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Richardthughes



Posts: 10756
Joined: Jan. 2006

(Permalink) Posted: Aug. 26 2008,14:35   

Here:

http://debunkingchristianity.blogspot.com/2008....on.html

this cat writes:

Quote
Just in casual terms, complexity is a description of the "number of discrete and differentiated parts", and information is "reduction in uncertainty". Complexity and information are related on some level, and those terms do often occur together in computing and information theoretic contexts. But complexity is not information, any more than mass is acceleration.


is this a fair statement, especially concerning the layman definitions?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Henry J



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(Permalink) Posted: Aug. 26 2008,15:12   

That definition for "complexity" seems reasonable to me.

On information, I'd say that in casual usage, information is data that's useful to somebody. So whether a datum is information or not is relative; it depends on whether the entity possessing it finds it useful.

Seems like the concepts are referring to entirely different things.

Henry

  
jeannot



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(Permalink) Posted: Aug. 26 2008,15:22   

Quote (Henry J @ Aug. 26 2008,15:12)
That definition for "complexity" seems reasonable to me.

On information, I'd say that in casual usage, information is data that's useful to somebody.

Which is why "information" is subjective and irrelevant to the reality of evolution.

  
Richardthughes



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(Permalink) Posted: Aug. 26 2008,15:36   

I'd agree. Let X = "the complete works of Shakespeare"

Does X now have more information? Sorta.. but only by context.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
SoonerintheBluegrass



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(Permalink) Posted: Aug. 26 2008,16:04   

If i'm not horribly mistaken-- and there's something like a 99.9% certainty I am-- in theoretical physics, isn't information in a very broad sense defined as everything in the universe (i.e., all matter/energy)?  The only difference, then, between one particle and another is how it is organized, either as the bits and pieces that make up an atom, and/or some particle/wave in the EM spectrum or a manifestation of the weak/strong force/gravity (at least in some hypotheses).  And that a corollary of this is effectively that no information is ever lost (except, maybe, in a black hole, although IIRC, the jury's still out on that one).  

But even if I were somehow right, it wouldn't mean squat to the IDists with regard to biology.  It's doubtful that any real chemist or physicist would say some intelligence was required to have this information organized in such a way or complexity in some special way to produce a living organism-- or at least not self-replicating molecules that could provide the basis for what a biologist would call life.

--------------
"And heaven will smell like the airport
But I may not get there to prove it
So let's not waste our time thinking how that ain't fair."

Neko Case

  
dnmlthr



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(Permalink) Posted: Aug. 26 2008,16:34   

Does compressibility play into this? That is, how much do you need to know to recreate a document*?

Consider a document containing the complete works of Shakespeare, I'd expect it to be reasonably compressable, likewise a document of the same size containing only the same letter over and over again. But how about a document of the same size that contains completely random characters?

Which one of these contain the most information? Which one is the most complex? The Shakespeare document would certainly seem to contain the most usable information (in the context of a human reader), but I'd expect it to not be the least compressible.

It's getting late, so I'll just leave you with this confused comment, hopefully to come back at a time when my brain isn't mush.

* For the sake of discussion, I'll talk about a simple text document sans metadata

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Guess what? I don't give a flying f*ck how "science works" - Ftk

  
Richardthughes



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(Permalink) Posted: Aug. 26 2008,16:47   

There's still context in the compressibility - in your example it might be the rules for English and a semantic understanding, in pure technology it may be adequately described by the codec - or maybe not, perhaps it is also the operating system the codec runs on?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
stevestory



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(Permalink) Posted: Aug. 26 2008,17:03   

Quote (dnmlthr @ Aug. 26 2008,17:34)
Does compressibility play into this? That is, how much do you need to know to recreate a document*?

Consider a document containing the complete works of Shakespeare, I'd expect it to be reasonably compressable, likewise a document of the same size containing only the same letter over and over again. But how about a document of the same size that contains completely random characters?

To test this in a first-order, amateurish way, I got the full text of Hamlet and saved it in a text file. It was 197 kb. When I zipped it, the zip file was 72kb. 36% the size of the original. I also made a text file of one letter over and over about 180,000 times, roughly the same length as Hamlet, and the file size was around 176 kb. When I zipped that, the file was 4kb, around 2% of the original. And in fact it's probably less and 4kb is just some kind of minimum file size on my machine. A file that was completely, truly random would be basically incompressible, and the zipped file would be 100% the size of the original.

(various caveats go here: zipping isn't perfect compression, I are not a information theorist, etc etc.)

   
dogdidit



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Joined: Mar. 2008

(Permalink) Posted: Aug. 26 2008,17:11   

Lossless compression simply eliminates the redundancy. Shannon estimated the redundancy of English at 50%, so 2:1 reduction should be possible without loss of information.

As for dnmlthr's question, the text with random symbols by definition has more "information" than a similarly sized copy of Shakespeare. Semantically, it could be reduced to RAND(N) for all any human reader would care, but (per Shannon) the "semantic aspects of communication are irrelevant to the engineering problem". In contrast, the document consisting of "AAAAAAAAA" is readily compressed to a couple of parameters (namely "A" and the number of A's).

Compression (and for that matter, coding) does need to know what set of symbols to be used.

If stevestory repeats his test with a string of random characters, I'll bet he sees no file size reduction after zipping. That's because the message has no redundancy to be removed.

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"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
stevestory



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(Permalink) Posted: Aug. 26 2008,17:32   

Quote (dogdidit @ Aug. 26 2008,18:11)
If stevestory repeats his test with a string of random characters, I'll bet he sees no file size reduction after zipping. That's because the message has no redundancy to be removed.

Interestingly that didn't happen. Having read an Erv post recently, I went to google and said "Gives me the random numbars pleez" and it sent me to Random.org and I got 10,000 numbers in a single column and put that in a text file and it said "Your filez are 38.2 kilobytes LOLZ" and when I zipped it it became 16 kilobytes. Not sure what's going on there. Maybe, because i had the numbars delivered in 1 columnz, there was like an End of Line charactar that was stripped out and that was the compressian diffarance. Kthanxbi!

   
steve_h



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(Permalink) Posted: Aug. 26 2008,17:35   

Shakespeare's works don't just contain information and they are not just complex - they contain complex specified information!!one! For instance, in Macbeth, the number of possible arrangements of the words is, from the arse, more than 10^1050. But M. is also independantly specified by the short spec, "Scottish dude meets pushy wife, ghost, Kristinewitches, spot,  maybe a knife and (*spoiler alert*) gets deaded", which can probably be further reduced by zipping.

  
stevestory



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(Permalink) Posted: Aug. 26 2008,17:39   

We should kick back with some beverages. We've already, on this thread, done more actual Information Theory work than the IDiots have done in 15 years.

   
Louis



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Joined: Jan. 2006

(Permalink) Posted: Aug. 26 2008,17:42   

Quote (stevestory @ Aug. 26 2008,23:39)
We should kick back with some beverages. We've already, on this thread, done more actual Information Theory work than the IDiots have done in 15 years.

And you have conveniently duplicated your post. Mutate just one copy and you've INCREASED the information in this thread.

Which of course we know is impossible because it violates the SLOT or something.

Louis

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Bye.

  
stevestory



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(Permalink) Posted: Aug. 26 2008,17:46   

That's okay. I heard from Davetard that every time he writes a sentence he violates the SLoT.

   
Louis



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(Permalink) Posted: Aug. 26 2008,17:50   

Quote (stevestory @ Aug. 26 2008,23:46)
That's okay. I heard from Davetard that every time he writes a sentence he violates the SLoT.

Impossible, because anything Davetard does is, by definition, not an intelligently designed act.

;-)

Louis

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Bye.

  
dogdidit



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Joined: Mar. 2008

(Permalink) Posted: Aug. 26 2008,17:51   

Quote (stevestory @ Aug. 26 2008,17:32)
 
Quote (dogdidit @ Aug. 26 2008,18:11)
If stevestory repeats his test with a string of random characters, I'll bet he sees no file size reduction after zipping. That's because the message has no redundancy to be removed.

Interestingly that didn't happen. Having read an Erv post recently, I went to google and said "Gives me the random numbars pleez" and it sent me to Random.org and I got 10,000 numbers in a single column and put that in a text file and it said "Your filez are 38.2 kilobytes LOLZ" and when I zipped it it became 16 kilobytes. Not sure what's going on there. Maybe, because i had the numbars delivered in 1 columnz, there was like an End of Line charactar that was stripped out and that was the compressian diffarance. Kthanxbi!

Lost my bet. Farg. I shall now eat me a beer.

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Doc Bill



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(Permalink) Posted: Aug. 26 2008,17:54   

Romeo and Juliette compressed:

Misunderstanding results in young lovers committing suicide.

Now, the original play provides a lot more details but, basically, that's what happens.

Could one argue that my short synopsis is the "information" and the complete play only adds noise?

Or, if I randomly included paragraphs from Moby Dick into Romeo and Juliette would that be adding information?

The problem that ID faces is that the cdesign proponentists are unable to define either "information" or "complexity" or "design" objectively which would prove or disprove my silly examples. They rely upon layman subjectivity to skirt the rigor that is required.

Oh, Ishmael, Ishmael!  Where for art thou Ishmael!

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Aug. 26 2008,17:55   

Quote (stevestory @ Aug. 26 2008,17:32)
 
Quote (dogdidit @ Aug. 26 2008,18:11)
If stevestory repeats his test with a string of random characters, I'll bet he sees no file size reduction after zipping. That's because the message has no redundancy to be removed.

Interestingly that didn't happen. Having read an Erv post recently, I went to google and said "Gives me the random numbars pleez" and it sent me to Random.org and I got 10,000 numbers in a single column and put that in a text file and it said "Your filez are 38.2 kilobytes LOLZ" and when I zipped it it became 16 kilobytes. Not sure what's going on there. Maybe, because i had the numbars delivered in 1 columnz, there was like an End of Line charactar that was stripped out and that was the compressian diffarance. Kthanxbi!

Heywaitaminnit. Random numbers .ne. random text. Winzip cheeted. Or cheeto'd. Or something.

*eats another beer*

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Richardthughes



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(Permalink) Posted: Aug. 26 2008,18:13   

Quote (Doc Bill @ Aug. 26 2008,17:54)
Romeo and Juliette compressed:

Misunderstanding results in young lovers committing suicide.

Now, the original play provides a lot more details but, basically, that's what happens.

Could one argue that my short synopsis is the "information" and the complete play only adds noise?

Or, if I randomly included paragraphs from Moby Dick into Romeo and Juliette would that be adding information?

The problem that ID faces is that the cdesign proponentists are unable to define either "information" or "complexity" or "design" objectively which would prove or disprove my silly examples. They rely upon layman subjectivity to skirt the rigor that is required.

Oh, Ishmael, Ishmael!  Where for art thou Ishmael!

in this case theirs a qualitative aspect to information, which is subjective.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Wesley R. Elsberry



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(Permalink) Posted: Aug. 26 2008,18:14   

Antievolutionists want to confuse and conflate meaning and information. Spetner, Gitt, Truman, and Dembski... all of them want meaning to be folded within whatever sort of "information" they propose.

Shannon's discussion of information explicitly excluded meaning. Algorithmic information theory only cares about one aspect of meaning: what is the shortest program and input that can generate a string?

Critique of Dembski's "complex specified information"

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

    
midwifetoad



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(Permalink) Posted: Aug. 26 2008,20:07   

Quote
A file that was completely, truly random would be basically incompressible, and the zipped file would be 100% the size of the original.


Just to show how screwed up intuitive concepts can be, the digits of pi are believed to be "random" in the sense that an arbitrary sequence of digits taken from pi cannot be distinguished from a sequence generated by quantum phenomena. In another sense, the digits of pi are believed to contain every possible string of finite length.

And yet pi can be generated by a simple algorithm.

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

  
dhogaza



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(Permalink) Posted: Aug. 26 2008,20:20   

Quote
Heywaitaminnit. Random numbers .ne. random text. Winzip cheeted. Or cheeto'd. Or something.

Even worse, they're not random BYTES.  You need a file filled up with bytes which randomly contain the values 0-255, not random values from the subsite 0 through 9 plus newline.

Try your zip on a JPEG, for instance.

  
midwifetoad



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(Permalink) Posted: Aug. 26 2008,20:54   

Actual data, image size 100x100 pixel, White square, and same size square after Photoshop noise filter applied (looks like confetti). Saved with no compression and two kinds of lossless compression.


    Object              .bmp      .tif         .psd
white, 100x100 px   29.3k     7.83k      8.25k
Noise, 100x100 px   29.3k    35.40k     44.60k

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

  
Richardthughes



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Joined: Jan. 2006

(Permalink) Posted: Aug. 26 2008,21:21   

Quote (midwifetoad @ Aug. 26 2008,20:54)
Actual data, image size 100x100 pixel, White square, and same size square after Photoshop noise filter applied (looks like confetti). Saved with no compression and two kinds of lossless compression.


    Object              .bmp      .tif         .psd
white, 100x100 px   29.3k     7.83k      8.25k
Noise, 100x100 px   29.3k    35.40k     44.60k

clearly there's a market for a metaformat that dynamically pics the best compression format - the added carrier cost for the 'format switch' would be minuscule...

