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Author Topic:   coded information in DNA
Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 286 of 334 (512327)
06-16-2009 1:16 PM
Reply to: Message 285 by Blue Jay
06-16-2009 1:04 PM


Re: Snowmen are actually made by snowclouds!
In reality, I'm pretty sure the waggle-dance code is genetic: queens do not dance, and so, there is no one from whom the first batch of workers in a hive can learn the dance. Yet, the workers can do the dance. Thus, it is probably an innate, rather than a learned, behavior.
I have a feeling you're wrong about this; there is variation in bee waggle dances and, IIRC, it's cultural rather than genetic in transmission.
I don't have time to go hunting for references right now. I'll look later.

This message is a reply to:
 Message 285 by Blue Jay, posted 06-16-2009 1:04 PM Blue Jay has replied

Replies to this message:
 Message 288 by Wounded King, posted 06-16-2009 4:52 PM Dr Jack has not replied
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Richard Townsend
Member (Idle past 4731 days)
Posts: 103
From: London, England
Joined: 07-16-2008


Message 287 of 334 (512345)
06-16-2009 4:30 PM
Reply to: Message 252 by WordBeLogos
06-13-2009 11:11 PM


Is it possible to deduce that the law of conservation of matter and energy is true because we have no evidence to the contrary? Because it's only based on 100% of human observation? Because not one human has observed evidence to the contrary?
It is violated on the quantum scale provided the violation is within the limits of the Heisenberg uncertainty relationm ie not directly detectable. But this violation does have observable consequences, e.g. quantum tunnelling. So in effect violations have been observed.
Note also that in the classical world, there were two separate conservation laws, conservation of energy and conservation of momentum. These were merged in relativity because they can individually be violated in relativity, but not in aggregate. In the 19th century, someone could have made your argument based on energy conservation - and they would have been wrong.
This shows the danger of induction. In effect I'm saying that we can't use induction to justify any physical law. How can we know that it will apply in all circumstances? We can't. We believe (or at least adopt) theories because they provide deep explanations for things, and are consistent with evidence.
In this case you've not only used induction but you've made an unjustified generalization. From 'by humans' to 'by intelligence'. We have no evidence of any intelligence other than human, and that any other intelligence has created codes, so what justification is there for this generalization?
Also, there is no fundamental principle involved in your statement about codes. Conservation laws, on the other hand, are powerful vehicles for exploring physics, they correlate to the existence of symmetries, and so they have a powerful role in our explanations.
Your statement has no correlation to any deep explanatory principle.
I suspect your statement is designed solely to support your already-held beliefs. Do you know any people who hold your belief about codes who are not already believers in God?

This message is a reply to:
 Message 252 by WordBeLogos, posted 06-13-2009 11:11 PM WordBeLogos has not replied

Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 288 of 334 (512346)
06-16-2009 4:52 PM
Reply to: Message 286 by Dr Jack
06-16-2009 1:16 PM


Not knowing about the bees, possibly birds as well.
You are correct to doubt WordBeLogos on his biology. Queens which fly off to found new hives, with swarms of workers, are generally old queens. The new virgin queen is born into a hive of workers that already know how to forage and dance, and the 1st generation of workers that she produces will be able to learn from the previous queen's offspring.
TTFN,
WK

This message is a reply to:
 Message 286 by Dr Jack, posted 06-16-2009 1:16 PM Dr Jack has not replied

Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 289 of 334 (512350)
06-16-2009 6:23 PM
Reply to: Message 286 by Dr Jack
06-16-2009 1:16 PM


