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The Minkowski Challenge

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AlbertGodwin

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The Minkowski Challenge:
A practical challenge to evolution


I have just taken the permission of Fady Bahig to submit the full text of the Minkowski project and the full text of the chapter that discusses it.

Now the people who support evolution : Here is the challenge. Can you make this program become encrypted ?

NB: The project and the chapter are taken from Bahig's Novel 'The Journey of The Fool':

lulu.com/content/438633
 

AlbertGodwin

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Here is the chapter where two characters discuss the Project, Marcus Minkowski and Faust Amoyo,

5

Watching the blind watchmaker

Note: This chapter includes deep details that need a basic knowledge of evolutionary biology and computer programming. If you are not experienced in those fields please skip to the next chapter. Bypassing this chapter will not prevent you from following the storyline.

Note: You can find the full commented sources of the project in the appendix.


“So Marcus,” I said as I opened my eyes, Marcus was sitting on his wheelchair in front of the PC, “What’s your newest victory?”

“I did it!” he said with enthusiasm as he was almost jumping on his wheelchair with joy, “W.B.W! The program evolved. Now I have a functional, non detectable program!”

“Marcus, I don’t remember much about your project. Will you please remind me of the basics?”

“Sure!” cried Marcus with enthusiasm, I knew how Mary Shelly could speculate about mad scientists; perhaps a distant ancestor of Marcus was her neighbor, “I chose to write the program in assembly. Assembly shares many features with our own biological code. In our bodies, each three letters of DNA bases form a single amino acid. In assembly, most instructions arise as collaboration between two or three bytes. When a DNA base mutates the produced amino acid will most probably be altered. In assembly, if a byte changes the instruction will also change. Now I have made a new folder called ‘EDEN’. In this folder I have put two files. GEN.COM and SELECT.EXE. Now look! Are there any other files?”

“No.”

“Great.” Said Marcus as he switched to DOS.

“Why did you leave windows?”

“I don’t like it. I honestly think that windows is a cheap tool for newbies. OK, sure it helps me work. But I only feel at home with the tough, manly climate of DOS.”

“Ok! Ok! Go on!”

“Now I will execute GEN.COM. See what happens?”

“Oh!” I cried as I watched a flood of COM files being created.

“Now GEN.COM has created COM files from AA.COM to ZZ.COM. Those files are almost perfect copies of GEN.COM but they have some altered bytes. When GEN.COM makes those files, it creates copies of itself. But it sometimes, totally randomly make some intentional copying ‘mistakes’. This is supposed to emulate the imperfection of the DNA copying procedure in our body. So some copies will have altered, extra or missing bytes of the original program.”

“Yes, ok. Go on!” I said trying to suppress my laughter. I didn’t understand anything.

“Now watch what happens.” Said Marcus as he executed SELECT.EXE with a certain large parameter.

“Wow!” I said, “This program is deleting all the files. What did we get of all that?”

“No!” cried Marcus angrily as a teacher who spent a couple of hours teaching a kid alphabetic, “Not all the files were erased! Only those carrying a certain sequence of bytes! Look!” He said as he executed a certain command, ‘Dir ??.COM’. 38 generated files were not eliminated.

“The originally created files are from AA to ZZ,” he said, “That means that they are 26*26 files, making 676 files.”

“Yes, that’s right.”

“Now out of the 676 files only 38 survived the massacre. You know why?”

“Why?” I asked with wide innocent stupid eyes.

“Because they are unrecognizable!” cried Marcus angrily, “GEN.COM made some mutations when it was copying the targeted sequence of bytes. So each and every one of those 38 copies doesn’t have the targeted sequence of bytes. They were all unrecognizable and thus, not eliminated.”

“So they are all evolved programs?”

“No!” said Marcus sadly, “Most of them are not functional. Mutations are usually harmful, they corrupt the instructions and so the mutant copies usually crash. Now comes the hard part. I will copy each file of those mutants into a new folder and execute it. All the copies that will crash or fail to reproduce will be erased manually. If a copy can reproduce smoothly and produce functional offspring as well, it will be considered an evolved file. So there is a double challenge, the file must be undetectable and at the same time it must be functional. Now Faust I want you to notice something. Can you see this text?”