© 2008 - AtBC Labs

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Aug. 26 2008,21:28   

Quote
Having read an Erv post recently, I went to google and said "Gives me the random numbars pleez" and it sent me to Random.org and I got 10,000 numbers in a single column and put that in a text file and it said "Your filez are 38.2 kilobytes LOLZ" and when I zipped it it became 16 kilobytes. Not sure what's going on there.


Numbers are easy to compress. The only characters involved are digits, maybe a period, maybe a + or - sign, and a separator between entries. Represent each of those by a value from 0 to 15, and each character fits in one nibble (4 bits) instead of the byte (8 bits) needed for the whole ASCII character.

Now about compressing that string of random characters - whether that can be compressed depends on how many character code values are used. If it's limited to ASCII characters, then only 96 of the 256 possible values are used, so it would be possible to store it so that the average bits used per character is 6 and a fraction. Not a terribly large compression, but not zero.

Henry

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Aug. 26 2008,21:32   

Quote (Wesley R. Elsberry @ Aug. 26 2008,18:14)
Antievolutionists want to confuse and conflate meaning and information. Spetner, Gitt, Truman, and Dembski... all of them want meaning to be folded within whatever sort of "information" they propose.

Shannon's discussion of information explicitly excluded meaning. Algorithmic information theory only cares about one aspect of meaning: what is the shortest program and input that can generate a string?

Critique of Dembski's "complex specified information"

Well, they are certainly free -- and more power to 'em -- to extend Claude Shannon's seminal work and the field of information theory in general to incorporate mathematically sound concepts of "functional", "complex", and "specified" to go along with "information". Big Claims require Big Proof, though. So far:
- Big Claims: many
- Big Proof: not so much.

I will give them credit for spurring me to tackle Shannon's classic paper. Not my primary speciality (which is radar) but I can occasionally brane when I don't haz the dumb.

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
midwifetoad



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Joined: Mar. 2008

(Permalink) Posted: Aug. 26 2008,22:05   

Quote (Richardthughes @ Aug. 26 2008,21:21)
Quote (midwifetoad @ Aug. 26 2008,20:54)
Actual data, image size 100x100 pixel, White square, and same size square after Photoshop noise filter applied (looks like confetti). Saved with no compression and two kinds of lossless compression.


    Object              .bmp      .tif         .psd
white, 100x100 px   29.3k     7.83k      8.25k
Noise, 100x100 px   29.3k    35.40k     44.60k

clearly there's a market for a metaformat that dynamically pics the best compression format - the added carrier cost for the 'format switch' would be minuscule...

© 2008 - AtBC Labs

Saving the same two files as .gif, the solid white takes 156 bytes and the noise file takes nearly as much space as the lossless compression files.

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

  
Richardthughes



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Joined: Jan. 2006

(Permalink) Posted: Aug. 26 2008,23:11   

http://en.wikipedia.org/wiki/Image_compression

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"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
J-Dog



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(Permalink) Posted: Aug. 27 2008,10:20   

This post is why I love this site!

Well, that and the secrets that Maya reveals.  And the beer and wine and spice tips, and the pictures of Denyse and Dembski.  And the Tardelogues, and Mornington Crescent Death-matches.

:)

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Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Tracy P. Hamilton



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Joined: May 2006

(Permalink) Posted: Aug. 27 2008,10:27   

Quote (stevestory @ Aug. 26 2008,17:39)
We should kick back with some beverages. We've already, on this thread, done more actual Information Theory work than the IDiots have done in 15 years.

Q: Is there more information in a copy of a message, such as the second copy of steve story's post?
A: Yes.  That information is that stevestory had already kicked back with some beverages before posting.    ;)

--------------
"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

  
goalpost



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(Permalink) Posted: Aug. 27 2008,12:21   

Ok, so I send two messages:

Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T. This message is non-compressible. It has maximum complexity as I understand it.

Message one's sequence codes for a protein.
Message two's contains junk DNA.

Does message 1 contain more information?

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Aug. 27 2008,13:17   

Quote (goalpost @ Aug. 27 2008,12:21)
Ok, so I send two messages:

Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T. This message is non-compressible.

Actually, it is very compressible if it is a DNA sequence, since codons (triplets of base pairs) code for only 22 possible states - start, stop, and twenty amino acids - even though the symbol set could accommodate 64. So the real measure of information in DNA is no more than 4.5 bits (log2 of 22) for every three base pairs, not 6 bits (log2 of 64).

(There may be other functional purpose by the apparent redundancy in the DNA code. For starters, it confers some point mutation error immunity to -some- amino acids...but that's an archival storage relieability issue, not a communication issue. The error imunity redundancy could be restored at the receiver but the inital information would be lost. That might matter to molecular biologists who want to use the genome data and point mutation distributions for cladistics and synteny and other cabbalistic darwinian materialist evolander corruptions...)

Quote
It has maximum complexity as I understand it.

What is your measure of complexity?

Quote

Message one's sequence codes for a protein.
Message two's contains junk DNA.

Does message 1 contain more information?

Difficult question. What you're asking is how much entropy (uncertainty) is there in the sequence of amino acids (our message set) in the proteins that make up the human proteome. Are some amino acids rarer than others? Are some amino acids sequences more likely than others? If the answer is yes, then the entropy of the source will be less than that of a source whose symbols have equal probability. That would reduce the information content from 4.5 bits per codon to something less.

Junk DNA, assuming it is not under selection pressure (else why would it be "junk"?), would be likely to accumulate mutations more rapidly than DNA related to the proteome, yes? Those mutations should help to "shuffle the deck" and over time one would expect the symbol set to drift toward equiprobability. (But never quite get there - equally random sequences of base pairs does not code for equally random sequences of amino acids.) So my guess is that yes, the junk DNA has more information (as defined by information theory) than DNA that codes for proteins.

BTW IANAB. I are uh injineer.

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Richardthughes



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(Permalink) Posted: Aug. 27 2008,13:24   

Just to mess things up further:

you can have 10 coders write 10 programs to do the same thing. They are all different and of varying length. Then you can compress them. The shortest initial program may not still be the shortest after compression - possibly due to luck, or perhaps the structure of reusable common elements with the code. So which program has the most information, given that bigger can be smaller, and should we be measuring the code or the inputs and outputs?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
slpage



Posts: 349
Joined: June 2004

(Permalink) Posted: Aug. 27 2008,13:57   

Quote (dogdidit @ Aug. 27 2008,13:17)

Quote

Actually, it is very compressible if it is a DNA sequence, since codons (triplets of base pairs) code for only 22 possible states - start, stop, and twenty amino acids - even though the symbol set could accommodate 64. So the real measure of information in DNA is no more than 4.5 bits (log2 of 22) for every three base pairs, not 6 bits (log2 of 64).


Yes, but isn't the compression you write of 'conceptual' (I can't think of a better word)?
Sure, you can run a computer file through a compression algorithm and all that, but DNA is physical - more akin to trying to 'compress' a CD as opposed to the 'information' ON the CD, if my point is making any sense.

Quote
Quote

Message one's sequence codes for a protein.
Message two's contains junk DNA.

Does message 1 contain more information?

Difficult question. What you're asking is how much entropy (uncertainty) is there in the sequence of amino acids (our message set) in the proteins that make up the human proteome. Are some amino acids rarer than others? Are some amino acids sequences more likely than others? If the answer is yes, then the entropy of the source will be less than that of a source whose symbols have equal probability. That would reduce the information content from 4.5 bits per codon to something less.

Junk DNA, assuming it is not under selection pressure (else why would it be "junk"?), would be likely to accumulate mutations more rapidly than DNA related to the proteome, yes? Those mutations should help to "shuffle the deck" and over time one would expect the symbol set to drift toward equiprobability. (But never quite get there - equally random sequences of base pairs does not code for equally random sequences of amino acids.) So my guess is that yes, the junk DNA has more information (as defined by information theory) than DNA that codes for proteins.


OK, so while we are discussing hypotheticals, how about this one.

Two DNA sequences, both 1000 bps long, both identical with one exception - one sequence starts with TAA instead of TAC.
The 'functional sequence' has a measured information content of (just tossing out a number here to make it simple) 1000.
Would the non-functional sequence have a content of 999 or 0?

  
Richardthughes



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(Permalink) Posted: Aug. 27 2008,14:03   

food for thought, the compressibility of PI:

http://en.wikipedia.org/wiki/Leibniz_formula_for_pi

PI is a non-recurring non terminating decimal.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Aug. 27 2008,14:07   

Quote (goalpost @ Aug. 27 2008,13:21)
Ok, so I send two messages:

Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T. This message is non-compressible. It has maximum complexity as I understand it.

Message one's sequence codes for a protein.
Message two's contains junk DNA.

Does message 1 contain more information?

proteins often have repetitive subunits, so that's another reason the DNA for a protein would be compressible.

   
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,15:43   

Quote (Wesley R. Elsberry @ Aug. 26 2008,18:14)
Antievolutionists want to confuse and conflate meaning and information. Spetner, Gitt, Truman, and Dembski... all of them want meaning to be folded within whatever sort of "information" they propose.

Shannon's discussion of information explicitly excluded meaning. Algorithmic information theory only cares about one aspect of meaning: what is the shortest program and input that can generate a string?

Critique of Dembski's "complex specified information"

Wes, the one exception to what you say is the Kolmogorov structure function of algorithmic information theory, which I have seen Paul Vitanyi relate to "meaning."

For criticism of the morph of CSI that came after the one you and Shallitt addressed, see this.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Turncoat



Posts: 128
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(Permalink) Posted: Aug. 27 2008,16:55   

The two leading notions of the quantity of information in an object are the self-information of Shannon and the algorithmic information of Solomonoff, Chaitin, and Kolmogorov (working more or less independently). Algorithmic information is widely known as Kolmogorov complexity, so distinctions between "complexity" and "information" are not clear-cut. What self-information and algorithmic information have in common is relation of information to description.

For Shannon, there is an objective probability distribution p on a set of outcomes of a random experiment, and the information in outcome x is -log p(x). (Let's say that the logarithm is base-2, and the unit of information is the bit.) A justification for regarding this as the intrinsic information in x is that if you want to transmit messages indicating the outcomes of repeated experiments to a receiver, and you want to minimize the average number of bits you transmit per outcome, then you and the receiver ideally agree on a code that associates a binary description of length -log p(x) with each possible outcome x.

A problem with Shannon's self-information is the issue of how we know the objective (actual) distribution p in terms of which ideal description length is defined. In algorithmic information theory, description is defined in terms of computation instead of probability. That is, the algorithmic information of a string (finite sequence) of symbols is the length of the shortest binary computer program that outputs the string and halts. To be more specific, the computer is a universal computer, equivalent in "computing power" to a universal Turing machine. If we restrict ourselves to "simple" universal computers, the program length varies little from one computer to the next. To make this more concrete, and to relate it to earlier comments, the program is like a self-extracting zip archive. The program is a compact description of the string x it outputs.

From the equality

description_length = -log p(x),

we may obtain

p(x) = 2^-description_length.

In algorithmic information theory, it is common to define probability in terms of description (shortest program) length. What is known as the universal distribution corresponds roughly to the latter of the equalities I just gave you. So, in a sense, information (ideal description length) "comes from" probability in Shannon's information theory, and probability comes from information (shortest-program length) in algorithmic information theory.

I'm sure I've just thrown way too much at some of you. But some of you have been in the ballpark with your remarks, and I hope this helps a bit.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



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(Permalink) Posted: Aug. 27 2008,17:00   

Thanks for your posts, turncoat. Now, if you can put your empirical hat on, why don't we see CSI calculations?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
dogdidit



Posts: 315
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(Permalink) Posted: Aug. 27 2008,17:24   

Quote (slpage @ Aug. 27 2008,13:57)
       
Quote (dogdidit @ Aug. 27 2008,13:17)
Actually, it is very compressible if it is a DNA sequence, since codons (triplets of base pairs) code for only 22 possible states - start, stop, and twenty amino acids - even though the symbol set could accommodate 64. So the real measure of information in DNA is no more than 4.5 bits (log2 of 22) for every three base pairs, not 6 bits (log2 of 64).

Yes, but isn't the compression you write of 'conceptual' (I can't think of a better word)?
Sure, you can run a computer file through a compression algorithm and all that, but DNA is physical - more akin to trying to 'compress' a CD as opposed to the 'information' ON the CD, if my point is making any sense.

The OP spoke about using bits to encode the nucleotides:
Quote (goalpost @ Aug. 27 2008,12:21)
Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T.

...so I was responding to that. I would agree that compressing functional DNA does not seem possible. Perhaps a very large steam press...

Quote
Quote
Quote

Message one's sequence codes for a protein.
Message two's contains junk DNA.

Does message 1 contain more information?

Difficult question. What you're asking is how much entropy (uncertainty) is there in the sequence of amino acids (our message set) in the proteins that make up the human proteome. Are some amino acids rarer than others? Are some amino acids sequences more likely than others? If the answer is yes, then the entropy of the source will be less than that of a source whose symbols have equal probability. That would reduce the information content from 4.5 bits per codon to something less.

Junk DNA, assuming it is not under selection pressure (else why would it be "junk"?), would be likely to accumulate mutations more rapidly than DNA related to the proteome, yes? Those mutations should help to "shuffle the deck" and over time one would expect the symbol set to drift toward equiprobability. (But never quite get there - equally random sequences of base pairs does not code for equally random sequences of amino acids.) So my guess is that yes, the junk DNA has more information (as defined by information theory) than DNA that codes for proteins.