Honeybee Behavior and Genetics
Hi, Mr Jack.
Mr Jack writes:
I have a feeling you're wrong about this; there is variation in bee waggle dances and, IIRC, it's cultural rather than genetic in transmission.
Johnson et al 2002:
quote:
The results reported here are in agreement with previous findings that dance is a complex honey bee behavior under simple genetic control. This is not unusual in honeybees, as there are several examples of strong genetic influence of behavior in the genus Apis.
A lot of aspects of honeybee behavior are used in behavioral genetics because a lot of their behaviors are explained by simple Mendelian genetics.
However, Giurfa et al 2001 found insight learning in honeybees, too.
-----
But, Wounded King is right: honeybee queens have never been documented founding nests on their own. I thought I had read that solitary queens occasionally establish colonies, but I can't find it now, so I'll assume I was wrong.
(To WK: that was Bluejay's biology, not WordBeLogos's. And, Bluejay is an entomologist who recently took a course on insect behavior that included at least three weeks on honeybees. )
-----
The conundrum for WordBeLogos still stands: either way, the honeybee waggle-dance causes problems for his intelligence-only hypothesis for codes.
Edited by Bluejay, : Note to Wounded King

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 286 by Dr Jack, posted 06-16-2009 1:16 PM Dr Jack has not replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 290 of 334 (512356)
06-17-2009 1:14 AM


BluejayYou writes:
do realize the implication of this statement, right?
You've set the bar pretty low: if honeybees are sufficiently intelligent to create a code, then the Intelligent Designer need not be any more intelligent than a honeybee.
In your mind, what is the cut-off point?
How intelligent must something be to create a code?
Please note, just because a bee could be smart enough to make a code, doesn't mean it's smart enough to make THE genetic code.
We can posit bees have some level of intelligence. After all they are smart enough to get mad at us when we mess with their nest.
So for the discussion lets say they did create the dance themselves. They still may only be 0.0000000001% as intelligent as humans. But they are still infinitely more intelligent than pebbles, because pebbles have zero intelligence. Pebbles have zero ability to create codes whatsoever.
So pmarshalls thesis still stands. Codes ONLY come from other codes or intelligent beings. There are many codes hard coded in DNA, mating calls of insects for example. DNA is the Mother Code.
lyx2no writes:
The hill is the encoder: it writes the path of the ball. The ball is the decoder: it reads the shape of the hill.
The USGS lists the symbols.
Code is defined as communication between an encoder a "writer or speaker" and a decoder a "reader or listener" using agreed upon symbols.
In your example of a ball rolling down hill, there is no set of comunicated symbols. The USGS symbols are *ONLY* used by humans to describe the ball. And not used *BY* any ball. This is totally different from DNA , the base pairs are used *BY* the DNA as symbols. GGG = Glycine. UUU = Phenylalanine.
DNA carries out the rules of the genetic code in addition to obeying the laws of physics. The ball rolling down the hill has no such code and simply obeys the laws of physics.
Percy writes:
About information and meaning Shannon says on page 1 of his paper A Mathematical Theory of Communications:
Shannon writes:
The fundamental problem of communication is that of reproducing at one point either exactly or approximately a message selected at another point. Frequently the messages have meaning; that is they refer to or are correlated according to some system with certain physical or conceptual entities. These semantic aspects of communication are irrelevant to the engineering problem.
In response, Word simply quotes Perry Marshall claiming that meaning does exist in Shannon information:
Word quoting Perry Marshall in Message 279 writes:
In Shannon’s system, meaning DOES exist. It is extremely simple: the only meaning that we need to be concerned with here is whether the message is encoded or decoded properly. In DNA, the meaning of GGG is Glycine. That meaning is real and black and white and quantifiable. In ASCII, the meaning of 100001 is capital A.
For WordBeLogos, Shannon stating that meaning is irrelevant to the problem of communicating information can be trumped by Internet denizen Perry Marshall claiming Shannon is wrong to have said this.
For Shannon, DNA’s ‘GGG’ is information. ‘GGG’ can be interpreted as meaning Glycine, but this meaning is irrelevant to the information itself. ‘GGG’ can be interpreted as having literally any meaning one wants, and the machinery in cells actually attach more than one meaning to ‘GGG’. During protein production ‘GGG’ means Glycine, but during fission (cell division) ‘GGG’ means match up with ‘CCC’.
Until Word begins taking seriously Shannon’s unambiguous statement that meaning is irrelevant to the information problem, this discussion will not be able to make progress.
Percy you might want to read all of what Shannon says instead of quotemining his paper.
Mr.Marshall addresses all these questions at Semantics of DNA.
Specifically he says: ‘Weaver has stated that his theory cannot quantify semantical meaning. There is no debate about that. But you have carried this further and now said that semantical meaning therefore does not exist. Shannon and Weaver have most certainly NOT stated that semantical meanings don’t exist; in fact when Weaver says In fact, two messages, one of which is heavily loaded with meaning and the other of which is pure nonsense this is a direct acknowledgement that meaning is real and that it is important.’
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