“Now creating?”

“Yes, That’s it. Now if the search string was that text the program would have much easily evolved, since the text was to be only altered. The program will still be executable if the text was carrying a spelling mistake.”

“I see…”

“But definitely I intended to make the program scan executable code, it would have been totally uninteresting if I made that text my search string.”

“So now you will test the mutant copies one by one?”

“Yes. This will take sometime, you can do anything until I am done.”

“Ok, I’ll go and…”

“Wait!” Marcus cried in enthusiasm.

“What is it?”

“There is an interesting thing that I had thought of as I was talking to you about that text.”

“I’m all ears!”

“You see, Faust. There is a very strong selective force that protects the executable part of the program. If any part failed to operate the copy will not be functional.”

“Ok.” I replied gladly, I understood what he meant.

“But if a certain copy was undetectable, functional, yet the text ‘Now creating’ was corrupted, it will still ‘live’ peacefully.”

“That’s right.”

“You see, as if mutations are ‘noise’ that is constantly bombarding a message, trying to corrupt it. When they hit the wrong place, the individual dies, or is not even born. But there are some varying degrees of ‘tolerance’. In case of the text, there is much freedom. No matter how badly that text is mutilated, the individual will live normally.”

“I bet this has a parallel in the biological version of life!”

“Exactly! You see, there are VIGs, very important genes, like those responsible for the replication of cells…etc. You will see quite few differences between the human and the, say, plant copy. Because such genes are not to be toyed with, the least alteration and the fetus will die. But other genes are quite ‘tolerant’, like the genes determining hair color. It won’t kill you to have a different hair color. That’s why humans have a good mix. But there is more, some genes are totally unused. They are simply fossil genes. Those are just like this text, they are absolutely tolerant to each and every mutation. Scientists determine when those genes ceased to be used by seeing how much they were deformed by the constant ‘noise’ of mutations.”

“Oh my God! I got it! You mean that if the text was ‘Nbw creatong’ then perhaps this is the 20th generation while if the text was ‘Nzigcreltinq’ then this is perhaps the 200th or 300th generation?”

“Exactly!” Cried Marcus with immense pleasure.

“Wow! It felt really good to understand that. I could feel a certain pleasure… I can’t describe it…”

“Not as juicy as sex but far more sublime, almost as exotic as mysticism but ways more realistic, denuding the thought of God through his own game of life… the erotic ecstasy of being the first to know.”

“Wow!” I cried with great pleasure, “I didn’t know that you are a poet, too!”

“Well,” said Loki in anger, “I’d really appreciate it if you’d stop dancing striptease with the universe and feed yourself a little, I am getting hungry!”

I brought myself a sandwich and sat for about half an hour watching Marcus isolate and test each file. Every time that he executed a file the PC crashed and he had to reboot the PC and erase the copy. So he decided to investigate each file using a debugger to see if it will probably execute. Finally, all the copies were eliminated.

“Well,” said Marcus awkwardly, “I was not so lucky this time, but it’s OK. Evolution needs too many trials till a good thing is acquired.”

“But didn’t this indicate that your species became extinct? All the files failed, no?”

“No, that’s wrong!” cried Marcus angrily, “Because here I am selecting for mutations that I have just created. In real life numerous mutants exist long time before selective pressures are applied to an organism.”

“Yes, I must admit I missed that!”

“Now let me show you the copy that I have evolved this morning when you was still asleep.”

Marcus swiftly moved to another folder where a single file, GJ.COM, was present. He quickly entered the instruction ‘Debug GJ.COM’. Then he entered ‘u 122’ quickly a small bunch of assembly instructions appeared.

