Uncommon Descent Serving The Intelligent Design Community

Berlinski’s Question Remains Unanswered

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In a recent post I asked the following question.

I have a question for non-ID proponents only and it is very simple: Is there even one tenet of modern evolutionary theory that is universally agreed upon by the proponents of modern evolutionary theory?

Then I waited for the answers to come in. I was not disappointed, and I would like to express a hearty “thank you” to the proponents of modern evolutionary theory who participated in the exercise.

I have gone through the comments, and the proponents have nominated the following list as tenets on which all proponents of modern evolutionary theory agree:

1. Common descent

2. Modern organisms descend from very ancient ones.

3. The differences among related lineages have accumulated over many generations of change.

4. The basis of (some of) the differences among individuals is heritable.

5. The relative success of those heritable traits is the basis of evolutionary change.

6. Selection is an important evolution force.

7. Populations connected by gene flow evolve together absent very strong selection pull each population in different directions.

8. Selection is important (I am not sure how this is different from 6).

9. Drift exists.

10. Allopatric speciation is possible.

11. Most speciation processes fit somewhere between the extremes of sympatric speciation and allopatric speciation.

12. All of modern life shares common ancestry, HGT and orphan genes notwithstanding.

13. The following mechanisms of genetic change cause change in lineages, with a bias against reversal:
Mutation (point, indel, duplication and rearrangement)
Gene Conversion
Recombination (several mechanisms including HGT)

14. A parallel process of concentration/dilution of such variant alleles occurs (concentration of one is inevitably dilution of the other), by both sample error (drift) and systematic bias (selection).

15. Only frequency-dependent selection can oppose the progress of such an allele through to the fixation of one variant and elimination of the other. This is rare, so origin-fixation is the norm, long-term. [Later withdrawn]

16. Iterated occurrences of such fixations inevitably change lineages.

17. Isolated gene pools diverge.

18. Species differences are fundamentally due to the tendency of this divergence to proceed beyond the point of interfertility (isolation through prezygotic and postzygotic mechanisms).

19. Higher taxa result from ongoing divergences of historic species.

20. Transition-transversion biases in substitution are due to a biochemical tendency increasing yields of one product over the other.

21. Codon position biases occur and are due to the relative effects of selection and drift on synonymous vs nonsynonymous sites.

OK then. Let’s take a look at this list. They seem to fall into the following five categories.

Category 1: Who doesn’t believe that?

Pretty much everyone on the planet would agree with the following proposition: Animals and plants are different now than they were in the past. Thus, the proposition – while at some trivial level a tenant of modern evolutionary theory – is not that which sets it apart from other theories and accounts for its unique purported explanatory power. Even young earth creationists believe it. Therefore, these propositions cannot be the basis for any claim that the theory (as opposed to some other theory) is true. From the above list the following fall into this category: 1, 2, 3, 7, 9, 10, 12, 14, 16, 17, 18, 19, 20 and 21.

Category 2: Trivial

4. The basis of (some of) the differences among individuals is heritable.

Yes, all evolution proponents agree that genetics exists.

Category 3. It is simply not true that all evolution proponents believe it

It is simply not true, for example, that all evolution proponents believe that natural selection plays more than a non-trivial role in the process. It is also not true that all proponents believe sympatric speciation occurs. 5, 8 and 11 fall into this category. See here and here.

Category 4. I Don’t know what claim is being made

13. The following mechanisms of genetic change cause change in lineages, with a bias against reversal:
Mutation (point, indel, duplication and rearrangement)
Gene Conversion
Recombination (several mechanisms including HGT)

Is the proponent of this claim stating that genetic change and only genetic change causes change in a lineage? If so, it is clearly not the case that all proponents of the theory agree with this; indeed most of them would dispute it. Is the proponent claiming merely that genetics change occurs and somehow that gets fixed in a species? If that is the case, it would fall under category 1.

Catategory 5. Withdrawn: claim 15.

CONCLUSIONS

My suspicions have been confirmed. Proponents of modern evolutionary theory all agree on a set of propositions that even most fervent young earth creationist would also agree on. And nothing more as far as I can tell.