Replies to this message:
 Message 291 by Percy, posted 06-17-2009 7:20 AM WordBeLogos has not replied
 Message 292 by Percy, posted 06-17-2009 7:58 AM WordBeLogos has not replied
 Message 293 by Blue Jay, posted 06-17-2009 8:18 AM WordBeLogos has not replied
 Message 294 by lyx2no, posted 06-17-2009 8:53 AM WordBeLogos has not replied
 Message 296 by Dr Adequate, posted 06-18-2009 1:44 AM WordBeLogos has not replied

Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 291 of 334 (512382)
06-17-2009 7:20 AM
Reply to: Message 290 by WordBeLogos
06-17-2009 1:14 AM


WordBeLogos writes:
Percy you might want to read all of what Shannon says instead of quotemining his paper.
Mr.Marshall addresses all these questions at Semantics of DNA.
Specifically he says: ‘Weaver has stated that his theory cannot quantify semantical meaning. There is no debate about that. But you have carried this further and now said that semantical meaning therefore does not exist. Shannon and Weaver have most certainly NOT stated that semantical meanings don’t exist; in fact when Weaver says In fact, two messages, one of which is heavily loaded with meaning and the other of which is pure nonsense this is a direct acknowledgement that meaning is real and that it is important.’
Word, at some point you've got to stop parroting Perry Marshall and think for yourself. You've just quoted Marshall rebutting someone who apparently claimed that semantic meaning doesn't exist. I never claimed that semantic meaning doesn't exist, therefore your response is a complete non sequitur.
What I did do is quote Shannon stating that semantic meaning is irrelevant to the problem of communicating information, and Perry Marshall completely agrees. As he says right at the top of your link (Semantics of DNA):
Perry Marshall writes:
Claude Shannon's information theory does not mathematically quantify semantics - because so far as we know it's impossible to do so.
I couldn't have said it better myself. You can't say that Shannon information supports your claims about semantic meaning because Shannon information cannot say anything about semantic meaning.
But Marshall goes on to say things that are totally bogus:
However, Shannon and Weaver explicitly acknowledge the existence and importance of semantics. A message, after all, must mean something or it's not a message.
I don't know why Marshall thinks that Shannon and Weaver would ever feel the need to explicitly state something that no one in their right mind denies, that semantics exist and is important. In his paper Shannon mentions semantic meaning only to state that it doesn't play a role in communicating information. But anyway, a message definitely does not have to have meaning. The simplest example would be testing a communication system where you'd likely begin by sending simple sequences of bits that mean nothing semantically.
I continue to suggest that you learn what formal information theory actually says instead of what Perry Marshall says it says. Think for yourself.
--Percy

This message is a reply to:
 Message 290 by WordBeLogos, posted 06-17-2009 1:14 AM WordBeLogos has not replied

Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 292 of 334 (512386)
06-17-2009 7:58 AM
Reply to: Message 290 by WordBeLogos
06-17-2009 1:14 AM