OK, so while we are discussing hypotheticals, how about this one.

Two DNA sequences, both 1000 bps long, both identical with one exception - one sequence starts with TAA instead of TAC.
The 'functional sequence' has a measured information content of (just tossing out a number here to make it simple) 1000.
Would the non-functional sequence have a content of 999 or 0?

1000. That assumes a C is as likely as an A. Functionality ("semantic content") is irrelevant.

@Turncoat: yep, I am using Shannon's definition (and thanks for not mentioning my errors).

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,17:27   

Almost all binary strings x have no program ("self-extracting zip archive") much shorter than themselves. A string that is in this sense incompressible is algorithmically random by definition. The definition makes sense, though, because an algorithmically random string x passes all computable tests of randomness. In essence, there is no effective procedure that allows you to say that the bits in x did not come from a random source.

The problem some of you have had in experimenting with compression of texts is that you haven't taken into account the fact that you're working with strings of (presumably) 8-bit characters. If I recall correctly, the bzip utility compresses to bit strings instead of character strings. This is what you need for your experiments.

For large N, a string of N digit-bytes (8 bits per byte) coming from a random source will compress from 8N bits (always) to about N log 10 bits (almost always). The high compression ratio comes only from the inefficiency of an 8-bit representation of textual digits.

There are similar considerations with Macbeth. There are not 2^8 = 256 letters, spaces, and punctuation marks in Shakespeare's text, so you get some compression simply because the initial 8-bit representation of characters is inefficient. At first blush, I would say that the number of distinct characters is no more than 64. Thus to get a better estimate of the compressibility of Macbeth, count 6 bits per byte of the source text, not 8. Count 8 bits per byte of bzip output. (Bzip may tell you the number of bits in the output -- I haven't used it in a long time.)

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Henry J



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(Permalink) Posted: Aug. 27 2008,17:55   

Turncoat,

That's kind of what I was getting at in my post last night.

Henry

  
Turncoat



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Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,18:08   

Quote (Richardthughes @ Aug. 27 2008,17:00)
Thanks for your posts, turncoat. Now, if you can put your empirical hat on, why don't we see CSI calculations?

RIP those who were waiting with bated breath to see Dembski's computation of CSI for the bacterial flagellum.

To apply CSI, you have to come up with an upper bound on the probability that a configuration of matter arose by purely natural processes. In principle, that does not reduce to argument from ignorance. In practice, you run afoul of argument from ignorance whenever you go from something like coin tossing to the  flagellum. We know all we're going to know about outcomes of tossing a fair coin, but we don't know how much we might eventually know about natural processes giving rise to the flagellum. From a Bayesian perspective, scientific learning generally increases the probability of observed phenomena. How is Dembski going to place an upper bound on the probability a future model might assign justifiably to the emergence of the flagellum by natural processes?

I think that assignment of probabilities to explanations of historical events that occurred under largely unknown circumstances is a philosophical quagmire. Dembski complains that evolutionary models are not sufficiently detailed. I would contend that evolutionary models are correct in reflecting our ignorance of the details. We cannot turn the emergence of the flagellum into a repeatable, controlled experiment, and I have no idea how Dembski justifies his frequentism in the development of CSI.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



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(Permalink) Posted: Aug. 27 2008,18:35   

They have compressed it to "bac flag", though. Progress!
???

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,18:47   

Quote (Henry J @ Aug. 27 2008,17:55)
Turncoat,

That's kind of what I was getting at in my post last night.

Henry

Yep. Hadn't read that far yet.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,18:53   

Quote (Richardthughes @ Aug. 27 2008,18:35)
They have compressed it to "bac flag", though. Progress!
???

I saw "BF" yesterday. You may see that as further progress, but I say that when the information content of the message is zero, the waste of bandwidth is infinite.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
steve_h



Posts: 533
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(Permalink) Posted: Aug. 27 2008,20:29   

Quote
There are similar considerations with Macbeth. There are not 2^8 = 256 letters, spaces, and punctuation marks in Shakespeare's text, so you get some compression simply because the initial 8-bit representation of characters is inefficient. At first blush, I would say that the number of distinct characters is no more than 64. Thus to get a better estimate of the compressibility of Macbeth, count 6 bits per byte of the source text, not 8. Count 8 bits per byte of bzip output. (Bzip may tell you the number of bits in the output -- I haven't used it in a long time.)

I just downloaded Macbeth from Project Gutenberg and compressed it with the latest version of WinZip.  It reduced from 116kb to 31.5kb. Instead of one character being stored in eight bits, it required a little over two bits. That's rather better than what you'd get by saving random six-bit characters.

  
Richardthughes



Posts: 10756
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(Permalink) Posted: Aug. 27 2008,20:52   

All this experimenting is not very congruent with ID, folks. back to navel-gazing and hand-waving, please.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,21:44   

Quote (Richardthughes @ Aug. 27 2008,20:52)
All this experimenting is not very congruent with ID, folks. back to navel-gazing and hand-waving, please.

Have you forgotten how amazingly "creative" one can be with MatLab?

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 27 2008,22:26   

Here's a little shell script for getting word counts (case insensitive) from a text:
Code Sample
#!/bin/sh

tr -d "'" |
tr -cs "[:alpha:]" "\n" |
tr "[:upper:]" "[:lower:]" |
sort |
uniq -c |
sort -rn |
awk '{ cum += $1; print  $1, cum, $2; }'


It says that Macbeth contains 18596 instances of 3379 distinct words. Here are the ten most frequent words:

740 740 the
579 1319 and
385 1704 to
368 2072 of
335 2407 i
284 2691 macbeth
253 2944 a
233 3177 that
207 3384 in
202 3586 you

The first column is word frequency, and the second is cumulative frequency. Applying this command
Code Sample
awk '{h += $1 / 18596 * -log($1/18596)/log(2)} END{print h}'

to the output, I get per-word entropy of about 9.357 bits. It would have been nice to treat punctuation marks as words, but I don't happen to have a script on hand that does that.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



Posts: 10756
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(Permalink) Posted: Aug. 27 2008,22:32   

Quote
It would have been nice to treat punctuation marks as words, but I don't happen to have a script on hand that does that.


I'm guessing they have low compressibility given their single character nature? You could perhaps make capitalization at the start of a sentence a rule and then compress that way?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 28 2008,01:05   

Quote (Richardthughes @ Aug. 27 2008,22:32)
 
Quote
It would have been nice to treat punctuation marks as words, but I don't happen to have a script on hand that does that.


I'm guessing they have low compressibility given their single character nature? You could perhaps make capitalization at the start of a sentence a rule and then compress that way?

Periods and commas have low self-information (are given short encodings) because they are of high probability. Most capitalization can be recovered from punctuation. My transformation to lowercase of words that are always capitalized (e.g., "Macbeth") has no effect on the entropy calculation.

My brain is fried, so I'm not good for any real work. Perhaps I'll diddle a bit with punctuation.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 28 2008,01:59   

Here is a preprocessing script. Run Macbeth through this first, and then run the output through the filter (script) I gave above.
Code Sample
#!/bin/sh

# Spell out punctuation marks. Leave apostrophe as part of word.
# Treat end-of-line as punctuation for processing of verse.
# This works well for Shakespeare from Gutenberg Project.
# Manually remove copyright notice prior to each act.

sed '/^ *$/d'   |
sed "
s/'/papostrophe/g
s/,/ pcomma /g
s/\./ pperiod /g
s/\!/ pbang /g
s/\?/ pquestion /g
s/-/ phyphen /g
s/\[/ plbracket /g
s/\]/ prbrackt /g
s/;/ psemicolon /g
s/:/ pcolon /g
s/(/ plparenthesis /g
s/)/ prparenthesis /g
s/$/ pendofline/"

I decided that end-of-line should be treated as punctuation in verse. I also noticed that there were copyright notifications prior to Acts II-V that I had not removed in my previous analysis. Now there are 25,307 "words," and the per-word entropy is 8.228 bits. Yes, the per-word entropy went down because the empirical distribution concentrates  a great deal of probability mass on punctuation pseudo-words. Here are the twenty most frequent words and pseudo-words:

2625 2625 pendofline
1873 4498 pperiod
1646 6144 pcomma
736 6880 the
567 7447 and
385 7832 to
356 8188 of
318 8506 i
284 8790 macbeth
253 9043 a
238 9281 pquestion
229 9510 that
208 9718 psemicolon
208 9926 pbang
207 10133 in
202 10335 you
192 10527 my
183 10710 is
164 10874 not
155 11029 with

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



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(Permalink) Posted: Aug. 28 2008,08:58   

WRT punctaution rules, which become part of the codec in our examples - I guess this sort of thing works if:

1) The rule is lossless
2) Compressing the rule < compressing the examples?

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Wesley R. Elsberry



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(Permalink) Posted: Aug. 28 2008,09:42   

Quote (Turncoat @ Aug. 27 2008,21:44)
Quote (Richardthughes @ Aug. 27 2008,20:52)
All this experimenting is not very congruent with ID, folks. back to navel-gazing and hand-waving, please.

Have you forgotten how amazingly "creative" one can be with MatLab?

That was fun, though the creative folks just turned around and re-asserted everything just on their say-so rather than rely on the authority of their script.

I once actually had a program that worked properly (that is, the results were computed accurately), but I had failed to initialize pointers. Everything worked fine up until the program ended, at which point my computer would reboot itself. The uninitialized pointers apparently happily pointed into memory regions used by MS-DOS... worked fine while my program was doing its thing, but it hammered the in-memory parts of some system stuff, COMMAND.COM and MSDOS.SYS or similar bits. That, though, was enough of an inducement to track down the problem.

I would have thought that coming up with results so starkly inconsistent with decades of peer-reviewed research would have given the MATLAB programmer(s) pause, but apparently since the error went in a direction parallel to their prejudices, it seemed not to raise any alarm bells.

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

    
Wesley R. Elsberry



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(Permalink) Posted: Aug. 28 2008,09:46   

That reminds me... has anyone seen the Marks/Dembski collaborations appear in print anywhere yet?

Though I suppose that if they do, notice is likely to be given the IDC equivalent of a ticker-tape parade, appearing on the DI blog, the ID-the-Future blog, UD, TT, and however many DO'L blogs there are at the time.

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

    
slpage



Posts: 349
Joined: June 2004

(Permalink) Posted: Aug. 28 2008,11:06   

Quote (dogdidit @ Aug. 27 2008,17:24)

Quote
The OP spoke about using bits to encode the nucleotides:
 
Quote (goalpost @ Aug. 27 2008,12:21)
Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T.

...so I was responding to that. I would agree that compressing functional DNA does not seem possible. Perhaps a very large steam press...


Indeed.

This has always sort of bugged me in these discussions - talk of compressability and information and DNA.  
Quote
Quote
OK, so while we are discussing hypotheticals, how about this one.

Two DNA sequences, both 1000 bps long, both identical with one exception - one sequence starts with TAA instead of TAC.
The 'functional sequence' has a measured information content of (just tossing out a number here to make it simple) 1000.
Would the non-functional sequence have a content of 999 or 0?

1000. That assumes a C is as likely as an A. Functionality ("semantic content") is irrelevant.

@Turncoat: yep, I am using Shannon's definition (and thanks for not mentioning my errors).


Interesting.  Funny - when I present IDcretos with similar scenarios, then get themselves into a tizzy and can never seem to even try to address the question.

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Aug. 28 2008,13:33   

Quote (Wesley R. Elsberry @ Aug. 28 2008,10:46)
however many DO'L blogs there are at the time.

That's a subject best left to the guy who managed to calculate Disaster Area's tax returns.

   
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 28 2008,15:55   

Quote (Wesley R. Elsberry @ Aug. 28 2008,09:46)
That reminds me... has anyone seen the Marks/Dembski collaborations appear in print anywhere yet?

Though I suppose that if they do, notice is likely to be given the IDC equivalent of a ticker-tape parade, appearing on the DI blog, the ID-the-Future blog, UD, TT, and however many DO'L blogs there are at the time.

Nothing in print that I know of. The fact is that I'll be obsoleting anything they publish, anyway.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



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(Permalink) Posted: Aug. 28 2008,15:58   

Quote (Turncoat @ Aug. 28 2008,15:55)
The fact is that I'll be obsoleting anything they publish, anyway.

*Proffers High-Five*  :p

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Turncoat



Posts: 128
Joined: Dec. 2007

(Permalink) Posted: Aug. 29 2008,00:59   

Quote (Richardthughes @ Aug. 28 2008,15:58)
 
Quote (Turncoat @ Aug. 28 2008,15:55)
The fact is that I'll be obsoleting anything they publish, anyway.

*Proffers High-Five*  :p

My results are solid -- I'm preparing a presentation and a paper.

--------------
I never give them hell. I just tell the truth about them, and they think it's hell. — Harry S Truman

  
Richardthughes



Posts: 10756
Joined: Jan. 2006

(Permalink) Posted: Aug. 29 2008,01:31   

The math may be beyond me but I'm sure folks like Wes could offer you a good critique, if you'd like.

--------------
"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Wesley R. Elsberry



Posts: 4807
Joined: May 2002

(Permalink) Posted: Aug. 29 2008,06:16   

Quote (Turncoat @ Aug. 28 2008,15:55)
Quote (Wesley R. Elsberry @ Aug. 28 2008,09:46)
That reminds me... has anyone seen the Marks/Dembski collaborations appear in print anywhere yet?