What I was really trying to get at was this: Is there any “core” proposition on which all proponents of modern evolutionary theory agree. By “core” proposition, I do not mean basic facts of biology that pretty much everyone from YECs to Richard Dawkins agrees are true. I mean a proposition upon which the theory stands or falls, and, as I said above, sets it apart from other theories and accounts for its unique purported explanatory power

I have in mind a proposition that would answer David Berlinski’s famous question:

I disagree [with Paul R. Gross’ assertion] that Darwin’s theory is as “solid as any explanation in science.” Disagree? I regard the claim as preposterous. Quantum electrodynamics is accurate to thirteen or so decimal places; so, too, general relativity. A leaf trembling in the wrong way would suffice to shatter either theory. What can Darwinian theory offer in comparison?

Indeed. What does modern evolutionary theory offer in comparison? How can the theory ever hope to be as “solid as any explanation in science” when its proponents cannot seem to agree on a single tenet, the falsification of which would, in Berlinski’s words, shatter the theory?

UPDATE:

In the comments eigenstate pulls Haldane’s famous “rabbit in the Cambrian” out of his hat. I will address that here:

Everyone knows there are no rabbit fossils in the strata that have been labeled “Cambrian.” First, eigen’s sputtering to the contrary notwithstanding, the primary reason a stratum would be called “Cambrian” in the first place is because of the absence of rabbit fossils.

Set that aside for the moment and consider this. The fact that there are no rabbit fossils in the Cambrian strata is a datum. It is a datum for evolutionary theory; it is a datum for young earth creationists; it is a datum for ID proponents. It is a fact on the ground in the same way that people are stuck to the earth with a force of 1G is a fact on the ground. Saying “a rabbit in a Cambrian stratum would destroy Darwinism” is equivalent to saying “if people start floating off into space it would destroy general relativity.” Well, people are not floating off into space and they are not about to. No rabbits have been found in the Cambrian strata and none ever will be. Haldane’s observation amounts to nothing more than “if the facts were different the theory to explain those facts would have to be different too.” It is trivially true and singularly unhelpful.

I take it that Berlinski’s point is very different. The mathematical models of quantum electrodynamics and general relativity make extremely precise predictions (13 decimal points). It follows that those theories have exposed themselves to an enormously high degree of “risk,” because if an observation were to vary from prediction by even an astronomically small degree it would falsify the theory.

Now consider the following exchange:

Barry: And yet unlike respectable scientific theories, there is not universal agreement on a single one of those details that sets [evolutionary] theory apart as an explanatory mechanism.

eigenstate: so what?

Well, here is what. Paul R. Gross’ asserted that Darwin’s theory is as “solid as any explanation in science.” Berlinski retorted that the assertion is preposterous. The point of the OP is that Berlinski is certainly correct. There is not even agreement among evolutionary theorists on what the model should be in the first place; far less has anyone developed a model that would make exquisitely precise predictions equivalent to those made by quantum electrodynamics and general relativity. Thank you eigenstate for confirming Berlinski’s point with your “so what.’