0B55:0122 BFB801 MOVDI,01B8
0B55:0125 BE0001 MOVSI,0100
0B55:0128 52 PUSHDX
0B55:0129 B9B800 MOVCX,00B8
0B55:012C E86500 CALL0194

“Look here, that’s where the byte sequence was altered!” said Marcus as his finger was about to penetrate the poor screen, “Oh poor me! How far I am from understanding the madness of mother nature! If anybody told me that an extra byte would have saved a copy from the massacre, I would have bet it would be a NOP, CLC, STC or something like fake one-byte instructions that polymorphic engines put. But a PUSH DX? That’s totally mad! Yet who cares! It works! That PUSH did not interrupt a PUSH/POP pair so the program still runs smoothly. That’s how evolution works. We are not the masterpiece of a great engineer; we are the result of numerous ‘layers’ of plumbing.”

“Plumbing?”

“Sure! Look at your body. It’s like a giant robot that was created in the industrial revolution and operated by steam, a medieval machine of endless features amalgamated with endless flaws. We have reached the moon, yet a small virus can send us to the graveyards. If we carefully consider our DNA, we will neither recognize the fingerprints of Ahura Mazda nor of Ahriman. There only reside the fingerprints of the fingerless blind watchmaker. In fact, evolution is not even a blind watchmaker, for it is ok with it to create cheap pencils instead of elegant watches. And what is the difference between pencils and watches to the blind, who can neither write nor see what time it is?”

“Eh, Marcus, is your leg feeling better now?” I cautiously asked.

“Ya! Sure! It doesn’t hurt at all. Things could have gone much worse if Roy had shot my heart or head, but a good strike of Madame Pauline’s frying pan secured him a trip to the stars.”

“I never knew that this guy was that mad! Kill you just for refusing to help him?”

“You know that his parents were going mad about his repetitive failures, and he was also half-drunk then.”

“Well, they shouldn’t be so worried about him now. He will spend a long time in jail.”

“Oh, no, he won’t,” replied Marcus in apathy, “His father’s gonna throw them a bunch of money sacks and they’ll be good to young poor Roy…”

“How can this happen!” I angrily asked.

“Well, it’s a dirty world,” said Marcus with a sigh, “In the American films the bad guys always go to the jail, because there is a story writer who always make sure that it will happen. But who’ll punish the baddies in our directorless world?”

“What am I saying?” cried Marcus as he quickly regained his cosmic spark, “I must tell everybody about the success of my project. It’s gonna be a big hit for the Nature Watcher and maybe Johan will send me more money for that one.”

“Oh, yeah, Johan…Wait a minute!” I suddenly cried.

“What?”

“You… I think that you told me that this program was supposed to evolve encryption, didn’t you.”

“Eh, well,” replied Marcus with a faint smile, “Yes, but that’s not obligatory. The program found that it was easier to slightly alter its code to avoid detection.”

“Aha!” I replied in a triumphal manner, “Now can you somehow direct the program into evolving encryption?”

“Well,” Marcus replied with his right hand rubbing his chin and his eyes gazing at the ceiling, “Perhaps I can make the selector detect numerous parts of the program… eh, I will also alter the elimination of the non-mutants from 100% to a lower probability. Yes this can make it. Eh…No! The program will most probably slightly alter all the targeted code snippets. I just don’t know…”

“So you can’t make this program evolve encryption, let alone polymorphism!”

“Well,” said Marcus as he adjusted his thin body on the wheelchair in an evident sense of unease, “No! I just can’t think of any selective force that would force my program into evolving encryption. If the selective pressure was very tolerant, most copies will be slightly altered. If the selective pressure was drastic, all the copies each time will be deleted. Even if I’d put many search sequences for the program, each sequence will be slightly altered. I can’t think of any selective strategy that would force the program to evolve encryption.”

“Well,” I said with a smile, glad to prove that I could once defeat Marcus’ genius mind, “Think a little! Perhaps you forgot about something!”