Though I suppose that if they do, notice is likely to be given the IDC equivalent of a ticker-tape parade, appearing on the DI blog, the ID-the-Future blog, UD, TT, and however many DO'L blogs there are at the time.

Nothing in print that I know of. The fact is that I'll be obsoleting anything they publish, anyway.

I will make a direct response whenever a paper shows up.

"Obsolete" doesn't seem the right word; it carries an implication that there was some period of time where the thing in question actually worked.

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

    
Wesley R. Elsberry



Posts: 4807
Joined: May 2002

(Permalink) Posted: Aug. 29 2008,07:18   

Quote (Richardthughes @ Aug. 29 2008,01:31)
The math may be beyond me but I'm sure folks like Wes could offer you a good critique, if you'd like.

I can at least speak to Dembski's history of claims with respect to information theory and evolutionary computation. I was the guy who set him the task of explaining away EC back at the 1997 NTSE conference. My example there was a GA that produces short tours for the Traveling Salesman Problem. It's an example Dembski has never come to grips with. The class of problem, NP-hard, sets both intelligent agents and evolutionary computation on the same level, seeking approximate solutions rather than exact optimal solutions for any non-trivial number of cities in the tour. The evaluation function is too simple to even try to claim that the solution state is incorporated into it: total cost for each tour. Instead, Dembski has been making a career out of misunderstanding even Dawkins' pedagogical example, the weasel program. So far, he has not even managed to describe the weasel program correctly.

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

    
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Aug. 29 2008,11:25   

Quote (Wesley R. Elsberry @ Aug. 29 2008,08:18)
Quote (Richardthughes @ Aug. 29 2008,01:31)
The math may be beyond me but I'm sure folks like Wes could offer you a good critique, if you'd like.

I can at least speak to Dembski's history of claims with respect to information theory and evolutionary computation. I was the guy who set him the task of explaining away EC back at the 1997 NTSE conference. My example there was a GA that produces short tours for the Traveling Salesman Problem. It's an example Dembski has never come to grips with. The class of problem, NP-hard, sets both intelligent agents and evolutionary computation on the same level, seeking approximate solutions rather than exact optimal solutions for any non-trivial number of cities in the tour. The evaluation function is too simple to even try to claim that the solution state is incorporated into it: total cost for each tour. Instead, Dembski has been making a career out of misunderstanding even Dawkins' pedagogical example, the weasel program. So far, he has not even managed to describe the weasel program correctly.

I get the impression that even DDrr.. Dembski's MESA program was more powerful than he bargained for, so he dropped it when it didn't give confirmatory answers.

All science so far!

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
midwifetoad



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(Permalink) Posted: Aug. 29 2008,12:54   

Quote (Wesley R. Elsberry @ Aug. 29 2008,07:18)
Quote (Richardthughes @ Aug. 29 2008,01:31)
The math may be beyond me but I'm sure folks like Wes could offer you a good critique, if you'd like.

I can at least speak to Dembski's history of claims with respect to information theory and evolutionary computation. I was the guy who set him the task of explaining away EC back at the 1997 NTSE conference. My example there was a GA that produces short tours for the Traveling Salesman Problem. It's an example Dembski has never come to grips with. The class of problem, NP-hard, sets both intelligent agents and evolutionary computation on the same level, seeking approximate solutions rather than exact optimal solutions for any non-trivial number of cities in the tour. The evaluation function is too simple to even try to claim that the solution state is incorporated into it: total cost for each tour. Instead, Dembski has been making a career out of misunderstanding even Dawkins' pedagogical example, the weasel program. So far, he has not even managed to describe the weasel program correctly.

I have been wondering whether the weasel program could be run as a web page where viewers could vote on the strings to live and reproduce based not on a match to a given string, but on arbitrary criteria known only to each participant.

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

  
Wesley R. Elsberry



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(Permalink) Posted: Aug. 29 2008,13:17   

Quote

I have been wondering whether the weasel program could be run as a web page where viewers could vote on the strings to live and reproduce based not on a match to a given string, but on arbitrary criteria known only to each participant.


The only "why not" there would be the high degree of interaction required. If web weasel loads in consensus-making on top of the usual weasel evaluations, I expect that one could have closer to ten times the usual number of evaluations needed. I'm not sure how to attract enough user attention to do that not just once, but often enough to get good statistics on the dynamics.

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

    
Richardthughes



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(Permalink) Posted: Aug. 29 2008,13:20   

Do you have a ballpark estimate?


Richard Dawkin's website readers are quite numerous.

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Wesley R. Elsberry



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(Permalink) Posted: Aug. 29 2008,13:31   

Actually, thinking about it a bit more, I don't know that it would require more evaluations. If most strings collect no votes at all, that is a default evaluation of no merit. It is only if one requires that all candidate strings get some evaluation that the very large number of evaluations comes in. OK, it might not be infeasible.

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

    
Turncoat



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(Permalink) Posted: Aug. 29 2008,14:22   

Quote (Wesley R. Elsberry @ Aug. 29 2008,07:18)
     
Quote (Richardthughes @ Aug. 29 2008,01:31)
The math may be beyond me but I'm sure folks like Wes could offer you a good critique, if you'd like.

I can at least speak to Dembski's history of claims with respect to information theory and evolutionary computation. I was the guy who set him the task of explaining away EC back at the 1997 NTSE conference. My example there was a GA that produces short tours for the Traveling Salesman Problem. It's an example Dembski has never come to grips with. The class of problem, NP-hard, sets both intelligent agents and evolutionary computation on the same level, seeking approximate solutions rather than exact optimal solutions for any non-trivial number of cities in the tour. The evaluation function is too simple to even try to claim that the solution state is incorporated into it: total cost for each tour. Instead, Dembski has been making a career out of misunderstanding even Dawkins' pedagogical example, the weasel program. So far, he has not even managed to describe the weasel program correctly.

Personally, I would stay away from using solution of traveling salesperson problems with genetic algorithms as an example. TSP is the prototype of problems for which GA researchers have designed custom representations and reproduction operators. David Goldberg's Genetic Algorithms in Search, Optimization, and Machine Learning (1989) gives special attention to TSP.

The Dembski-Marks paper with the misrepresentation of the weasel program (and, trivially, the misspelling of "methinks" as "me thinks" in the target string) has been "forthcoming" in the Wistar Retrospective proceedings for quite a time. Dawkins' program is an instance of what folks in evolutionary computation know as a (1, ?)-ES [evolution strategy].

How does the weasel program know the space of strings on which fitness is defined? How does it know that fitness evaluation of some strings is not impractically slow? How does it know that lower "fitness" values are better than higher values? How does it know to terminate when it obtains a string of zero fitness? The weasel program, like most optimization programs, is highly informed of the optimization problem. (And I have said nothing about the fitness function guiding the program to the target string.)

Dembski is blinkered by his agenda, but he's not wrong in all points he raises. He got me to ponder what optimization procedures know about problems, and this led me to see that the NFL analytic framework predicates considerable prior knowledge. Take away some of that prior knowledge, and there are huge performance distinctions among optimization procedures. This is not a fine theoretical point. Wolpert and Macready's constraints on optimization problems are in no sense natural.

Wes, I told you last fall that I thought I had major results on the way. It turned out that I had to beat my sub-genius head against the wall quite a few more times to "break on through to the other side." At the moment, I'm preparing for a job interview, and I'm trying to work what I have into a crystal-clear presetation. When I'm through with that, I'll write a paper. I would appreciate it if you were to read a draft and give me feedback.

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midwifetoad



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(Permalink) Posted: Aug. 29 2008,14:27   

I have no idea what the population size is in weasel, but let's say it's too large for inspection by a human over the Internet.

Suppose each page view is treated as and encounter with a reasonable sized tribe, and the web player is designated as a predator, choosing some to eliminate, or food, choosing some to survive and replace those that are eliminated. The host would dole out the roles so that the population size remains stable.

On any given page view, the host program selects an individual at random and builds a tribe of those most nearly matching it. The player sees the tribe -- say 50 or 100 individuals -- and selects some for reproduction or elimination.

At the host end the population would be in continuous flux; there would be no "rounds" affection the entire population at once.

From the player's perspective, the "genome" would be beyond the control of any particular player. Depending on the population size, a player might never see the same string or same tribe twice.

OK, so I'm nuts, but I think with some tinkering, you could build a game that would have interesting results.

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Richardthughes



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(Permalink) Posted: Aug. 29 2008,14:48   

Of course, ID's victory will be 'stimulating more research' ergo "teach the controversy"...

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goalpost



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(Permalink) Posted: Aug. 29 2008,15:30   

Quote (dogdidit @ Aug. 27 2008,13:17)

 
Quote (goalpost @ Aug. 27 2008,12:21)
Ok, so I send two messages:

Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T. This message is non-compressible.

Actually, it is very compressible if it is a DNA sequence, since codons (triplets of base pairs) code for only 22 possible states - start, stop, and twenty amino acids - even though the symbol set could accommodate 64. So the real measure of information in DNA is no more than 4.5 bits (log2 of 22) for every three base pairs, not 6 bits (log2 of 64).

You're quite correct, I forgot about that bit. Let me rephrase the question, then:
I send 2 messages, both DNA sequences as before. Each is coded in such a way that it may not be further compressed. Each is of the same length, and contains the same number of DNA triplets.

One has 'usefulness'  - it codes for a protein. The other doesn't.
Does the 'useful' message contain any more information by virtue of its 'usefulness'?

  
oldmanintheskydidntdoit



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(Permalink) Posted: Aug. 29 2008,15:46   

Quote (goalpost @ Aug. 29 2008,15:30)
Does the 'useful' message contain any more information by virtue of its 'usefulness'?

When this comes up I'm always reminded of Hofstadter's example of sending a vinyl record into space.

I can't see where this is going  :p

  
dogdidit



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(Permalink) Posted: Aug. 29 2008,18:06   

Quote (goalpost @ Aug. 29 2008,15:30)
       
Quote (dogdidit @ Aug. 27 2008,13:17)

         
Quote (goalpost @ Aug. 27 2008,12:21)
Ok, so I send two messages:

Both messages contain a human DNA sequence - ACGT etc etc, each letter coded as two bits, ie 00 = A, 01 = C, 10 = G, 11 = T. This message is non-compressible.

Actually, it is very compressible if it is a DNA sequence, since codons (triplets of base pairs) code for only 22 possible states - start, stop, and twenty amino acids - even though the symbol set could accommodate 64. So the real measure of information in DNA is no more than 4.5 bits (log2 of 22) for every three base pairs, not 6 bits (log2 of 64).

You're quite correct, I forgot about that bit. Let me rephrase the question, then:
I send 2 messages, both DNA sequences as before. Each is coded in such a way that it may not be further compressed. Each is of the same length, and contains the same number of DNA triplets.

One has 'usefulness'  - it codes for a protein. The other doesn't.
Does the 'useful' message contain any more information by virtue of its 'usefulness'?

The challenge is coming to an acceptable definition of "information". Shannon's definition had to do with the entropy of the source, but this is a bit confusing because "entropy" is a poorly understood concept (at least, for me) so I prefer to think of the measure information as the reduction in uncertainty at the receiver (which is also consistent with Shannon's interpretation).

If you are sending me a symbol, and I have no idea what it might be, then each bit of information you send represents a reduction of 50% in my uncertainty. (I'm assuming that we are dealing with symbols selected from a finite and discrete set.) Let's assume you are sending a hexadecimal number in binary format. I expect to receive xxxx but I have no idea if the x's are 1's or 0's, so my uncertainty at the outset is that the symbol belongs to one of sixteen possible states, from 0 to 15. Your first bit -- let's assume it's a 1 -- cuts my uncertainty in half, since now I know that the symbol is of the form 1xxx and therefore the set [0 7] are ruled out and the symbol must lie in [8 15]. Eight possible states; half as many as before. Half the uncertainty.

Notice that at no time do I rule that your message is cogent or noise. A 1,000-character post on AtBC contains the same quantity of "information" as a 1,000-character post on UD (shudder!! except we also know that the UD can't be a post from kairosfocus) if both are written in the same language.

Applying this to DNA (and here I wander out of engineering and into microbiology - ALERT! ALERT!), mRNA (m = message!) is a message from the cell nucleus to the ribosome: "Here. Make this protein". The ribosome will read the mRNA three bases at a time and use those triplets (codons) to determine* which amino acid to append to the polymer it is assembling. It does not care whether the polymer is useful or toxic or garbage or a viroid. The semantics of the message are irrelevant to the measure of information.

* I'm overlooking the role of tRNA and the myriad other helper molecules that help make the magic happen.

In information theory, there is AFAIK no way to measure the "usefulness" of the message. (Is a viroid useful? To the virus, it is. Are point mutations useful?) The IDers might wish to extend information theory to do just that, but so far they've not come up with the goods. "FCSI" and other concoctions appear to me as just so much unsubstantiated wishful thinking. I appreciate their desire to distinguish between "useful" and "useless" information but the science does not help them and they have not extended the science to do so. Invoking "information theory" in the defense of their efforts is nothing more than intellectual hi-jacking.