Comments
And still no source code. Carpathian, you are not the first to ever write a Weasel program. Why is yours so special that you cannot release it into the public domain? Does it use a secret sauce?Mung
May 13, 2015
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Carpathian:
Notice that I am using 93 chars in my text char set. That is more than enough for getting the information I need.
In those few words, you have said more than you will ever likely know. You, the intelligent designer, have injected information into your program which drastically reduces the size of the search space. And ASCII supports 128 characters, not 93. (One of which is the NUL character.) So are you finally admitting that I was right all along? Carpathian: Here is the char set. It is text, not binary.
In computing, a character encoding is used to represent a repertoire of characters by some kind of an encoding system. Depending on the abstraction level and context, corresponding code points and the resulting code space may be regarded as bit patterns, octets, natural numbers, electrical pulses, etc. A character encoding is used in computation, data storage, and transmission of textual data. Terms such as character set, character map, codeset or code page are sometimes used as near synonyms; however, these terms have related but distinct meanings described in the article. http://en.wikipedia.org/wiki/Character_encoding
Mung
May 13, 2015
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Mung, Here is the char set. It is text, not binary. Marriage Mode Fitness string = 1234567890. CharSet = !"#$&'()*+,-./0123456789:;?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[]^_`abcdefghijklmnopqrstuvwxyz{|}~ 1234567890 - 10 GEN 1: 0 ??c??????? #Matches: 0 1234567890 Carpathian
May 13, 2015
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jw777: Autophagy in a fasted state uses far less energy to maintain cellular integrity and mitochondrial function than the creation of a new organism to have “fresh cells”. Sure, which is why most organisms won't reproduce when energy levels are low. However, they do have to eventually reproduce to continue the line. A single organism, even if otherwise immortal, and even if incredibly well-adapted, will eventually die either due to accumulated damage or extrinsic mortality. Because reproduction is essential, it becomes a matter of finding the right balance between survival and reproduction. jw777: APerceived stress (not real threat) also shortens life by sympathetic nervous pathways corrupting DNA transfer and shortening telomeres. The test wasn't of stress in an individual, but the evolution of populations over generations under differing rates of extrinsic mortality.Zachriel
May 13, 2015
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Mung:
Actually, for me, it’s something a bit simpler even that that. It’s about the decision to use a C string which does not permit the inclusion of an ASCII NUL within the string itself.
Again, if someone wanted to send binary data, from 0 to 255, he could write his own binary protocol. I don't need that. What I am demonstrating is that a Weasel type program doesn't need to be recompiled if you change the fitness string. Here is what I am concerned with: GEN 16: 40 AAAAA?AAAAAAAAAAA #Matches: 16 AAAAAAAAAAAAAAAAA GEN 17: 39 AAAAAAAAAAAAAAAAA #Matches: 17 AAAAAAAAAAAAAAAAA Population Size/Fitness Length = 17.647059 Size Char Set = 93 Number of generations = 17 Notice that I am using 93 chars in my text char set. That is more than enough for getting the information I need.Carpathian
May 13, 2015
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Carpathian:
This whole dialogue is not about any specific char at all, it is rather about using out-of-band chars for control, as ASCII defines.
Actually, for me, it's something a bit simpler even that that. It's about the decision to use a C string which does not permit the inclusion of an ASCII NUL within the string itself. Carpathian:
Your are reducing the ASCII spec to a binary look-up table.
Just what do you suppose goes on inside your computer? You have no answer to my questions @249? What does it even mean to say that one letter is greater than or less than a different letter? Is the computer comparing letters or numbers?Mung
May 13, 2015
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Carpathian:
You asked me to write a function to show you how to get a count of matching chars in two strings as if that were relevant to the question of whether a Weasel type program needed to be re-compiled if the target string changed.
And now you're just making things up.Mung
May 13, 2015
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Mung:
I am capable of compiling source code into an executable, but I would need the source code. Any reason you’re being coy about the source?
First of all, thanks to you I actually invested the time to do this. Secondly, you're not as capable as you think. You asked me to write a function to show you how to get a count of matching chars in two strings as if that were relevant to the question of whether a Weasel type program needed to be re-compiled if the target string changed. Now you're arguing about the use of ASCII chars that are defined by the standard to be communication and terminal control codes, chars whose standard use is accepted by the real world vendors and customers. Anything I show you will involve my experience trying to debate your inexperience over trivial things like zeros at the end of C strings.Carpathian
May 13, 2015
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Mung:
Carpathian: ..and the intent of the standard, was to make it an ignored character, the same as NUL (all zeroes).