WordBeLogos,
Unless there's two Perry Marshall's with the same middle initial, Perry sells his own line of website promotion books, DVDs and seminars: Perry Marshall's Products & Services. This is one good looking guy:
You could use Perry's photo as your avatar!
Perry's gift is his ability to sell ideas. He doesn't really know anything about information theory. I again suggest you read up a bit and learn what information theory really says, because it doesn't say anything about semantic meaning. All Perry's claims about semantic meaning are not supported by anything within the field of information theory.
--Percy

This message is a reply to:
 Message 290 by WordBeLogos, posted 06-17-2009 1:14 AM WordBeLogos has not replied

Blue Jay
Member (Idle past 2697 days)
Posts: 2843
From: You couldn't pronounce it with your mouthparts
Joined: 02-04-2008


Message 293 of 334 (512389)
06-17-2009 8:18 AM
Reply to: Message 290 by WordBeLogos
06-17-2009 1:14 AM


Hi, WordBeLogos.
WordBeLogos writes:
Please note, just because a bee could be smart enough to make a code, doesn't mean it's smart enough to make THE genetic code.
You're going to have to do better than that.
Here's what we have so far:
Premise 1: Honeybees can make codes.
Premise 2: The genetic code is a code.
Conclusion: Honeybees can make the genetic code.
Until you provide further evidence, we have to accept this as the logical conclusion of your own argument.
-----
Your dichotomous argument in relation to the waggle-dance ends with one of two conclusions:
  1. If the honeybee consciously created the waggle-dance code, the Intelligent Designer need not be any more intelligent than a honeybee.
  2. If the waggle-dance code resulted from a genetic mutation, the Intelligent Designer need not be any more intelligent than a genetic mutation.

-Bluejay (a.k.a. Mantis, Thylacosmilus)
Darwin loves you.

This message is a reply to:
 Message 290 by WordBeLogos, posted 06-17-2009 1:14 AM WordBeLogos has not replied

lyx2no
Member (Idle past 4716 days)
Posts: 1277
From: A vast, undifferentiated plane.
Joined: 02-28-2008


Message 294 of 334 (512390)
06-17-2009 8:53 AM
Reply to: Message 290 by WordBeLogos
06-17-2009 1:14 AM


Then You Fail
Code is defined as communication between an encoder a "writer or speaker" and a decoder a "reader or listener" using agreed upon symbols.
Then you fail:
  • The "writer" is the shape of the codon or the shape of the hill.
  • The "reader" is how an amino acid orients itself to a shape just as a ball follows a slope.
  • There are no symbols in either case. The carnation of my Message 214 is a symbol: the shape of these objects aren't symbols.
In your example of a ball rolling down hill, there is no set of comunicated symbols. The USGS symbols are *ONLY* used by humans to describe the ball. And not used *BY* any ball. This is totally different from DNA , the base pairs are used *BY* the DNA as symbols. GGG = Glycine. UUU = Phenylalanine.
The symbols GGG and UUU are *ONLY* used by humans to describe the codon. Ribosomes facilitate the fitting of a square peg into a square hole. They don't read a codon and then construct a protein in some other part of the cell base upon that information. The shapes of codons position amino acids just as the shapes of hills position balls (or better: rivers).
And why are you talking about base pairs? (It's because you don't actually understand what you're talking about so as you toss words about you fail to recognize when you're producing rubbish. I've tried subtle before, and it doesn't work.)
DNA carries out the rules of the genetic code in addition to obeying the laws of physics. The ball rolling down the hill has no such code and simply obeys the laws of physics.
DNA carries out the rules of the genetic code *BY* obeying the laws of physics.