Claude Shannon was a brilliant man, and Bell Labs was the "Google" of it's day. Interestingly enough, his doctoral thesis was An Algebra for Theoretical Genetics. However, as far as I can tell he earned only one doctorate.

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Daniel Smith



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(Permalink) Posted: Aug. 29 2008,22:37   

I think what you guys need is a real IDer here so that you don't become all back-slapping and self-congratulatory with no one to challenge your silliness.  So for this I offer my services.

The problem I have with the weasel example is that it uses a predetermined and easily obtainable goal - so it really does nothing to bolster the argument for the power of RM+NS.  I think that a realistic model--one that has many more obstacles to overcome--would be much more convincing.  

Are there any genetic algorithms that you can point me to that closely resemble the actual processes involved in RM+NS evolution of something as complex as a cell?  Or say part of a cell - mitochondria?  Or maybe just a flagellum?  Or maybe just the flagellar motor?

I think we all can agree that our 26 letter alphabet, along with punctuation, spaces, etc., are a pretty close analogue (for this purpose anyway) for the amino acids used in life's systems.  And that words, phrases, sentences, etc., are a fairly good analogue for proteins.  While paragraphs, chapters, books, etc., make a passable analogue for cellular systems.

Therefore, I would think that a better selection criteria (as far as mimicking RM+NS and real world evolution) would be to start with a string of random letters, punctuation marks and spaces--maybe a million characters long--under constant mutation; select from this anything that functions as a word, a phrase, or a sentence; combine these fragments randomly into longer passages, selecting all the while for grammatical function, until you have cohesive paragraphs, then chapters, with the end result being a cohesive novel.

Wouldn't that be more in line with the origin of a simple cellular system via RM+NS?

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

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midwifetoad



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(Permalink) Posted: Aug. 29 2008,22:50   

The travelling salesman problem does not have a predetermined solution. It doesn't even have a single solution.

There's a patent issued for an electronic circuit designed by a genetic algorithm.

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Richardthughes



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(Permalink) Posted: Aug. 29 2008,23:35   

Hi Daniel. Did you see the steiner tree debate or have you seen Zach's word mutagenation?

http://www.zachriel.com/mutagenation/

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Henry J



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(Permalink) Posted: Aug. 29 2008,23:37   

Quote
I think we all can agree that our 26 letter alphabet, along with punctuation, spaces, etc., are a pretty close analogue (for this purpose anyway) for the amino acids used in life's systems.


I would be very surprised if a biologist were to agree with that. A letter is a symbol with no intrinsic meaning of its own. An amino acid is a chemical that reacts with other chemicals.

Quote
The problem I have with the weasel example is that it uses a predetermined and easily obtainable goal


The only point to that program was selection vs. random search; it was never intended as a simulation of real evolution.

Quote
I think that a realistic model--one that has many more obstacles to overcome--would be much more convincing.


That I'd agree with. In natural evolution there are bound to be lots of those obstacles, and the "solutions" sometimes conflict with each other, if only in that using more resources for one thing reduces the resources that are available for other things. If the situation remains stable long enough some sort of equilibrium might occur among the various factors.

Henry

  
oldmanintheskydidntdoit



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(Permalink) Posted: Aug. 30 2008,04:44   

Quote (Daniel Smith @ Aug. 29 2008,22:37)
Wouldn't that be more in line with the origin of a simple cellular system via RM+NS?

Would it? Why don't you tell us Daniel, you just suggested it.

Tell me, what "function" would this Novel that you suggest that will evolve, perform?

EDIT:
Quote
The problem I have with the weasel example is that it uses a predetermined and easily obtainable goal


Daniel, simple question - have you read the book that the weasel example appears in?

If you had I suspect that you would not be making the statements you are making.

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
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if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
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Daniel Smith



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(Permalink) Posted: Aug. 30 2008,12:47   

To answer the questions:  No I have not read "The Blind Watchmaker" so I don't know what Dawkins' purpose was.  I'm assuming it was an attempt to show that RM+AS could produce meaningful information.

As for Zach's word mutagenation, I haven't read the whole thing, but I'm starting to see how equating words to real evolution might be problematic.  What do the letters represent?  Do they represent amino acids?  Are words proteins?  If so, then how do these examples from the English language mirror real world biochemical systems?  For instance, words can be put together rather randomly and give some sort of meaning, but can biological systems be built this way - especially within living organisms?  Can you randomly insert new proteins into a cascading systems such as blood clotting and have it work?  Or is the English language much more forgiving than living systems are?  Let's just say that you can insert a new protein into the blood clotting system and have the system actually change its function to something besides blood clotting.  What are the side effects of such a change?  The organism has a new function, yet it bleeds to death.  Is it selected for?  Doubtful.  I think that all in all, the English language is more forgiving.  No one dies when words are jumbled.  Of course there are peripheral, non-essential systems for which random changes might be tolerated - much more in keeping with the English language.  But this merely slides the problem sideways.  How did the essential systems originate?  Were all essential systems at one time non-essential?  If so, how did they become essential?

I guess my problem is one of accuracy: what do these examples represent in regard to real world evolution?

For instance, what is the purpose of the weasel example?  How does it apply to any argument about origins?  After all isn't that what all the debate is really about anyway?  It's not about whether random mutations can modify or improve something: it's about whether or not random mutations can create something new.  It's about the process--including all the intermediate steps--by which random mutations creates new functional biochemical systems.  So, with the weasel example, what does METHINKS IT IS LIKE A WEASEL  represent?  Is it like a chain of amino acids that makes up a specific protein?  Perhaps the last piece of a "protein puzzle" that will alter the way an organism fights disease?  If so, then what does ME SOMNSISN HE L DHIEJWEAMFK represent?  Some of the letters are in the correct places, so is it an amino acid chain that doesn't quite become a protein, or one that folds into a different shape with different charges and characteristics?  More importantly, why would the second example be selected?  Are amino acid chains that don't make up specific proteins selected for - simply because they show potential?  If some of the amino acids are in the correct place for a future, potential protein, does the cellular machinery set it aside for future use?  Is that mutation guaranteed to be passed on?  On what basis?  I don't think so, but I could be wrong.

Of course the weasel example could have nothing to do with real world evolution, so none of the above would apply.  If so, then why bother bringing it up?  Why is it even out there?  What does it prove?  Why is it relevant to the discussion?

As far as I'm concerned, all this talk about information, complexity, and specificity is irrelevant if it doesn't apply to real world biochemical systems.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
jeannot



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(Permalink) Posted: Aug. 30 2008,13:30   

Quote (Daniel Smith @ Aug. 30 2008,12:47)
 Are amino acid chains that don't make up specific proteins selected for - simply because they show potential?  

No, a gene (not a protein) is "selected" if its product improves its replication rate in the population, by definition.

And whether it contains more or less "information" is completely irrelevant.

  
oldmanintheskydidntdoit



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(Permalink) Posted: Aug. 30 2008,15:37   

Quote (Daniel Smith @ Aug. 30 2008,12:47)
 Were all essential systems at one time non-essential?  If so, how did they become essential?



How to build an arch

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Wesley R. Elsberry



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(Permalink) Posted: Aug. 30 2008,15:38   

Quote

For instance, what is the purpose of the weasel example?


RTFB.

You'd be whining ad nauseum if someone were offering an opinion on Schindewald without reading his work, so suck it up and learn something about what you presume to criticize.

All I've seen from you is trollage.

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Wesley R. Elsberry



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(Permalink) Posted: Aug. 30 2008,15:44   

Uninformed trolling is being automatically redirected to the Bathroom Wall.

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Zachriel



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(Permalink) Posted: Aug. 30 2008,16:34   

Quote (Daniel Smith @ Aug. 30 2008,12:47)
As for Zach's word mutagenation, I haven't read the whole thing...

Try the open source software instead. (Requires Excel. Unzip before running.)

Quote (Daniel Smith @ Aug. 30 2008,12:47)
... but I'm starting to see how equating words to real evolution might be problematic.

Quite so. Word Mutagenation doesn't represent biological evolution. It represents claims frequently made by Intelligent Design Advocates. In particular, Sean Pitman claimed that if you "start with a short 2 or 3-letter word and see how many words you can evolve that require greater and greater minimum sequence requirements. No doubt you will quickly find yourself coming to walls of meaningless or non-beneficial potential options that separate you from every other meaningful and beneficial option." So I tested it.

Quote (Daniel Smith @ Aug. 30 2008,12:47)
Or is the English language much more forgiving than living systems are?

Words can be very fragile. The proportion of valid 10-letter words among 10-letter sequences is only about one in ten billion. Testing at a few thousand per second (the working rate of Word Mutagenation) would take days to find even one 10-letter word. Yet, Word Mutagenation does it easily in seconds. The reason the "Big Number Calculation" is misleading is because the assumptions about how an evolutionary algorithm works are wrong.

The concept is that words may be separated in the vastness of sequence space, but that they are joined by a common descent to much shorter sequences and are composed of common subunits that can be combined in various ways. What results are very subtle combinations of letters and syllables—which are often irreducibly complex! Once you understand this, then you will see why the ID Argument is faulty.

I have also tested this with Phrasenation. It is even more fragile as sequences must be exact matches from Hamlet. Sequences beyond Dembski's Universal Probability Bound are possible. And that with a toy running very inefficient software.

Quote (Daniel Smith @ Aug. 30 2008,12:47)
I think that all in all, the English language is more forgiving.  No one dies when words are jumbled.

Actually, in Word Mutagenation, that's exactly what happens. Let's say we have a word "can". It mutates to "pan". It lives and competes for space in the population. Let's say it mutates to "cxn". It's still-born.

Quote (Daniel Smith @ Aug. 30 2008,12:47)
I guess my problem is one of accuracy: what do these examples represent in regard to real world evolution?

Not much, but Word Mutagenation is one of a class of evolutionary algorithms, and biological evolution can be modeled, in part, as an evolutionary algorithm.



Quote (Daniel Smith @ Aug. 30 2008,12:47)
As far as I'm concerned, all this talk about information, complexity, and specificity is irrelevant if it doesn't apply to real world biochemical systems.

You have it now! That's why most such claims made by ID Advocates are vacuous, or just false.

--
Edited Big Number Arithmetic above.

Length     Big Number    Mutagenation

10-letter      7 days        2-3 seconds
11-letter    239 days        5-10 seconds
12-letter     25 years       minute or two


There's a random element so Mutagenation results vary somewhat.


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oldmanintheskydidntdoit



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(Permalink) Posted: Aug. 30 2008,17:12   

Quote (Daniel Smith @ Aug. 30 2008,12:47)
Of course the weasel example could have nothing to do with real world evolution, so none of the above would apply.  If so, then why bother bringing it up?  Why is it even out there?  What does it prove?  Why is it relevant to the discussion?

By demolishing things that weasel never claimed to prove in the first place and by attaching undue importance to it and making all sorts of misrepresentations about what it claims to represent, then "disproving" those claims, well it gives people who've no better arguments then that who want to disprove "evolution" something to feel good about. And it's "disproof" is useful for those doubters who need to be fooled by a bit of science "find the lady" con trickery, rather then just take Dembski et al at their word. Some won't be fooled.

Many will. For example:

site:http://www.uncommondescent.com weasel



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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



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(Permalink) Posted: Aug. 31 2008,14:34   

Quote (Wesley R. Elsberry @ Aug. 30 2008,13:38)

You'd be whining ad nauseum if someone were offering an opinion on Schindewald without reading his work, so suck it up and learn something about what you presume to criticize.

Did you mean "Schindewolf"?  
I don't remember anyone here actually reading Schindewolf's book all the way through before they took to criticizing his work.  I know some who read a few chapters, others read Gould's foreword, yet I don't remeber one who began a counterargument with the statement "I'm thoroughly familiar with Schindewolf's work and I find it..."  Did you read his book?
If not, then don't be a hypocrite: allow the uninformed debate to continue.

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



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(Permalink) Posted: Aug. 31 2008,15:02   

Quote (Zachriel @ Aug. 30 2008,14:34)
         
Quote (Daniel Smith @ Aug. 30 2008,12:47)
I guess my problem is one of accuracy: what do these examples represent in regard to real world evolution?

Not much, but Word Mutagenation is one of a class of evolutionary algorithms, and biological evolution can be modeled, in part, as an evolutionary algorithm.

This is really the only debate I'm interested in.  I'd be intensely interested in an algorithm that mirrors real biological evolution.  I'm not really that interested at all in the debate about words - unless there's something that can be shown analogous to real world (non-theoretical) evolution.  (Although I will download and play with your program.)

I guess what I'm saying is that every living organism and every organ is said to be the result of evolution.  What I'd like to see is a detailed account of how any one of these organs or organisms (or even the most basic biochemical systems within them) originated via evolution.  I'd like to see a step-by-step analysis of evolution in action.  What was the precursor?  What were the intermediate steps?  Why were they selected?  

For instance, it's often said that lungs evolved from swim bladders.  So...
What were the specific biochemical steps?  Are lungs and swim bladders made of the same proteins?  What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab?  Are these steps able to be specified down to the biochemical level?  What is the evidence in support from other fields such as paleontology?  

IOW, can you get here from there?  Are there any biological algorithms that will let you plug in "swim bladder" and get "lungs" as a result?  Is anyone even working on the problem?  Or are the conclusions assumed?

