapping to evolve given the three specified rewarded simpler functions.
Finally, Nelson Alonso says "If it was one of the complex forms of EQU, which Lenski report required way more than 3 intermediates, then I would need to look at the data, ...". Actually, Lenski, et al.'s control conditions did not cover the full range of number of intermediates, and they did not report that evolving the mapping corresponding to EQU "required way more than 3 intermediates." They tested environments in which either one or a pair of the full set of intermediates were not rewarded, and concluded that the EQU mapping evolved with as few as 6 simpler functions being rewarded. Since they did not test with fewer than 6 rewarded simpler functions, they cannot have reported that it "required way more than 3 intermediates;" they didn't do all of the control conditions necessary to make that statement.
Once again, given Nelson Alonso's repeated misinterpretations and misrepresentations of both the published literature and my own postings, I believe that I am wasting my time here.
RBH
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Nel
Member
Member # 614
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posted 30. July 2003 19:33
RBH,
I chopped the first part off because it was irrelevant. I wrote it exactly as you wrote it, with the exception that in between the two quotes, I wrote that you wrote one after the other.
RBH wrote:
quote:
Does Nelson Alonso truly not know that a "two-input logic function" is a function that takes two inputs (e.g., A AND B, where "A" and "B" are the two inputs), and is not "two functions"?
Nothing in my post implied that I do not know what a "two-input logic function is" and so I have no idea why RBH would even imply such a thing. I only assumed it was two because RBH uses the plural, the minimum of a plural word for "function" is two:
quote:
The remainder of the two-input logic functions were not rewarded
So again, were these functions required and yet not rewarded?
RBH wrote:
quote:
I can only say that this is incoherent. The minimum numbers of instructions required to perform mappings corresponding to the various logic functions are available: Those will provide minimum estimates of the probabilities of chance formation. Calculate those and any evolved program that is more complex will be less probable.
I don't know what the other two (or more) functions were, nor do I know how to write EQU with only three functions. So thats why I would need the data that you say is "gone" in order to calculate anything.
RBH writes:
quote:
Nelson complains that he would have to know exactly how many intermediates were rewarded. I have repeated that information twice in this thread. Let him read for comprehension.
I stated this in the context of my own testing and not in light of anything that you said (because you have said nothing).
RBH wrote:
quote:
They tested environments in which either one or a pair of the full set of intermediates were not rewarded, and concluded that the EQU mapping evolved with as few as 6 simpler functions being rewarded. Since they did not test with fewer than 6 rewarded simpler functions, they cannot have reported that it "required way more than 3 intermediates;" they didn't do all of the control conditions necessary to make that statement.
In all the runs that Lenski et. al. did, none of them came out requiring only 3 intermediates. None. There is no need to "test" for this, in fact, I would be very suspicious if they did something in their starting conditions that would end up with an EQU that had only 3 intermediates. If it is truly a stochastic process, then a 3 intermediate EQU would have shown up (in fact, that none showed up shows that it is an unlikely event). None were reported.
[ 30. July 2003, 19:52: Message edited by: Nelson-Alonso ]
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RBH
Member
Member # 380
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posted 30. July 2003 21:39
I'll try just once more. If three simpler logic functions are rewarded, and there are eight total simpler logic functions (see the Lenski, et al., paper, Table 1), then obviously five simpler functions were not rewarded. I still have no idea where Nelson Alonso got his notion about two non-rewarded functions "persisting."
Nelson Alonso wrote quote:
In all the runs that Lenski et. al. did, none of them came out requiring only 3 intermediates. None. There is no need to "test" for this, in fact, I would be very suspicious if they did something in their starting conditions that would end up with an EQU that had only 3 intermediates. If it is truly a stochastic process, then a 3 intermediate EQU would have shown up (in fact, that none showed up shows that it is an unlikely event). None were reported.
Unfortunately for Nelson's interpretation, Lenski, et al., did not analyze their runs to determine whether the final program/lineage that evolved to perform the EQU mapping incorporated whole subprograms that performed one, two, three, or or all eight simpler logic functions. Nelson Alonso's description of what Lenski, et al., did is simply incoherent. In the Lenski, et al., experiment, in the experimental and control runs varying numbers (six to eight, with zero in one case) of the simpler logic functions were rewarded by the fitness function. In all conditions except the 'zero simpler functions rewarded' condition, at least one lineage evolved to perform the input-output mapping corresponding to EQU. Beyond that, they did not vary the simpler functions that were available in the simulation.
Lenski, et al., did not analyze each of the assembly language programs that evolved to perform the EQU mapping to ascertain which simpler programs that performed simpler logic functions were incorporated whole into those EQU-performing programs. It is possible to tell from the knockout procedure that there were some single instructions and sequences of instructions that were shared with the EQU program by programs performing several other functions, suggesting cooption, but there was no analysis of how many (or which) of the programs that performed the various simpler logic functions were coopted whole into the programs that performed the EQU mapping. Lenski, et al., say "However, no particular function was essential for the subsequent evolution of EQU, because each one was absent from at least one of the parent genotypes" (p. 142). That is the extent of their analysis of that topic.
So Nelson Alonso's remark that "If it is a truly stochastic process, then a 3 intermediate EQU would have shown up ..." bears no relationship to the procedures of the experiment and the analyses performed. Essentially, when Nelson Alonso says "None were reported" he is telling us that Lenski, et al., did not report the results of data analyses that they did not perform for experimental conditions that were not run.
Once again, Nelson Alonso's postings show an often mistaken representation of the technology of the Avida platform, the design of the Lenski, et al., study, what its output data were and how they were analyzed, and what the results of those analyses were. Hence this discussion has become a waste of my time and I doubt that I will bother to post further in response to him.
RBH
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