“No!” he said nervously as he boxed the chair arm, “Encryption requires a decryptor to decipher the encrypted body and it also needs a part to encrypt the program before it is copied. Each part consists of a handful of bytes. I didn’t put blank places for any of the two. And even if I filled the appropriate sequences with NOPs it will make no difference. It’s too improbable that either of the two would emerge ‘just like that’. And even if any of the two would ‘miraculously’ exist it would still be useless, in fact it would even be fatal for the file that holds it.”

“Why?”

“If the decryptor evolves alone, it will decrypt bytes that are already unencrypted, thus it will corrupt the main body of the program. And if the encryptor evolves alone, it will produce encrypted offspring that lack a decryptor to decipher them. Thus the offspring will be actually corrupted files.”

“I see…”

“Even if I’d put in the whole encryptor and decryptor and just put the XOR key as zero the resulting program will be practically unencrypted and thus be eliminated by the selector, for the byte sequence will still be visible.”

“Wow! Things are so complicated!” I said as I drank some coke in delight, “So what about real evolution. Can we force a unicellular organism to become a multicellular one?”

“I don’t know. In fact I don’t know much about the fine mechanisms involved there, perhaps a certain gene can decide if the two dividing cells should stay attached to each other after division or just swim away.”

“And how can we selectively force the cells to stay united?”

“Eh, I don’t know, perhaps if a certain organism can eat each alone but fail in eating both together…”

“Maybe, but I think it’d be easier then for the cells to evolve some toxins or flagella.”

“Well, there are many features that would have proven to be exceedingly useful if they evolved. But they simply didn’t. Because, as you said, there is almost no selective way to force them to exist.”

“Like…?”
 
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AlbertGodwin

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“Like a TVs in your trunk. Let’s suppose that a certain animal identified a new vicious carnivore. If it could make the rest of the herd see the picture of that carnivore, it would be very useful.”

“There are already animals that can change the color of their skin.”

“Yes, chameleons. But reptiles are solitary animals. They needn’t broadcast anything on their TVs, because there are no spectators around to watch. See why their already incredible feature couldn’t be further stretched into becoming an awesome one?”


“That makes sense. But I doubt that the evolution of many existing organs is less improbable.”

“What do you want by this?” Asked Marcus with a thoughtful look.

“I think that all the selective challenges will only trigger minor improvements. I just can’t think of any selective force that’d force an organism into evolving major capabilities.”

“Like what for instance?”

“Hmm, like rational thinking. You can put more obstacles, more predators and more challenges. They will at best result in more speed, more camouflaging abilities, and perhaps some tricky behavior… but logic?”

“Well, I must admit that the evolution of logical thinking is the biggest challenge out there…”

“I don’t think so,” I replied with a proud deducing smile, seeing how my philosophical background could help me challenge the more scientifically-oriented Marcus, “Perhaps the most challenging feature is self awareness, consciousness. An animal can have eyes that would see an approaching lion, and then send the image to a system that would realize that this means ‘danger’ and order the legs to run, but why would there be an ‘I’ that watches all that?”

“Well, this reminds me of solipsism, the philosophical position that says that I am the only ‘really conscious’ one here, all other people react to sounds and pictures quite normally without having real consciousness; without really seeing or hearing. They are just zombies. Now as far as I understand you are asking why evolution didn’t only produce human and animal zombies to save effort.”

“Exactly, why?”

“Well, perhaps one way to respond is to argue that consciousness is necessary for such complex computational processes in the mind, that no animal can react with such vividness unless it does have a certain ‘I’ inside. The other way is to say that this is simply the way things happened, because our common ancestor just happened to be conscious, and that there could have been a planet where evolution produced only zombie creatures.”

“Wow,” I thought, “This guy is smarter than what I thought.”

“Eh, So!” I attackingly resumed, “Now let’s get back to the main point. You did experience the difficulty, and perhaps the impossibility, of evolving an encrypted program or virus. Do you really think that all the features that we and other animals have are easier to explain and to be selectively chosen than mere encryption?”
 
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AlbertGodwin

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And Now Comes the Source code of the project

1

W.B.W. Commented Sources

Those are the commented sources of the W.B.W project discussed by Marcus Minkowski and Faust Amoyo in the first and fourth chapters of the Romanian section of the novel.

