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Author Topic:   coded information in DNA
WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 1 of 334 (509882)
05-25-2009 7:13 PM


Hi guys, I couldn't find a thread on this specific question which I'm sure has been mentioned somewhere, please forgive me. But how do we account for the coded symbolic information in DNA through the laws of physics and chemistry?

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 3 of 334 (509890)
05-25-2009 9:39 PM
Reply to: Message 2 by AdminNosy
05-25-2009 8:27 PM


Re: Much More Detail Please
Hello AdminNosy,
Coded information = a system of symbols used by an encoding / decoding mechanism that transmits a message which is seperate from the communication medium itself.
Examples would be english, computer languages, radio signal and music and yes, DNA. All known codes always involve a system of symbols which represent a idea, concept or plans etc.
As far as my view on this, I don't see how the laws of physics and chemistry alone can account for the coded information contained in DNA. All known codes that we know the origin of always come from intelligent activity.
The next question I suppose is will we all agree DNA contains coded information or not. I say it most surely does based on information theory itself. We can start here I guess, thx.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 5 of 334 (509907)
05-26-2009 1:36 AM
Reply to: Message 4 by AdminNosy
05-25-2009 9:50 PM


Re: Much More Detail Please
Seperate in the sense that paper and ink does not account for the information in a book. Books cannot be reduced to paper and ink and DNA is not reducible to chemicals.
A book containing random letters contains no message. A hypothetical DNA molecule with random bases contains no plan / instructions for an organism. But a real book and a real DNA molecule both contain real codes represented by symbols composed of real matter that represent real useful information and uniquely specify external objects, processes and ideas. The code itself is an immaterial entity.
Naturalistic explanations may provide the materials, but still fail to explain the origin of the code. Why? Because coded information is an immaterial entity and based on all known observation, is only created by mental processes.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 8 of 334 (509921)
05-26-2009 5:44 AM
Reply to: Message 7 by AdminNosy
05-26-2009 2:18 AM


AdminNosy,
1- DNA is not merely a molecule with a pattern, it is a code, a language, and an information storage mechanism.
2- All codes are created by a conscious mind, there is no natural process known to science that creates coded information.
3- Therefore DNA was designed by intelligence.
If you can provide an example of a code or language that occurs naturally you can prove this false. All you need is one.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 10 of 334 (509924)
05-26-2009 6:03 AM
Reply to: Message 9 by Dr Adequate
05-26-2009 5:49 AM


Hi Dr,
The genetic code is the very thing in question.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 18 of 334 (510005)
05-26-2009 4:30 PM


Definition of coded information - a system of symbols used by an encoding/ decoding mechanism which transmits a message representing a idea, plan or instructions etc., that are independent of the communication medium.
The book Information Theory - Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in electrical engineering, and is not subjective, it is not debatable or even controversial. It is a brute fact:
Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies. (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
Code is defined as communication between an encoder, a writer or speaker and a decoder, a reader or listener using agreed upon symbols.
DNA's definition as a literal code and not a figurative one is nearly universal in the entire body of biological literature since the 1960's.
DNA code has much in common with human language and computer languages
DNA transcription is an encoding/decoding mechanism isomorphic with Claude Shannon's 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins.
Information theory terms and ideas applied to DNA are not metaphorical but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.
In the same way, you can prove that President Obama is white --- if I will only grant you the premise that all American Presidents (in which we include President Obama) are white.
It's very easy to prove anything if you are allowed to postulate, without proof, a premise that includes your conclusion.
Correct, except here, we can observe Obama himself to know otherwise.
Let's be more specific, all codes are made by man.
Besides human language we also observe animal mating calls, bee waggle dances, bird songs, whale songs,and ant communication by pheromone etc., using coded information. Since all the above are derivatives of DNA, the challenge to the naturalist is to provide a single example of coded information that occurs naturally, outside the realm of life, outside the realm of DNA. All you need is one example.
brb,..