Ridicule is the only weapon which can be used against unintelligible propositions. Ideas must be distinct before reason can act upon them.
Thomas Jefferson

This message is a reply to:
 Message 290 by WordBeLogos, posted 06-17-2009 1:14 AM WordBeLogos has not replied

bluegenes
Member (Idle past 2477 days)
Posts: 3119
From: U.K.
Joined: 01-24-2007


Message 295 of 334 (512398)
06-17-2009 11:45 AM
Reply to: Message 279 by WordBeLogos
06-16-2009 2:10 AM


WordBeLogos writes:
You are doing precisely what you are acusing me of doing, assuming without proof. I freely admit I can't put God in a laboratory and test Him. I only claim to infer. But you are trying to get away with an assumption that you cannot prove. There is *NO* inference to a natural explanation of DNA. None. Just because it's here, and we observe it, doesn't mean it's natural. You can't have it both ways.
You're finally catching on, but you've still got it wrong. Both of us are making observation based inferences, and both of us would be assuming our conclusions if we claimed to be proving anything. Yet your friend Marshall claims to have "proof" of his god.
My argument is a parody of yours. I can phrase it in many ways.
"All known intelligent designers have code as a prerequisite. From this evidence, we can infer that code must precede intelligence, and therefore not all codes can be intelligently designed."
Now, from "all codes that we know the source of are intelligently designed" it does not follow that "all codes are intelligently designed", and from "all known intelligent designers have code as a prerequisite" it does not follow that "code must precede intelligence".
If you're going to make observation based inferences that mean anything, you need to take all the observations available into account. Ignoring the fact that code precedes all known intelligent designers when you're trying to argue that all codes are the product of intelligent design makes your inference useless.
The only way to actually discover the origin of the DNA code is via origin of life research.
I'll give you another illustration of your type of argument.
Birds are flying things with wings. When we can directly observe the origin of things with wings that fly, they are intelligently designed. Therefore, we can infer that all birds are intelligently designed.
Do you think it's a good one? (You probably do!).
There are hundreds of things that humans make and for which we can see analogies in nature. Of course we can directly observe our own actions. We make artificial hills; do you want to try one based on that? Or do we know too much about hill formation to stick a god in the gaps?
Incidentally, your claim (or P. Marshall's claim) that "there is no natural process known to science that creates coded information" would make your argument a "god of the gaps" argument, along with its other faults. On top of that, it's arguably not much of a gap, because natural selection can organize information, and codes are organized information. The selection of better organized or more useful information can be observed, and so can the creation of new information by natural mechanisms of variation in biology.
I recommend that you follow the origins of life research closely, as interesting things are happening. If you're an honest person, then I think that the next time you communicate with your god, you should address him as "dear gaps in human knowledge", and you could also consider that gaps in knowledge are not usually considered to be sentient beings.
You should also listen to Doc Adequate above. The laws of physics don't tell you how mountains are formed, or how rivers are formed, or how chemical codes are formed, but all those things are in keeping with those laws. Interestingly, the existence of intelligent designers without some kind of organized information as a prerequisite probably would break numerous scientific laws!
And a final tip. Never listen to religious people trying to prove the existence of the father figure of their desires to themselves or anyone else. It's all emotional, not rational, and they practise obvious self-deception.

This message is a reply to:
 Message 279 by WordBeLogos, posted 06-16-2009 2:10 AM WordBeLogos has replied

Replies to this message:
 Message 310 by WordBeLogos, posted 06-21-2009 5:44 AM bluegenes has replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 296 of 334 (512433)
06-18-2009 1:44 AM
Reply to: Message 290 by WordBeLogos
06-17-2009 1:14 AM


DNA is the Mother Code.
All hail the Great Mother!
How should we worship the Mother Code of DNA?
Oh ... wait ... was that not what you meant?

This message is a reply to:
 Message 290 by WordBeLogos, posted 06-17-2009 1:14 AM WordBeLogos has not replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 297 of 334 (512435)
06-18-2009 3:11 AM


Gentlemen,
Here is some suggested material before this discussion can make any more progress... view all parts
https://www.youtube.com/watch?v=d1xkpncGHEQ&feature=related
...please do not simply watch one or two parts and cherry pick an isolated statement or two and continue on with more ad hominem attacks.
-Word
Edited by WordBeLogos, : No reason given.