According to the novel, the whole project was written by Marcus Minkowski to illustrate evolution. He read Dawkins’ ‘The Blind Watchmaker’ and became obsessed with the biomorphs. Later, Marcus decided to make an even more powerful illustration of evolution by watching a living creature evolve. And what can that living creature be but the only life form that humans created? A computer Virus!

Marcus later Decided that he should remove the viral code and replace it with a benign program that replicates in its own-created files, thus he could openly take credit for the program. An extra bonus for that move turned out to be a faster, safer and easier testing.

The Project consists of two files. The first one is a COM file, called GEN.COM. This COM file is written in assembly. It generates files from AA.COM to ZZ.COM. These files resemble the mother file almost completely. Yet they carry certain mutations. Mutations can be either extra bytes, deleted bytes or altered bytes.

The Second file is a program written in Basic. It is called SELECT.BAS. It can be executed via Qbasic or turned into an EXE file with QuickBasic. It will scan all the generated files, from AA.COM to ZZ.COM, for a certain sequence of bytes and will eliminate each and every copy where that code is present. This program is supposed to emulate the antivirus software and may represent a predator or a parasite. Yet it is not the only selective force involved. Marcus would also try to execute all the copies that survived the scanner massacre and test them for smooth execution. Most of the mutants were, as he did expect, nonfunctional and would usually result in system crash. Marcus also deleted all those copies. Yet, he was not troubled at all by their presence for they emulated the defected offspring that were spontaneously aborted.

Watching The Blind Watchmaker
===
How it works:
1- Make a new folder. Put in it the file GEN.COM and the file SELECT.EXE (or SELECT.BAS and Qbasic if you didn’t compile it).
2- Run GEN.COM, you will see files created from AA.COM to ZZ.COM
3- Run SELECT.EXE, you will see that most of the files will be eliminated.
4- Manually test the few remaining files for proper execution. Copy each into another empty folder, rename it to GEN.COM and execute it. Delete all the files that fail to reproduce or crash the system.
5- If you are left with a file that still works and replicates giving functional offspring, then the program did indeed evolve. That’s what happened with me, and with Marcus in the novel. I believe that this confirms microevolution. Yet can you force this program to evolve encryption? This is the Minkowski challenge. He failed and gave up, saying that the microevolution he watched happen was enough. I also didn’t end up with any encrypted version of this file in my numerous trials. For theoretical discussion of the consequences of this program please read the discussion in the fourth chapter of the Romanian section of the novel.

; Watching The Blind Watchmaker
; ===
; First: The Replicator (GEN.ASM)
;
; Copyright © 2006 by Fady Bahig
; This program was written by Fady Bahig in 2006
; for the novel ‘The Journey Of The Fool’
; The W.B.W project was supposed to be written
; in the fiction by Marcus Minkowski
; This is the replicator part of the project
; Upon executing this COM file it will generate
; Mutated Copies of itself from AA.com till ZZ.com
; Mutants can be missing bytes, with an extra bytes
; or with altered bytes.
; To compile put in GEN.ASM then compile with A86
; GEN.COM will be then produced.

Code_begins:
jmp Code_start
Message: db "Now creating "
Filename: db "AA.COM",0 ;File name of the first file
db 13,10, "$"

Code_start:
push cs
push cs
pop ds
pop es

; BUG! Marcus should have put some NOPs here to avoid the
; jump in a smaller mutant from going to the above instructions.
Make_next_file:;This loop generates files
nop ;Those nops are necessary here because if a byte is
nop ;added the backwards jump location will be
nop ;corrupted. So I decided to put them for safety.
nop

; The following 4 instructions are the search string.
; For any copy to avoid being detected and deleted,
; the following 12 bytes must be altered somehow
; to avoid detection.

lea di,offset Code_ends;Make a copy at the heap
mov si,offset Code_begins;A copy of myself
mov cx,(Code_ends-Code_begins);My size
copy_loop:
call Get_random_number;Will I mutate this byte?
cmp al,1h
je Mutate;Yes?