..the same as NUL.. This whole dialogue is not about any specific char at all, it is rather about using out-of-band chars for control, as ASCII defines. If you have ever programmed on a multi-drop platform you would know this. I've written code for clearing credit cards and the bank I had to communicate with used ASCII control codes with a very specific protocol that I and everyone else involved had to follow. Standards are written for a reason, so that everyone uses them in a standard way thus allowing computers to talk to each other with a known protocol. Your are reducing the ASCII spec to a binary look-up table.Carpathian
May 13, 2015
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Thank you Zachriel @ 238. I'm hearing you on the energy argument. But it seems a little unconvincing. Autophagy in a fasted state uses far less energy to maintain cellular integrity and mitochondrial function than the creation of a new organism to have "fresh cells". Sleep, in order to repair dendritic health, uses far less energy than the production of a new nervous system. Maintaining a stable adult organism requires orders of magnitude less energy than the nascent life cycle stages. And it doesn't pan out with reference to similar genus and species. All things being equal, big fish live longer than small fish. Small dogs live longer than big dogs. And I get it: we have to factor in extrinsic mortality. But even that seems a little simplistic. Perceived stress (not real threat) also shortens life by sympathetic nervous pathways corrupting DNA transfer and shortening telomeres. We have genetic anxious mice who die younger under no threat than genetically fearless mice who endanger themselves all the time. Q @ 239: I'm just trying to see where the dots connect and where they don't. I'm not looking to dismiss the entirety of Z's proposition even if it falls apart when overlaid in certain domains of life.jw777
May 13, 2015
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Mung: Unfortunately, only you know what you mean by “evolution.” Replication with variation and selection. This occurs in nature, and can be simulated with computers.Zachriel
May 13, 2015
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Zachriel: Across non-chaotic landscapes, evolution is much faster than random guessing or a random walk. Unfortunately, only you know what you mean by "evolution." If you mean an algorithm that guides the search toward specific areas that have a higher probability of success, yes. We know that from intelligently designed programs.Mung
May 13, 2015
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EugeneS: The current population is composed by the progammer with neighbourhood operators known to be successful in the past. 'Knowing' they were successful in the past isn't required. That's within the blackbox of the evolving population. We surmise that's the case based on our knowledge of how evolution works. EugeneS: The value of the fitness is the key. In nature you have two ‘values': ‘survive’ and ‘die’. That is incorrect. In evolution, healthy offspring is the measure of success. http://www.alternet.org/files/story_images/salmon_run.jpg EugeneS: Blind search does work. But it does not go far especially given the limited time budget. Across non-chaotic landscapes, evolution is much faster than random guessing or a random walk.Zachriel
May 13, 2015
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Zachriel, "Evolutionary algorithms have no foresight". The current population is composed by the progammer with neighbourhood operators known to be successful in the past. GAs model artificial selection, not natural selection. The value of the fitness is the key. In nature you have two 'values': 'survive' and 'die'. Blind search does work. But it does not go far especially given the limited time budget. Natural selection is nowhere near artificial selection. You have no idea what you are talking about.EugeneS
May 13, 2015
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Carpathian, you're a hoot. I'll give you that. Your article @ 252 is not a history of NUL. It's about DEL. Further, this:
Secondly, ASCII defines the purpose of chars in the code.
So it is ASCII that defines the purpose of an A or of a 6? Prior to ASCII the purpose of ringing a bell had never been revealed?
There is no need to send a zero value across a communications link over even to another task on your own computer.
Not true. Say your program was running on my computer. I'd want to send it a NUL value just to see how it was programmed to handle NUL. Don't want to reveal your source? Create a web site with an interface. I might want to send a NUL to see if I could hack your siteMung
May 12, 2015
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Carpathian, I am capable of compiling source code into an executable, but I would need the source code. Any reason you're being coy about the source? There are web sites that will host your source code for free. If you don't like GitHub (assuming a Gist won't suffice) there is also BitBucket. Want more? Alternatively, I could write the code in a language of my choosing and post it online and you can tell me how to modify it to be like yours. But that seems to be a rather silly approach to this, since you already have source code that compiles and runs.Mung
May 12, 2015
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Querius: Perhaps someone should have informed you that in science or any other intelligent endeavor, your opinion to the contrary does not constitute irrefutable proof. Perhaps someone should have informed you that ignoring evidence that is provided doesn't make the evidence go away. As noted above, see Watve at al., Aging may be a conditional strategic choice and not an inevitable outcome for bacteria, PNAS 2005. See also Ackermann et al., Senescence in a Bacterium with Asymmetric Division, Science 2003; and Stewart et al., Aging and death in an organism that reproduces by morphologically symmetric division, PLOS Biology 2005;.Zachriel