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"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Aug. 31 2008,18:33   

Quote (Daniel Smith @ Aug. 31 2008,14:34)
 
Quote (Wesley R. Elsberry @ Aug. 30 2008,13:38)

You'd be whining ad nauseum if someone were offering an opinion on Schindewald without reading his work, so suck it up and learn something about what you presume to criticize.

Did you mean "Schindewolf"?  
I don't remember anyone here actually reading Schindewolf's book all the way through before they took to criticizing his work.

Did you read it all the way through before touting it, Dan?
Quote
I know some who read a few chapters, others read Gould's foreword, yet I don't remeber one who began a counterargument with the statement "I'm thoroughly familiar with Schindewolf's work and I find it..."

Would one have to have done so to counter any of your inane arguments?

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Aug. 31 2008,18:43   

Quote (Daniel Smith @ Aug. 31 2008,15:02)
 
Quote (Zachriel @ Aug. 30 2008,14:34)
           
Quote (Daniel Smith @ Aug. 30 2008,12:47)
I guess my problem is one of accuracy: what do these examples represent in regard to real world evolution?

Not much, but Word Mutagenation is one of a class of evolutionary algorithms, and biological evolution can be modeled, in part, as an evolutionary algorithm.

This is really the only debate I'm interested in.  I'd be intensely interested in an algorithm that mirrors real biological evolution.

Hmmm...then why is it that you aren't at all interested in real biology?
Quote
I'm not really that interested at all in the debate about words - unless there's something that can be shown analogous to real world (non-theoretical) evolution.

So we agree that the IDers' claims that the "genetic code" (which is not a code in biology; it's only a code when we offer letters to replace chemical structures) implies intelligence are bogus?
Quote
I guess what I'm saying is that every living organism and every organ is said to be the result of evolution.

Your obsession with organs appears to be sexual.
Quote
What I'd like to see is a detailed account of how any one of these organs or organisms (or even the most basic biochemical systems within them) originated via evolution.

It's in the sequences that you botched so badly. But as for seeing how complex organ systems can differ dramatically based on the dosage/activity/presence/absence of a very small number of genes, I suggest that you examine the dimorphism of human sexual organs.
Quote
I'd like to see a step-by-step analysis of evolution in action.  What was the precursor?

The undifferentiated system.
Quote
What were the intermediate steps?  Why were they selected?

Because they helped in reproduction. 
Quote
For instance, it's often said that lungs evolved from swim bladders.  So...
What were the specific biochemical steps?

Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means.
Quote
Are lungs and swim bladders made of the same proteins?

Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions.
Quote
What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab?

No. Your request is stupid. What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite?
Quote
Are these steps able to be specified down to the biochemical level?

More BS. You don't know what you're talking about.
Quote
What is the evidence in support from other fields such as paleontology?  

The most important field is comparative genomics, one you ran away from studying, remember?

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Aug. 31 2008,21:22   

Quote (Daniel Smith @ Aug. 30 2008,12:47)
As far as I'm concerned, all this talk about information, complexity, and specificity is irrelevant if it doesn't apply to real world biochemical systems.

Erm - well, it does seem relevant in light of the attempts of the ID community to make various claims that the genetic code shows evidence of complex specified information having been injected into it (shh! don't say by who!) without a shred of science or measurement behind the words "complex" or "specified" and predicated on a listener's confusion or lack of understanding as to what "information" is and how it is measured in statistical terms. So the first order of business would be to clear the cobwebs of obfuscation out of the way. "Information" has a solid mathematical foundation beneath it; it even gets to be a "theory"! "Complexity"? "Specified"? Jury still out.

As for:  
Quote
I'd be intensely interested in an algorithm that mirrors real biological evolution.

Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough?

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"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Richardthughes



Posts: 10756
Joined: Jan. 2006

(Permalink) Posted: Aug. 31 2008,21:27   

GAs have incredible utility as seen by their application in optimization. Funny how they're modelled on this thing that doesn't work, yet they do so well.

Sure, we might completely understand the mechanism, but at least we have one.

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"Richardthughes, you magnificent bastard, I stand in awe of you..." : Arden Chatfield
"You magnificent bastard! " : Louis
"ATBC poster child", "I have to agree with Rich.." : DaveTard
"I bow to your superior skills" : deadman_932
"...it was Richardthughes making me lie in bed.." : Kristine

  
Wesley R. Elsberry



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Joined: May 2002

(Permalink) Posted: Aug. 31 2008,22:09   

Quote (Daniel Smith @ Aug. 31 2008,14:34)
Quote (Wesley R. Elsberry @ Aug. 30 2008,13:38)

You'd be whining ad nauseum if someone were offering an opinion on Schindewald without reading his work, so suck it up and learn something about what you presume to criticize.

Did you mean "Schindewolf"?  
I don't remember anyone here actually reading Schindewolf's book all the way through before they took to criticizing his work.  I know some who read a few chapters, others read Gould's foreword, yet I don't remeber one who began a counterargument with the statement "I'm thoroughly familiar with Schindewolf's work and I find it..."  Did you read his book?
If not, then don't be a hypocrite: allow the uninformed debate to continue.

It's not my standard that is a basis for a charge of hypocrisy; I've never stated that one cannot address particular issues on the basis of having read a relevant subset of someone's work. You, on the other hand, have been copiously documented saying that criticism of any issue cannot be done unless all of some book or all of someone's work has been read by the critic, at least for certain privileged sources. Others apparently don't merit even the minimal amount of respect that reading the material relevant to your completely uninformed claims would require.

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

    
Quidam



Posts: 229
Joined: Mar. 2008

(Permalink) Posted: Aug. 31 2008,22:26   

Quote (Daniel Smith @ Aug. 31 2008,14:02)
I'd be intensely interested in an algorithm that mirrors real biological evolution.

How about a program that in each iteration generates an array of artificial life creatures  by mutations in its building rules ('genes') from a parent. The user selects one of the children in each generation to become the parent of the next generation. The user decides subjectively what sorts of traits  to select for. This simulates artificial, rather than natural, selection.

I know where such an algorithm can be found.

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The organized fossils ... and their localities also, may be understood by all, even the most illiterate. William Smith, Strata. 1816

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Sep. 01 2008,02:55   

Quote (Daniel Smith @ Aug. 31 2008,15:02)
I guess what I'm saying is that every living organism and every organ is said to be the result of evolution.

I guess what I'm saying is that every living organism and every organ is said to be the result of Jesus.  What I'd like to see is a detailed account of how any one of these organs or organisms (or even the most basic biochemical systems within them) originated via Jesus.  I'd like to see a step-by-step analysis of Jesus in action.  What was the precursor?  What were the intermediate steps?  Why were they selected?  

Well?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 01 2008,15:21   

I found a program called Stylus that attempts to bridge the gap between language and real biological function by using Chinese characters.  I've only just begun to read the article, but it appears to be an honest attempt at a realistic evolutionary algorithm.
Abstract:  
Quote
The study of protein evolution is complicated by the vast size of protein sequence space, the huge number of possible protein folds, and the extraordinary complexity of the causal relationships between protein sequence, structure, and function. Much simpler model constructs may therefore provide an attractive complement to experimental studies in this area. Lattice models, which have long been useful in studies of protein folding, have found increasing use here. However, while these models incorporate actual sequences and structures (albeit non-biological ones), they incorporate no actual functions—relying instead on largely arbitrary structural criteria as a proxy for function. In view of the central importance of function to evolution, and the impossibility of incorporating real functional constraints without real function, it is important that protein-like models be developed around real structure–function relationships. Here we describe such a model and introduce open-source software that implements it. The model is based on the structure–function relationship in written language, where structures are two-dimensional ink paths and functions are the meanings that result when these paths form legible characters. To capture something like the hierarchical complexity of protein structure, we use the traditional characters of Chinese origin. Twenty coplanar vectors, encoded by base triplets, act like amino acids in building the character forms. This vector-world model captures many aspects of real proteins, including life-size sequences, a life-size structural repertoire, a realistic genetic code, secondary, tertiary, and quaternary structure, structural domains and motifs, operon-like genetic structures, and layered functional complexity up to a level resembling bacterial genomes and proteomes. Stylus is a full-featured implementation of the vector world for Unix systems. To demonstrate the utility of Stylus, we generated a sample set of homologous vector proteins by evolving successive lines from a single starting gene. These homologues show sequence and structure divergence resembling those of natural homologues in many respects, suggesting that the system may be sufficiently life-like for informative comparison to biology.


Unfortunately, the software only runs on Unix/Linux operating systems so I have no way of testing it.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 01 2008,16:22   

Quote (Wesley R. Elsberry @ Aug. 31 2008,20:09)

It's not my standard that is a basis for a charge of hypocrisy; I've never stated that one cannot address particular issues on the basis of having read a relevant subset of someone's work. You, on the other hand, have been copiously documented saying that criticism of any issue cannot be done unless all of some book or all of someone's work has been read by the critic, at least for certain privileged sources. Others apparently don't merit even the minimal amount of respect that reading the material relevant to your completely uninformed claims would require.

Well, without going out and buying the book, I think I've managed at least a rudimentary understanding of Dawkins' purpose for the weasel algorithm.  He uses it solely as a demonstration for the power of cumulative selection vs. single step selection.  He also is quite clear that it does not mirror biological evolution:  
Quote
Although the monkey/Shakespeare model is useful for explaining the distinction between single-step selection and cumulative selection, it is misleading in important ways. One of these is that, in each generation of selective 'breeding', the mutant 'progeny' phrases were judged according to the criterion of resemblance to a distant ideal target, the phrase METHINKS IT IS LIKE A WEASEL. Life isn't like that. Evolution has no long-term goal. There is no long-distance target, no final perfection to serve as a criterion for selection, although human vanity cherishes the absurd notion that our species is the final goal of evolution. In real life, the criterion for selection is always short-term, either simple survival or, more generally, reproductive success.

Dawkins admitted (according to the Wiki article I read anyway) that there has not been enough time since the universe began to produce the phrase METHINKS IT IS LIKE A WEASEL randomly via single/step selection.  So his phrase--of only 28 character length--required cumulative selection (of one letter resolution) in order to be produced from a random generator within a realistic time frame.  It would seem to me then that any biological system at least as complex as METHINKS IT IS LIKE A WEASEL, would require cumulative selection of each of its individual elements in order to be produced via random mutation in a sufficient amount of time.  Thus, each element must confer a selective advantage.  This would mean that each point mutation would have to confer an advantage in order to produce a specific 28bp sequence.  You could not just pull a good 28bp sequence out of space (single selection) as a starting point.  In fact, you could not pull an 8bp sequence out of space without significantly increasing the amount of time required to produce the functional sequence.

Where have I gone wrong?

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 01 2008,16:26   

Why is it that anytime I post a reply I'm redirected to the Bathroom Wall thread?  Is that a joke?  Some sort of warning perhaps?  Or is it happening to everyone and I'm just being paranoid?

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Lou FCD



Posts: 5402
Joined: Jan. 2006

(Permalink) Posted: Sep. 01 2008,20:52   

Quote (Daniel Smith @ Sep. 01 2008,17:22)
Well, without going out and buying the book, ...

Wait, weren't you just...

nevermind.

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Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Sep. 01 2008,23:34   

Quote (Daniel Smith @ Sep. 01 2008,16:26)
Why is it that anytime I post a reply I'm redirected to the Bathroom Wall thread?  Is that a joke?

Speaking of jokes, I'd like an answer to my question: did you read all of Schindewolf's book?

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Sep. 02 2008,02:57   

Quote (Daniel Smith @ Sep. 01 2008,16:22)
Dawkins admitted (according to the Wiki article I read anyway) that there has not been enough time since the universe began to produce the phrase METHINKS IT IS LIKE A WEASEL randomly via single/step selection.  

Would you like us to club together and purchase then send you a copy of the book?

It'll only be a few $$$.

There are many copy's.

I'm in for $1.

If you are in the UK I can post my copy today.

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 02 2008,19:07   

Quote (JAM @ Sep. 01 2008,21:34)
Speaking of jokes, I'd like an answer to my question: did you read all of Schindewolf's book?

Yes JAM I did.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 02 2008,19:46   

Quote (JAM @ Aug. 31 2008,16:43)
     
Quote (Daniel Smith @ Aug. 31 2008,15:02)
  I'd like to see a step-by-step analysis of evolution in action.  What was the precursor?

The undifferentiated system.
     
Quote
What were the intermediate steps?  Why were they selected?

Because they helped in reproduction.


Why is it JAM, that whenever I ask for specifics about evolution in forums like these, the answers get more vague?
 
   
Quote
     
Quote
For instance, it's often said that lungs evolved from swim bladders.  So...
What were the specific biochemical steps?

Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means.

I don't think it's that hard a word to understand, it's just the chemicals that life is made of.  I know that all of life is essentially biochemical reactions.  A lot of it is dependent on a chemical's reaction to water molecules.  Protein folding seems to be largely dependent on keeping the correct amino acids on the outside for their ready interactions with water (among other things) and keeping the "oily" amino acids separated from water (among other things as well).  The strength/weakness of chemical bonds is probably the most important quality.

   
Quote
   
Quote
Are lungs and swim bladders made of the same proteins?

Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions.
     
Quote
What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab?

No. Your request is stupid.

Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution?
Surely you have specific, lab-tested evolutionary pathways for scores of living systems.  After all, you are a scientist, correct?  Why not break one out for my amusement?  

"Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous." (from Wiki)

So what was the original sequence for the undifferentiated ancestor of modern lung/swim bladder species?

You should be able to re-create the steps - correct?  What were they?

   
Quote
What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite?

Is this a dodge?  Are you attempting to change the subject?  You have not answered my questions with anything above the vaguest vaguery, yet you want me to get specific.

     
Quote
   
Quote
Are these steps able to be specified down to the biochemical level?

More BS. You don't know what you're talking about.


Humor me.

     
Quote
The most important field is comparative genomics, one you ran away from studying, remember?


I don't remember "running away" from anything JAM.  A lot of it is over my head, but I am perfectly willing to discuss anything you have the patience to discuss with me.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Sep. 02 2008,22:41   

Quote
Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution?


Asking a question isn't stupid. But, mplying that the validity of a theory depends on scientists having a detailed history of a particular series of event (esp. for events between .5 and 4.5 billion years ago) - that's unrealistic.

It isn't so much that scientists "firmly believe" their conclusions, but (as I understand it) that they (1) note that the general concepts of the theory is consistent with all the relevant evidence (2) that is very unlikely to be the case if the theory is wrong, and (3) some of the implications of the theory were recognized before the confirming data was available (not all of the implications by any means; there will always be some implications that can't be directly tested).

Henry

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Sep. 03 2008,00:46   

Quote (Daniel Smith @ Sep. 02 2008,19:46)
   
Quote (JAM @ Aug. 31 2008,16:43)
           
Quote (Daniel Smith @ Aug. 31 2008,15:02)
  I'd like to see a step-by-step analysis of evolution in action.  What was the precursor?

The undifferentiated system.
           
Quote
What were the intermediate steps?  Why were they selected?

Because they helped in reproduction.


Why is it JAM, that whenever I ask for specifics about evolution in forums like these, the answers get more vague?

There was nothing vague about my answer. How can an intelligent person demand a step-by-step analysis of something in action that took hundreds of millions of years, Dan?

And why can't you supply any specifics about design, given that you believe in it with your heart and soul?

Your demand is a dishonest one and you know it.
      
Quote
 
Quote
           
Quote
For instance, it's often said that lungs evolved from swim bladders.  So...
What were the specific biochemical steps?

Biochemical steps? You're just BSing now. You clearly don't even understand what the word "biochemical" even means.

I don't think it's that hard a word to understand, it's just the chemicals that life is made of.  I know that all of life is essentially biochemical reactions.

Right. So please explain why EVOLUTION would involve ANY "biochemical steps." You don't know what you're talking about.
 
Quote
A lot of it is dependent on a chemical's reaction to water molecules.  Protein folding seems to be largely dependent on keeping the correct amino acids on the outside for their ready interactions with water (among other things) and keeping the "oily" amino acids separated from water (among other things as well).

"Keeping"? There's no "keeping" going on at all. You're assuming design from the start, because you're afraid to test a design hypothesis. You have no real faith.
 
Quote
The strength/weakness of chemical bonds is probably the most important quality.

This is so vague as to be meaningless.
 
Quote
         
Quote
         
Quote
Are lungs and swim bladders made of the same proteins?

Almost entirely--but not the same proteins, orthologous proteins. There's a difference, but understanding that is probably beyond your curiosity, because you are afraid of learning enough to test your assumptions.
           
Quote
What are the differences?  How was each difference created step by viable step?  What was the selective advantage for each?  Can these steps be recreated or verified in the lab?

No. Your request is stupid.

Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of evolution to explain how one of them came to be via evolution?

Now you're being dishonest again. It's not a matter of firm belief like yours, it's a conclusion based on the evidence, none of which supports your firm belief. That's why you run away from evidence.
 
Quote
Surely you have specific, lab-tested evolutionary pathways for scores of living systems.

Why would I? We only have specific pathways for subsystems. The problem for you is, when we analyze a new subsystem, we don't find anything inconsistent with evolutionary pathways. You, of course, deal with this evidence by never analyzing any systems or subsystems. You are afraid to do so.
 
Quote
After all, you are a scientist, correct?

I am, and you reject the scientific method itself, correct?
 
Quote
"Homologous sequences are orthologous if they were separated by a speciation event: when a species diverges into two separate species, the divergent copies of a single gene in the resulting species are said to be orthologous." (from Wiki)

Cut/paste doesn't equal understanding.
 
Quote
So what was the original sequence for the undifferentiated ancestor of modern lung/swim bladder species?

This is gibberish. Sequence of what? Are you saying that lungs and swim bladders are species?
 
Quote
You should be able to re-create the steps - correct?

Why should I be able to do so?
 
Quote
What were they?

We extrapolate back to the nearest species to a common ancestor and it becomes obvious.
 
Quote
 
Quote
What were the design steps, Dan? What was the intelligent rationale behind each step? Why are you such a dishonest hypocrite?

Is this a dodge?

It's a question. You firmly believe that lungs and swim bladders were designed and not descended from a common ancestor, don't you?
 
Quote
Are you attempting to change the subject?

No, I'm addressing your lack of faith in your position.
 
Quote
You have not answered my questions with anything above the vaguest vaguery,...

That's a lie. I've pointed out why they are sleazy and ignorant in very specific ways.
 
Quote
 
Quote
         
Quote
Are these steps able to be specified down to the biochemical level?

More BS. You don't know what you're talking about.


Humor me.

There aren't "biochemical steps" in evolution, you arrogant fool.

           
Quote
 
Quote
The most important field is comparative genomics, one you ran away from studying, remember?


I don't remember "running away" from anything JAM.

You're delusional.
 
Quote
A lot of it is over my head, but I am perfectly willing to discuss anything you have the patience to discuss with me.

Then let's pick up your thread where it left off, and have you address the fact that not a single one of your predictions in comparative genomics were supported by the evidence. In fact, they all were completely inconsistent with the evidence.

How have you changed your hypothesis to accommodate the evidence?

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Sep. 03 2008,02:42   

Why?  Why is it "stupid" to ask someone who firmly believes that all of life's systems are the product of design to explain how one of them came to be via design?
Surely you have specific, lab-tested design pathways for scores of living systems.  After all, you are a Intelligent Design scientist, correct?  Why not break one out for my amusement?  


well? Can you explain how a single "system" came to be via design Daniel?

I expect it's turtles all the way down with your sort.

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Richard Simons



Posts: 425
Joined: Oct. 2006

(Permalink) Posted: Sep. 03 2008,17:40   

Quote
Surely you have specific, lab-tested evolutionary pathways for scores of living systems.

I have no idea what you mean by this. Do you mean someone must have carried out a selection program to, for example, convert a population of lunged organisms to a population with swim bladders? Have you the slightest idea of how much it would cost to maintain a suitable breeding population of lungfish to do what is essentially a pointless exercise? Even if this succeeds after millenia of selection (at a bare minimum), your spiritual descendents will complain that a detailed genomic analysis of each generation was not performed.

Perhaps you could tell us exactly what it is you expect to have been done.

--------------
All sweeping statements are wrong.

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 03 2008,19:09   

By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

I'm sure there are many other ways to test for viable pathways.  If you don't test for a pathway though, you have nothing but comparable sequences, which may show common ancestry but do nothing to show how evolution occurred.  It could've been gradual step-by-step, or it could've been saltational.  Who knows?  You've established nothing in regard to mechanism.

As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing, but on a nano-scale.  Only the very first cellular lifeform on earth would have to be designed--IF--the designer was able to program the cell to differentiate via evolutionary mechanisms.  The tricky part would not be the putting together of the actual pieces of that first cell so much as it would be putting together the information that would cause the cell to replicate, grow and evolve.  That every cell on earth contains coded information is irrefutable evidence for design, unless you can show a way to get coded information from natural forces working on earthly elements.  (Oh and JAM, we know that DNA is a code because we are able to decode it.)  One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically.  This is exactly what we do find - as outlined in this paper.  Abstract:    
Quote
From a mathematical point of view, the genetic code is a surjective mapping between the set
of the 64 possible three-base codons and the set of 21 elements composed of the 20 amino
acids plus the Stop signal. Redundancy and degeneracy therefore follow. In analogy with the
genetic code, non-power integer-number representations are also surjective mappings
between sets of different cardinality and, as such, also redundant. However, none of the nonpower
arithmetics studied so far nor other alternative redundant representations are able to
match the actual degeneracy of the genetic code. In this paper we develop a slightly more
general framework that leads to the following surprising results: i) the degeneracy of the
genetic code is mathematically described, ii) a new symmetry is uncovered within this degeneracy,
iii) by assigning a binary string to each of the codons, their classification into definite
parity classes according to the corresponding sequence of bases is made possible. This last
result is particularly appealing in connection with the fact that parity coding is the basis of the
simplest strategies devised for error correction in man-made digital data transmission systems.

Follow-up paper

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
G. cuvier



Posts: 2
Joined: Sep. 2006

(Permalink) Posted: Sep. 03 2008,21:18   

Quote (Daniel Smith @ Sep. 03 2008,19:09)
As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing,  (Oh and JAM, we know that DNA is a code because we are able to decode it.)  One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically.

Mmmmm.... that's some good tard. While berating actual scientists for vagueness, Daniel writes this incredibly specific prediction:

Quote
As for how things came to be via design; I'd imagine the methodology was very similar to the methods of design we observe and use every day.  We are able to take raw materials from the earth, refine them, and fit them together to make working machinery.  A cellular designer would do the same thing,


Of course, he then tops that off with this, the veritable cherry on top of his sundae of comedy:

Quote
One thing we might expect to find if cellular information was designed would be that the genetic code could be described mathematically.


It should be obvious to even the meanest Intelligence that the path of a falling stone can be "described mathematically". Since Daniel is probably not a believer in Intelligent Falling, I leave it to you all to work out the relative intelligence of the designer of this argument.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Sep. 03 2008,22:48   

The methods that human engineers use every day would not produce single consistent nested hierarchy - it would produce lots of different hierarchies. It also would not tend to cluster close relatives near each other geographically. And it would likely produce lots of cases of exact copying of sequences. Also human engineers like to modularize things so that they can change one part with minimal risk of disruption of other parts.

Henry

  
JAM



Posts: 517
Joined: July 2007

(Permalink) Posted: Sep. 04 2008,00:22   

Quote (Daniel Smith @ Sep. 03 2008,19:09)
By "lab tested" I mean something that is tested period.

So if I tested it outside the lab and in the field, you'd still call it "lab tested"?
Quote
For instance, if two sets of genes are known,...

This is meaningless unless you define "sets" in this context.
Quote
... and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.

We can extrapolate, but we can't be sure. But why extrapolate? Why not just take the gene from one species and see if it works in another?
Quote
Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

How would simply inserting a gene test it for viability? Do you even think about this stuff before you write it?
Quote
I'm sure there are many other ways to test for viable pathways.

I'm just as sure that you haven't thought carefully about any of them. You're just throwing shit at this point.
Quote
If you don't test for a pathway though, you have nothing but comparable sequences, which may show common ancestry but do nothing to show how evolution occurred.  It could've been gradual step-by-step, or it could've been saltational.  Who knows?  You've established nothing in regard to mechanism.

Gee, if we establish that homologous (not orthologous) biological phenomena have homologous mechanisms, what does that show?
Quote
As for how things came to be via design;...

What Henry and Cuvier said. Pure tard. You can't even discriminate between design and manufacture.

Psst...the term "code" is used metaphorically. There's nothing symbolic about it.

  
Mark Iosim



Posts: 27
Joined: Oct. 2007

(Permalink) Posted: Sep. 04 2008,21:31   

As long as scientists insist that there is no mystery in life phenomenon, ID proponents will have material to ridicule this science and promote their agenda.

I am not ID supporter, but I also can’t separate life (and even spontaneous processes in general) from some sort of purpose. Just think about thermodynamic description of a chemical reaction: it occurs TO ACHIEVE a state of minimum of free energy of system. Does is sound like metaphysics?

But I am more interested not in “ID vs. Natural Evolution” arguments, but in Complexity itself. If information is reduction in uncertainty, the complexity, I think, is a level of this uncertainty.

In my opinion, the main problem with defining Complexity is in treating it as an objective category, while it should be regarded as relative to observer only. The Complexity, of a problem or task, cannot be separated from a specific intelligence that is solving this problem. In the same time we can’t define (and measure) intelligence without referring to a particular problem. Therefore the definitions of Complexity and Intelligence (and Information probably also) are inseparable and both categories aren’t absolute, but are relative to each other.

The Intelligence is measured by interaction with a specific problem. For example if the problem to solve is a protein folding, then any single cell (or even molecule of protein) could be much more intelligent that we are.

The same way a complexity of a specific problem could be measured only in reference to a specific intelligence that attempts to solve this problem. For example, what is more complex: to build a house, surgically remove an appendix, or solve a linear differential equation? The answer depends on whom you ask- Carpenter, Surgeon, or Mathematician.

  
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 04 2008,22:27   

Quote (Daniel Smith @ Sep. 03 2008,19:09)
By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

Been done. Multiple times. Here's just one example:

Quote
J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5.

Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus.

Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.

Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote.


Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution!

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Sep. 05 2008,02:51   

Quote (qetzal @ Sep. 04 2008,22:27)
Quote (Daniel Smith @ Sep. 03 2008,19:09)
By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

Been done. Multiple times. Here's just one example:

 
Quote
J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5.

Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus.

Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.

Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote.


Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution!

Do you accept evolution now Daniel? Now that you've been given the evidence that you asked for?

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Sep. 05 2008,13:26   

Quote
As long as scientists insist that there is no mystery in life phenomenon,


Who the heck is claiming that there aren't any unanswered questions? If that ever happened, researchers would be out of jobs.

Henry

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Sep. 05 2008,14:54   

Quote (dogdidit @ Aug. 31 2008,22:22)
As for:      
Quote
I'd be intensely interested in an algorithm that mirrors real biological evolution.

Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough?

Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Sep. 05 2008,16:14   

Quote (dvunkannon @ Sep. 05 2008,14:54)
   
Quote (dogdidit @ Aug. 31 2008,22:22)
As for:            
Quote
I'd be intensely interested in an algorithm that mirrors real biological evolution.

Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough?

Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then.

No doubt by now Jebus has shown him where the CSI was injected.

edited for spelling

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
dvunkannon



Posts: 1377
Joined: June 2008

(Permalink) Posted: Sep. 05 2008,17:14   

Quote (dogdidit @ Sep. 05 2008,17:14)
Quote (dvunkannon @ Sep. 05 2008,14:54)
     
Quote (dogdidit @ Aug. 31 2008,22:22)
As for:              
Quote
I'd be intensely interested in an algorithm that mirrors real biological evolution.

Any simulation must be judged by the level of fidelity one is looking for, but would Blondie24 (Anaconda) fill the bill? Not an algorithm, really, but more of a process (which is what evolution is). Random variation and natural selection -- it's all there. No targets, no external fitness measure, no guidance, no CSI injected; just live (and spawn) or die. Close enough?

Gil Dodgen of UD fame gives an amazingly positive Amazon review to Blondie24, back in 2001. Maybe he wasn't saved back then.

No doubt by now Jebus has shown him where the CSI was injected.

edited for spelling

Artificial Chemistries - an old review, but might help Daniel if he wants to pursue the relevance of artificial models to the real world.

--------------
I’m referring to evolution, not changes in allele frequencies. - Cornelius Hunter
I’m not an evolutionist, I’m a change in allele frequentist! - Nakashima

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Sep. 05 2008,18:28   

Quote (qetzal @ Sep. 04 2008,20:27)
   
Quote (Daniel Smith @ Sep. 03 2008,19:09)
By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.

Been done. Multiple times. Here's just one example:

     
Quote
J Mol Biol. 2007 Jun 15;369(4):1060-9. Epub 2007 Apr 5.

Extremely thermophilic translation system in the common ancestor commonote: ancestral mutants of Glycyl-tRNA synthetase from the extreme thermophile Thermus thermophilus.

Shimizu H, Yokobori S, Ohkuri T, Yokogawa T, Nishikawa K, Yamagishi A.

Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Based on phylogenetic analysis of 16 S and 18 S rRNAs, the common ancestor of all organisms (Commonote) was proposed to be hyperthermophilic. We have previously tested this hypothesis using enzymes with ancestral residues that are inferred by molecular phylogenetic analysis. The ancestral mutant enzymes involved in metabolic systems show higher thermal stability than wild-type enzymes, consistent with the hyperthermophile common ancestor hypothesis. Here, we have extended the experiments to include an enzyme of the translation system, glycyl-tRNA synthetase (GlyRS). The translation system often shows a phylogenetic tree that is similar to the rRNA tree. Thus, it is likely that the tree represents the evolutionary route of the organisms. The maximum-likelihood tree of alpha(2) type GlyRS was constructed. From this analysis the ancestral sequence of GlyRS was deduced and individual or pairs of ancestral residues were introduced into Thermus thermophilus GlyRS. The ancestral mutants were expressed in Escherichia coli, purified and activity measured. The thermostability of eight mutated proteins was evaluated by CD (circular dichroism) measurements. Six mutants showed higher thermostability than wild-type enzyme and seven mutants showed higher activity than wild-type enzyme at 70 degrees C, suggesting an extremely thermophilic translation system in the common ancestor Commonote.


Note that it doesn't just show that the inferred ancestral sequence works. It shows that the inferred ancestral sequence has specific properties predicted based on evolution!

This is exactly what I've been looking for.  Thank you for posting that qetzal.  I only wish I could read the whole paper.  You say that experiments like these have been done multiple times: if you have any more links to papers such as this (preferably the full paper), I'm interested and would appreciate your posting them.

Thanks again.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Timothy McDougald



Posts: 1030
Joined: Dec. 2006

(Permalink) Posted: Sep. 06 2008,07:46   

Quote
By "lab tested" I mean something that is tested period.  For instance, if two sets of genes are known, and are said to be from a common ancestor, it should be possible to extrapolate the common ancestral gene (and intermediate genes) via computer simulation.  Then you should be able to test the resultant genes for viability by altering and inserting the DNA into the living organisms.


My favorite example (link goes to the pdf)

Here is the abstract:

 
Quote
A morphological or physiological trait may appear multiple times in evolution. At the molecular level, similar protein functions may emerge independently in different lineages. Whether these parallel functional changes are due to parallel amino acid substitutions has been a subject of debate. Here, I address this question using digestive ribonucleases (RNases) of two groups of foregut-fermenting mammals: ruminant artiodactyls and colobine monkeys. The RNase1 gene was duplicated twice in ancestral ruminants at least 40 MYA, and it was also duplicated in the douc langur, an Asian colobine, approximately 4 MYA. After duplication, similar functional changes occurred in the ruminant and monkey enzymes. Interestingly, five amino acid substitutions in ruminant RNases that are known to affect its catalytic activity against double-stranded (ds) RNA did not occur in the monkey enzyme. Rather, a similar functional change in the monkey was caused by a different set of nine substitutions. Site-directed mutagenesis was used to make three of the five ruminant-specific substitutions in the monkey enzyme. Functional assays of these mutants showed that one of the three substitutions has a similar effect in monkeys, the second has a stronger effect, and the third has an opposite effect. These results suggest that (1) an evolutionary problem can have multiple solutions, (2) the same amino acid substitution may have opposite functional effects in homologous proteins, (3) the stochastic processes of mutation and drift play an important role even at functionally important sites, and (4) protein sequences may diverge even when their functions converge.


--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
dnmlthr



Posts: 565
Joined: Mar. 2008

(Permalink) Posted: Sep. 06 2008,08:30   

Weird, where did afarensis' comment go?

--------------
Guess what? I don't give a flying f*ck how "science works" - Ftk

  
Timothy McDougald



Posts: 1030
Joined: Dec. 2006

(Permalink) Posted: Sep. 06 2008,09:50   

Quote (dnmlthr @ Sep. 06 2008,08:30)
Weird, where did afarensis' comment go?

Seems to be back now...

Just to follow up, Zhang has done several papers where he recreates ancestral genes and looks at mutations, selection, etc. as have a number of other labs.

--------------
Church burning ebola boy

FTK: I Didn't answer your questions because it beats the hell out of me.

PaV: I suppose for me to be pried away from what I do to focus long and hard on that particular problem would take, quite honestly, hundreds of thousands of dollars to begin to pique my interest.

   
qetzal



Posts: 311
Joined: Feb. 2006

(Permalink) Posted: Sep. 06 2008,10:16   

Quote (Daniel Smith @ Sep. 05 2008,18:28)
This is exactly what I've been looking for.  Thank you for posting that qetzal.  I only wish I could read the whole paper.  You say that experiments like these have been done multiple times: if you have any more links to papers such as this (preferably the full paper), I'm interested and would appreciate your posting them.

Thanks again.

You're welcome.

I found this quite quickly at PubMed by searching the phrase "ancestral sequence" (including the quote marks).

Not all the hits are what you want, but many are, and some have free full text links. See the little paper icons to the left of each hit? The ones with a green or orange bar at the top have free full text links.

Try other search phrases or word combos. Try using the Limits tab. You can limit searches to title words, even restrict your search to papers with free full text links if you want.

Also, if you find one reference you like, try using the "Related Articles" link to the right of it.

(Apologies if you're already familiar with PubMed.)

  
Patrickarbuthnot



Posts: 21
Joined: Feb. 2010

(Permalink) Posted: Feb. 24 2010,23:53   

Quote (Wesley R. Elsberry @ Aug. 26 2008,18:14)
Antievolutionists want to confuse and conflate meaning and information. Spetner, Gitt, Truman, and Dembski... all of them want meaning to be folded within whatever sort of "information" they propose.

Shannon's discussion of information explicitly excluded meaning. Algorithmic information theory only cares about one aspect of meaning: what is the shortest program and input that can generate a string?

Critique of Dembski's "complex specified information"

Hello Wesley R. Elsberry,
I have never posted on your site before this should prove to be very interesting.

--------------
Thomas Edison said: “The doctor of the future will give no medicine, but will interest her or his patients in the care of the human frame, in a proper diet, and in the cause and prevention of disease.”

  
Dr.GH



Posts: 2113
Joined: May 2002

(Permalink) Posted: Feb. 25 2010,00:15   

Quote (Patrickarbuthnot @ Feb. 24 2010,21:53)
Quote (Wesley R. Elsberry @ Aug. 26 2008,18:14)
Antievolutionists want to confuse and conflate meaning and information. Spetner, Gitt, Truman, and Dembski... all of them want meaning to be folded within whatever sort of "information" they propose.

Shannon's discussion of information explicitly excluded meaning. Algorithmic information theory only cares about one aspect of meaning: what is the shortest program and input that can generate a string?

Critique of Dembski's "complex specified information"

Hello Wesley R. Elsberry,
I have never posted on your site before this should prove to be very interesting.

Well, don't leave us in suspense.

PS, Welcome.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
sledgehammer



Posts: 533
Joined: Sep. 2008

(Permalink) Posted: Mar. 08 2010,20:23   

Creo Math.  Maybe Dembski can offer a course?
From here
Jonathon Bartlett is giving Nick Matzke a math lesson on how to add bits.  It's hilarious!
Nick:  
Quote
“Even if NS can only add 1 bit of information at a time to a genome, just repeat for millions of years and you’ve generated lots of new information. “

Bartlett:  
Quote
Again, you need to actually take a look at the math.  If natural selection adds 1 bit of information at a time to a genome, and does so each day for 20 billion years, at the end of it you will have 42.7 bits of information (because it is an order-of-magnitude measurement).

Huh???
Bartlett explains:  
Quote
Evolutionists often appeal to the vast age of the universe as justification for their improbable claims.  But the nice thing about mathematics is that you can use it to evaluate claims that would otherwise be incomprehensible.  While it might seem that adding 1 bit of information each day for 20 billion years would certainly add up to something past Dembski’s 500 bits, my trusty calculator calculates it to be 42.7 bits (the calculation is log2(365 * 20000000000) if you want to try it on your calculator).

Lessee, using Bartlett Math

1 bit+1 bit =log2(1+1)=1bit   (1+1=1)

2bits+2bits-log2(2+2)=2 bits  (2+2=2)

now it gets better:
4b +4b = log2(8) = 3

4b+4b=3b !!!! (Evolution destroys information. yay!)

A little math is a dangerous thing

--------------
The majority of the stupid is invincible and guaranteed for all time. The terror of their tyranny is alleviated by their lack of consistency. -A. Einstein  (H/T, JAD)
If evolution is true, you could not know that it's true because your brain is nothing but chemicals. ?Think about that. -K. Hovind

  
fnxtr



Posts: 2483
Joined: June 2006

(Permalink) Posted: Mar. 08 2010,21:32   

Quote (sledgehammer @ Mar. 08 2010,18:23)
Creo Math.  Maybe Dembski can offer a course?
From here
Jonathon Bartlett is giving Nick Matzke a math lesson on how to add bits.  It's hilarious!
Nick:  
Quote
“Even if NS can only add 1 bit of information at a time to a genome, just repeat for millions of years and you’ve generated lots of new information. “

Bartlett:  
Quote
Again, you need to actually take a look at the math.  If natural selection adds 1 bit of information at a time to a genome, and does so each day for 20 billion years, at the end of it you will have 42.7 bits of information (because it is an order-of-magnitude measurement).

Huh???
Bartlett explains:  
Quote
Evolutionists often appeal to the vast age of the universe as justification for their improbable claims.  But the nice thing about mathematics is that you can use it to evaluate claims that would otherwise be incomprehensible.  While it might seem that adding 1 bit of information each day for 20 billion years would certainly add up to something past Dembski’s 500 bits, my trusty calculator calculates it to be 42.7 bits (the calculation is log2(365 * 20000000000) if you want to try it on your calculator).

Lessee, using Bartlett Math

1 bit+1 bit =log2(1+1)=1bit   (1+1=1)

2bits+2bits-log2(2+2)=2 bits  (2+2=2)

now it gets better:
4b +4b = log2(8) = 3

4b+4b=3b !!!! (Evolution destroys information. yay!)

A little math is a dangerous thing

What. The. Hell.
?

My jade plant is 25 grams heavier today than yesterday. How many bits of information has it gained?

What complete bullshit.

--------------
"But it's disturbing to think someone actually thinks creationism -- having put it's hand on the hot stove every day for the last 400 years -- will get a different result tomorrow." -- midwifetoad

"I am in a rush to catch up with science work." -- Gary Gaulin

  
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