Movsb;No
cont_replicate:
loop copy_loop;Copy all the bytes
jmp continue

Mutate:
call Get_random_number;What is the type of the ;mutation?
cmp al,10h
jb add_byte;Will we add a byte?
cmp al,20h
jb sub_byte;Will we remove a byte?
call Get_random_number ;Will we change a byte
inc si
stosb
jmp cont_replicate

sub_byte:;We will remove a byte
inc si
jmp cont_replicate

add_byte:;We will add a byte

movsb

call Get_random_number
stosb
jmp cont_replicate

continue:
mov dx,offset Filename;Create a file
mov ah,03ch;with new name.
xor cx,cx;Copy all the data,
int 21h;And close.
xchg bx,ax
mov ah,040h
mov dx,offset Code_ends
mov cx,offset (Code_ends-Code_begins)
int 21h
mov ah,03eh
int 21h

mov ah,09h;Print message to say
mov dx, offset message;that the file is created
int 21h;successfully

cmp word ptr [Filename],"ZZ";Did we reach ZZ.COM?
jne stillmake;No? Make another file
int 20h

stillmake:

inc byte ptr [Filename+1];Calculate the
cmp byte ptr [Filename+1],"Z"+1;name of next file
jne skip_fix
mov byte ptr [Filename+1],"A"
inc byte ptr [Filename]
skip_fix:

jmp Make_next_file;Generate the next file


Get_random_number:;Get a random number
in al,40h;This procedure is
xchg al,ah;Used to make mutations
in al,40h;And see if we will make one.
xor al,ah
add al,ah
ror al,1
xor ax,bx
add ax,cx
sub ax,dx
xor al,ah
ret


db 10h dup (0) ; A reserve buffer so that if a mutant is longer
Code_ends: ; by a byte or two, it will still be copied

;GEN.ASM ends here

' Watching The Blind Watchmaker
' ===
' Second: The Selector.
' This program was written by Fady Bahig in 2006
' for the novel ‘The Journey Of The Fool’
' The W.B.W project was supposed to be written
' in the fiction by Marcus Minkowski
' This is the selector part of the project
' Upon executing this program it will scan for all the
' the generated COM files from AA.COM to ZZ.COM
' and will erase each and every copy carrying the search string:
' That is a certain sequence of bytes.
' This program can be run with Qbasic or can be
' turned into an EXE file by QB. In case you desire to
' turn it into an EXE, you must alter the first few lines. See
' comments for details
' To run with Qbasic put in SELECT.BAS and then open it
' with Qbasic and then choose start from run

DIM A AS INTEGER
'stext$ = COMMAND$
' activate if making EXE then run select.exe with the sequence of bytes as a parameter
' i.e. : Select BFB801BE0001B9B800E86500

stext$ = "BFB801BE0001B9B800E86500"
'Deactivate if EXE

IF stext$ = "/?" OR stext$ = "?" OR stext$ = "" THEN
PRINT "W.B.W Selector"
PRINT "Deletes all the ??.COM files"
PRINT "carring the byte sequence"
PRINT "enterd as a parameter."
PRINT ""
PRINT "And ..."
PRINT "Marcus Minkowski says to you all"
PRINT "VIVA ROMANIA ;)"
END
END IF

FOR l1 = 65 TO 90 ' Scan file names from AA to ZZ
FOR l2 = 65 TO 90
file$ = CHR$(l1) + CHR$(l2) + ".COM"


OPEN file$ FOR BINARY AS #1
b = -1 ' Make a text string of all the bytes
text$ = ""'In the file
DO UNTIL EOF(1)
b = b + 2
GET #1, b, A

b$ = HEX$(A)
IF LEN(b$) < 4 THEN b$ = STRING$(4 - LEN(b$), "0") + b$
b$ = RIGHT$(b$, 2) + LEFT$(b$, 2)

text$ = text$ + b$
LOOP
CLOSE

' If the byte sequence is present in the file, eliminate it and
' inform the user
IF INSTR(text$, stext$) <> 0 THEN
KILL file$
PRINT file$ + " was eliminated."
END IF

NEXT l2
NEXT l1
END

' SELECT.BAS ends here.
 