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

Replies to this message:
 Message 298 by Dr Adequate, posted 06-18-2009 3:13 AM WordBeLogos has not replied
 Message 299 by Percy, posted 06-18-2009 8:02 AM WordBeLogos has not replied

Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 298 of 334 (512436)
06-18-2009 3:13 AM
Reply to: Message 297 by WordBeLogos
06-18-2009 3:11 AM


In your own words please, according to the rules of this form.
Thank you.

This message is a reply to:
 Message 297 by WordBeLogos, posted 06-18-2009 3:11 AM WordBeLogos has not replied

Percy
Member
Posts: 22388
From: New Hampshire
Joined: 12-23-2000
Member Rating: 5.2


Message 299 of 334 (512454)
06-18-2009 8:02 AM
Reply to: Message 297 by WordBeLogos
06-18-2009 3:11 AM


WordBeLogos writes:
Here is some suggested material before this discussion can make any more progress... view all parts
You're pulling this stunt again? This thread is strewn with you making other people's arguments that you don't understand, and in this latest example there's no way to even tell who or what you're replying to.
If you want to offer a video as a supporting reference, fine, but first make the point in your own words. I watched the first few seconds, and it's Werner Gitt giving a lecture. So why don't you let us in on what you're up to. Perhaps finally understanding that you can't claim Shannon to support your claims about information and meaning, you're abandoning him for Gitt?
Dembski, Gitt and Spetner are all pushing their own non-scientific views on information, but none have bothered going to the trouble of actually connecting their ideas to reality.
--Percy

This message is a reply to:
 Message 297 by WordBeLogos, posted 06-18-2009 3:11 AM WordBeLogos has not replied

WordBeLogos
Member (Idle past 5392 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 300 of 334 (512765)
06-20-2009 6:53 PM


Gentlemen,
Bluejay writes:
Here's what we have so far:
Premise 1: Honeybees can make codes.
Premise 2: The genetic code is a code.
Conclusion: Honeybees can make the genetic code.
Premise 1: Honeybees can make codes.
Premise 2: HTML is a code.
Conclusion: Honeybees can write HTML and make web pages.
Again, because something makes code doesn't mean it can make *THE* genetic code.
bluegenes writes:
Incidentally, your claim (or P. Marshall's claim) that "there is no natural process known to science that creates coded information" would make your argument a "god of the gaps" argument, along with its other faults. On top of that, it's arguably not much of a gap, because natural selection can organize information, and codes are organized information. The selection of better organized or more useful information can be observed, and so can the creation of new information by natural mechanisms of variation in biology.
In order for natural selection to take place, self-replication has to occur.
Self replication requires code.
There must be code in the first place before you can even talk about evolution.
Yes, this is a God of the Gaps argument. But it is a different kind of argument. Because information is qualitatively and quantitatively different from matter and energy. As Norbert Weiner said, information is information, neither matter nor energy.
The DNA question is a how did information come to exist? question.
Which is similar to how did the universe come to exist except there’s only one universe and we have nothing else to compare it to.
With information we have thousands of examples to compare it to.
The burden is firmly on the shoulders of the materialist to account for the origin of information.
Your argument is a naturalism of the gaps argument. It is actually no different, you just use different terminology and sweep it under a rug called natural selection and call it science. You use that word no differently than most people use the word god. In actuality you have explained *NOTHING.* You have produced no model, no hypothesis, and there is nothing that you have provided which can be tested.
So again, I demand that you or anyone else *SHOW* one example of coded information arising naturally.
And yes the laws of physics *DO* tell you how mountains and rivers are formed . They tell you *EVERYTHING* you need to know.
But they don’t explain the coded information in DNA.
-Word

John 1:1 In the beginning was the Word, and the Word was with God, and the Word was God.

Replies to this message:
 Message 301 by RAZD, posted 06-20-2009 7:13 PM WordBeLogos has replied
 Message 319 by Blue Jay, posted 06-21-2009 9:05 PM WordBeLogos has replied

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