May 12, 2015
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Zachriel @ 243 . . .
Querius: Micro-organisms that reproduce by fission do not age. Zachriel: That is incorrect.
Perhaps someone should have informed you that in science or any other intelligent endeavor, your opinion to the contrary does not constitute irrefutable proof. Goodbye. -QQuerius
May 12, 2015
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>irb irb(main):001:0> "hello\u0000world".force_encoding("UTF-8").ascii_only? => true irb(main):002:0> "hello\u0000world".each_codepoint {|c| print c, ' '} 104 101 108 108 111 0 119 111 114 108 100 => "hello\x00world" irb(main):003:0> exitMung
May 12, 2015
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Mung: I could send the EXE to you if you give me an email address.Carpathian
May 12, 2015
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Carpathian:
I have written the program and the code you keep having trouble with runs just fine.
Good. Do we get to see it? There are sites where you can share code, such as GitHub. See also: https://gist.github.com/ [Can't recall if that requires having an account or not.]Mung
May 12, 2015
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Mung: Here is a little history of NUL: "Code 127 is officially named "delete" but the Teletype label was "rubout". Since the original standard did not give detailed interpretation for most control codes, interpretations of this code varied. The original Teletype meaning, and the intent of the standard, was to make it an ignored character, the same as NUL (all zeroes). This was useful specifically for paper tape, because punching the all-ones bit pattern on top of an existing mark would obliterate it.[28] Tapes designed to be "hand edited" could even be produced with spaces of extra NULs (blank tape) so that a block of characters could be "rubbed out" and then replacements put into the empty space. "Carpathian
May 12, 2015
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Mung: I have written the program and the code you keep having trouble with runs just fine. Secondly, ASCII defines the purpose of chars in the code. If I send another computer the value 7, it is supposed to ring the "bell" and not use that char for another purpose. That's what standards are for. I usually send and receive binary data when I expressly need it but I don't here. I use ASCII as the standard is defined both as data and as a means of control over that data. When you are dealing with modems, teletypes or other computers, if you don't comply with their protocol, it's your fault when your data doesn't get through. If I allow someone to log on to my computer through a modem, I can't assume that the modem will allow every char through. These are real world problems I have constantly dealt with in the field. There is no need to send a zero value across a communications link over even to another task on your own computer. If every other device my system talks to cannot handle a binary zero, how can I force them? Again, this has nothing to do with whether a Weasel implementation needs to be re-compiled when changing a target string as my program handles it fine. You simply just type in a new string.Carpathian
May 12, 2015
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EugeneS: Again you disregard the fact that in order for the ‘evolutionary’ algorithm to succeed it needs to be able to: 1. measure fitness with enough accuracy; 2. steer search towards better fitness according to the measured gradient (that is usually amplified in the algorithms to get what the programmer wants). Fitness doesn't have to be entirely accurate, can be balanced against other factors, and it is quite possible to include stochastic events. The "steering" is intrinsic due to the relationship of the evolving population and the fitness landscape, just like water is steered as it flows over a geographic landscape. EugeneS: For this, it needs foresight and knowledge of previous ‘hits and misses’. Evolutionary algorithms have no foresight. Whatever knowledge there of the past is entailed in the composition of the current population. EugeneS: Even the blind search algorithm needs to be able to know what it wants to achieve. The evolving population has no general knowledge of the fitness landscape, only the relative fitness value for a given individual at a given time.Zachriel
May 12, 2015
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Carpathian:
You are talking about ASCII as if it is purely binary.
No I am not. ASCII is an encoding. You seem to think that because you use a char pointer that your program is comparing, for example, an A to an A. It's not.
Convert text into ASCII number format. For example A is 065. Text in a computer is stored as numbers called ASCII numbers with each letter having its own number. Input text to convert to these ASCII numbers. ASCII is short for American Standard Code for Information Interchange. With applications in computers and other devices that use text, ASCII codes represent text. Based on the English alphabet, ASCII is a character-encoding scheme. ASCII was originally developed from telegraphic codes. Computers can only understand numbers, and ASCII codes are numerical representations of characters that a computer can understand. Examples of characters are a, 1, or >. For example, 097 is the ASCII numerical representation of the character a. ASCII covers over 100 characters with some of these characters being control characters that control how text appears. http://www.unit-conversion.info/texttools/ascii/