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Brennan

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HI AlbertGodwin.

1) I notice from the code that the program is limited in it's ability to evolve.
2) The selector program is 100% efficient - in reality this is not the case.
3)I am still not sure what the relevance of 'encryption' is.

In light of these objections, I am afraid this does not look like an adequate representation of evolution, therefore unless these objections can be overcome then this whole argument is a strawman.
 
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MatthewDiscipleofGod

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Brennan, are you an evolutionist? If so non fellowship posts like this one are not allowed here.

HI AlbertGodwin.

1) I notice from the code that the program is limited in it's ability to evolve.
2) The selector program is 100% efficient - in reality this is not the case.
3)I am still not sure what the relevance of 'encryption' is.

In light of these objections, I am afraid this does not look like an adequate representation of evolution, therefore unless these objections can be overcome then this whole argument is a strawman.
 
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chaoschristian

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The Minkowski Challenge:
A practical challenge to evolution


I have just taken the permission of Fady Bahig to submit the full text of the Minkowski project and the full text of the chapter that discusses it.

Now the people who support evolution : Here is the challenge. Can you make this program become encrypted ?

NB: The project and the chapter are taken from Bahig's Novel 'The Journey of The Fool':

lulu.com/content/438633

Brennan, are you an evolutionist? If so non fellowship posts like this one are not allowed here.

To be fair, please note the OP invited the open discussion of this.

If the OP does want open discussion of this, then may I ask that he request a Mod to move this to the open forum so that it may be discussed?
 
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laptoppop

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I agree - this is better for the main open forum. It actually sounds interesting in that context.

Following the links, there are apparently some other software alternatives - I don't know anything about this, and it would be interesting to know the positives and negatives.
 
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laptoppop

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OK, the way I see it is this is an attempt to model in software the actual working of evolution and mutations, etc. This sounds fascinating. In looking at the links, I see other efforts toward this as well. I just don't know anything about these efforts. Given my "day job" is heavy on software and IT, I am especially interested. Is there any online source for info - positive AND negative - about such efforts?
 
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Late_Cretaceous

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This is only helpful if you can get an evolutionist to agree with you about the definition of a mutation. They don't agree with the "harmful mutations" premise. They have redefined the word mutation. (That's all I know. Don't ask me to explain any more. It's just the most recent point I have been ridiculed on.)
From Freedictionary.com a handy little definition of the word mutation for you

mu·ta·tion (my
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n) n.1. The act or process of being altered or changed.
2. An alteration or change, as in nature, form, or quality.
3. Genetics a. A change of the DNA sequence within a gene or chromosome of an organism resulting in the creation of a new character or trait not found in the parental type.
b. The process by which such a change occurs in a chromosome, either through an alteration in the nucleotide sequence of the DNA coding for a gene or through a change in the physical arrangement of a chromosome.
c. A mutant.

4. Linguistics The change that is caused in a sound by its assimilation to another sound, such as umlaut.

Mutations are changes in the genetic code, nothing more. Some are harmful, some are neutral, some are beneficial.

Who has been trying to change that definition. It seems pretty strait forward. Can you provide a link to a post where someone tried to change the definition please.


An example of a mutation

On a string of DNA the "letters" UCC could be changed due to mutation to UCA. IN this case it would be a neutral mutation since both code for the amino acid Serine.

If UCC changed to UUC, you would wind up wit a different amino acid incorporated into the protein chain. This may result in a neutral, beneficial, or harmful mutation depending upon how it changes the characteristics of the protien.

Since proteins are composed of hundreds of amino acids linked together, the substitution of one amino acid may have no effect at all. On the other hand, it could be crititical in the overal shape of the protein (affecting protein folding) which could result in major changes to the nature of the protein.


Mutations occur when ever there is imperfect replication of a DNA sequence. Do you know of any system in anture that is 100% perfect?
 
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Late_Cretaceous

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How can someone justify accusing someone of intellectual dishonesty (i.e. changing the definition of a word), and not back up thier accusation with proof that this was actually ever said - without themselves becommming intellectually dishonest?
 
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Assyrian

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Let me get this straight, the claim is that if the computer program doesn't evolve encryption, then biological evolution can't happen??

Could there be a few non sequiturs in this, as well as a misunderstanding of how evolution actually works?
 
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shernren

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In the specifics of the challenge one must note that the challenger ("I") assumes that logical thinking has no adaptive purpose and therefore cannot be evolved. This may not be true; social behaviour is strongly observed among animals of all sorts, and logical thinking may be what is needed to robustly manage social behaviour, therefore providing a sort of adaptive motivation to evolve intelligence. Not that evolution can actually "want" something to evolve and have it evolve, but I am trying to engage the (slightly erroneous) concepts of the challenge itself, and even within that conceptual framework there would be a clear adaptive advantage to logical thinking.

I think one of the biggest problems to the computer sequence idea itself is the problem of specificity. In computer programming there is a discrete relationship between source codes and functions. What I mean is that in a computer program it is "all or nothing": either a particular instruction does something (whatever it is) or it does nothing (or crashes the system) and there is no possibility of gradualism because the meaningful codes are often separated by nonsense. For example:

Code Function
pop -------------------------
oop -
nop -------------------

(attempting to simulate a bar graph here)

You can see that if I graphed function against code, there would be a sort of spiky graph, and "evolution" would have to jump from one spike to another to get anywhere. Clearly that would be impossible.

When we talk about proteins, amino acids and genetic instructions, on the other hand, we are talking about real molecules with complex and subtle interactions, where it would certainly be possible for one thing to substitute for another. For example, consider the three amino acids alanine, glycine, and valine. (structural formulae here: http://upload.wikimedia.org/wikipedia/commons/c/c5/Amino_acids_2.png ) They all have small non-polar side-groups causing hydrophobic behaviour (for non-chem-geeks, hydrophobic means like how oil avoids mixing with water), and so I would reason that they can be suitably interchanged to give roughly equivalent behaviour, because if I changed say glycine with alanine, the affected region (of the side group) would still be hydrophobic but now slightly larger. (To mutate between one and the other would be easy, too: all three amino acids have U_ _ RNA codons, meaning that a single-base substitution in the second base would switch one to the other.)

That is why proteins can evolve satisfactorily even if programs cannot. Alanine is roughly similar to glycine, not identical so that there is no change, but not too wildly different that the protein is altogether upset. And it only takes a single-base mutation to substitute between any three of them. Is there any equivalent in computer programming? Is there another instruction which is roughly similar, but not identical to, say "PRINT", and can it be easily reached by mutation?

There are other problems as well, such as that in real evolution there are multiple niches and so multiple directions for an evolutionary pathway; the simulation has a static environment while in real life not only are environments dynamic but frequently changed by the evolving life itself; proteins do not evolve isolated functions but evolve in the context of surrounding functions performed by other proteins, and on a larger scale the same can be said of species. But I think there is a basic disconnect in terms of the difference between the discrete nature of digital information in programs and the continuous nature of analogue information in the chemical behaviour of a protein in its surroundings.
 
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Assyrian

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Not that evolution can actually "want" something to evolve and have it evolve,
I think this is one of the very basic flaws in the argument, misunderstanding of how evolution actually works. While it is a much more detailed and convoluted argument, it is basically the old:

If evolution is true, why didn't we evolve wings?
or
If evolution is true, why do mothers still only have one pair of hands?*

Evolution doesn't think to itself, "oh I know, wings would be handy I must evolve some of those" It doesn't plan ahead, "encryption would be handy, I'll go in that direction".

*Obviously a baby born with four pairs of arms would be seriously disadvantaged. The mother would never be able to get babygrows and cardigans to fit and the baby would be in risk of hypothermia.
 
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