I am not confusing characters with numbers, nor am I confusing numbers with what they represent. That is what you are doing. Further, you ought to be smart enough to know this since it's staring you in the face right there in your own code. if(Target[Position] == PopMember[Position]) Which of the following statements will evaluate to true, and why? 'A' > 'a' 'A' > 'a' C:projectsruby_scripts>irb irb(main):001:0> 'A' > 'a' => false irb(main):002:0> 'A' true What does it even mean to say that one letter is greater than or less than a different letter? Is the computer comparing letters or numbers?Mung
May 12, 2015
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Zachriel, Again you disregard the fact that in order for the 'evolutionary' algorithm to succeed it needs to be able to: 1. measure fitness with enough accuracy; 2. steer search towards better fitness according to the measured gradient (that is usually amplified in the algorithms to get what the programmer wants). For this, it needs foresight and knowledge of previous 'hits and misses'. In other words, every 'evolutionary' algorithm presupposes control and the existence of a target (or targets). Even the blind search algorithm needs to be able to know what it wants to achieve. Nothing of the sort is happening in life. Evolutionists don't realize that they are trying to sell Artificial Selection algorithms as 'algorithms that mimic natural selection'. They do not mimic it. The phrase 'evolutionary algorithm' is bogus. As soon as there is an algorithm, there is an intended target, fitness function and control that steers search towards the goal state. The fitness function may be implicit but in order for the 'evolutionary' algorithm to succeed in practice, it needs to be more than blind search, i.e. it needs to employ artificial selection. Everything else is the usual smoke in mirrors.EugeneS
May 12, 2015
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Mung:
I don’t think you can write the program that you apparently think you can write.
I have done just that. With all the frustration of talking to you I bit the bullet and started writing it Sunday night. I accept all printable chars and support command-line args. One of those args is to put it into what I call DNA mode where the set of chars accepted are restricted to 'ATCG'. It very quickly converges on the target string with only 4 codes.
But whether it will mean anything will depend on the claims you make for it. For example, what do you mean when you say we are wrong about the Weasel program?
Your claim and those of others is that a Weasel implementation cannot be written without re-compiling the code. That is wrong.Carpathian
May 12, 2015
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Mung:
Second, and this is a point you’ve still failed to admit to as far as I can tell, it will not accept any ASCII string as a target. And for it to do so, you will need to re-write the code.
You are talking about ASCII as if it is purely binary. I am using ASCII as per spec. ASCII is a specification for communication between computers, not simply a table of values. Chars such as ACK, NAK, STX, ESC, etc., are signaling and control chars, and are used for transmission control and are not printable. NUL is a special char that is neither a printable or control char. I will not treat any out of band data as data when ASCII doesn't define it as such. I am using ASCII as it was intended. I accept ASCII, not binary.Carpathian
May 12, 2015
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Carpathian:
... if I wrote a program that did everything that Weasel does, but accepted any input string without changing the algorithm, would that make any impact on you about this argument? To put it in a shorter way, if I could actually prove with running code that you are wrong about Weasel and Weasel type programs, would that mean anything?
By all means code something up. You can find weasel programs on the web coded in many different languages. http://rosettacode.org/wiki/Evolutionary_algorithm#C But whether it will mean anything will depend on the claims you make for it. For example, what do you mean when you say we are wrong about the Weasel program? I don't think you can write the program that you apparently think you can write. Perhaps start with a simple Weasel itself, a version of Dawkins original program, and we can go from there. That way we can track how the program needs to be modified from the original and how performance is affected. http://en.wikipedia.org/wiki/Weasel_program#Example_algorithm
With your reasoning floating point numbers are impossible to input to a computer since you can’t actually put floating point numbers into an array of type ‘char’.
You're missing the point. The question to ask is, can an ASCII NUL be entered from the keyboard?Mung
May 12, 2015
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Carpahtian:
The way this started is that you asked me what parts of the code had to be re-written if a different target was desired. I said none and you disagreed. After all we’ve talked about, do you still believe that to be true?
Yes, I still believe that to be true, and it should be obviously true. First and foremost you never had working code. It follows that your code would need to be re-written just to get it to compile much less function. Second, and this is a point you've still failed to admit to as far as I can tell, it will not accept any ASCII string as a target. And for it to do so, you will need to re-write the code. Third, you already admitted it would not accept just any target. So what are you arguing about? I ask if the target is changed will the code need to be modified, and your answer is not as long as the target isn't changed to something the code would have to be modified to handle?Mung
May 12, 2015
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