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

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 22 of 334 (510016)
05-26-2009 7:26 PM


Gravity. Gravity is the natural code or language that describes the forces on objects due to other objects.
The formal definition of a code according to Perlwitz and Waterman is a set of symbols that uniquely map a point in space "A" to a point in space "B." In other words there is special symbolic correspondence between a letter or word (idea) and a real physical entity. The word "coffee" represents a beverage made from cocoa beans for example. Symbolic relationships of this kind are only created in the mental world, they by definition do not exist in the purely material world.
Gravitational fields are fields, but not code, as it does not uniquely map a point in space A to a point in space B. Crystals and snowflakes, have edges and boundaries and growth patterns but do not contain any codes. Magma flows and layers of rock and ice, one might possibly argue that these things are encoding systems but they have no corresponding decoding system until someone shows up to inspect and interpret them, bee waggles and tree rings, yes, these things are most certainly codes - but they derive from DNA, and therefore don't count as examples of naturally occurring codes, since DNA has not been proven to have a naturalistic origin. Radioactive decay, same problem as gravity and magma flows, rhodopsin, an example of transduction, may be an encoding system but there is no decoding.
Our description of gravitys pull as 1/r^2 is a symbolic representation of its behavior but gravity itself is just a force. Gravity and tornados and sand dunes and water molecules contain no code, no symbols, no encoding/decoding mechanisms. DNA, however does symbolically represent something other than itself, a plan/ instructions for building a complete organism.
Does the description of gravity, 1/r^2, give us a big ellipse or a small one? An elongated one or a round one? An approximately parabolic path? Or a spiral, as the orbit comes closer and closer and the object crashes? Does 1/r^2 describe the crash itself, which may be extraordinarily complex? Gravity may cause the object to burn up in the atmosphere and never reach the ground. Gravity makes cool air drop, so hot air rises. Gravity holds my chair to the ground and me to the chair. The possibilities that a gravitational field can give rise to are legion. It contributes to all of these things, but which of these outcomes does it specify in advance?
The answer of course, is that it specifies none of these outcomes. It has no code that predetermines any single one of these things. It is simply one contributing force in all of them.
Why? because 1/r^2 describes the strength of the field as a function of radius from a single point, nothing more. The equation for an ellipse can be given in a number of different forms, but 1/r^ 2 itself does not specifically describe an ellipse. Nor does it specifically describe a spiral, or a crash, or cool air dropping as hot air rises.Thats because gravity is a force, not a code.
This is in contrast to DNA, which codes for every inheritable trait. It codes, in advance, whether your eyes are green or blue. Whether your skin is white or red or black or yellow. Whether you are male or female. Whether your blood is RH Negative or O Positive. Whether you go bald or not, whether your chest is hairy, whether you are short or tall. The physical characteristics and biochemical instructions that DNA specifies in any particular instance would fill a very large book. DNA codes for these characteristics the same sense that magnetic fields on your hard drive code for all our family pictures. That's because DNA is not a force, a field, or a boundary, it's a code.
I'm not asserting we will all agree that all codes have conscious minds as a designer. I'm just waiting for one naturalist to produce an actual empirical counterexample.
Ok, so these "codes" are created by animals without intelligence, but are actually derived from the genome. Our intelligence is derived from the genome, our codes come from our intelligence, so our codes are derived from our genome. Thus it is up to you to provide any codes that don't arise out of a genome.
That's just it, we know of none.
I'm a piece of "coded information" that entered this world naturally. If you follow the history of organisms you'll also find that they enter this world naturally, until you get to...your defalt position...the origin of the first "living" cell - RNA.
This is circular reasoning. You are already assuming, that you, consisting of information through DNA, arose naturally. The laws of physics and chemistry do not account for the coded information (unless you are willing to provide an example) any more then the paper and ink in a book account for the message it contains.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 25 of 334 (510019)
05-26-2009 7:34 PM
Reply to: Message 21 by Dr Adequate
05-26-2009 5:45 PM


Quite so. So we know that the style of reasoning you are using is fallacious, since when we can test it directly, it breaks down immediately.
Yes, we can find Obama to see for ourselves. But we have no known observable example of the laws of physics and chemistry producing coded information. All you need is one example.
And the challenge to the supernaturalist is to provide a single example of coded information that occurs by a miracle, outside the realm of life, outside the realm of DNA.
Not by miracle, but by intelligence. That's what we DO know, by empirical observation, that produces coded information. What we don't know is, can it arise without it. If you believe so, all you need is one example.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 27 of 334 (510021)
05-26-2009 7:44 PM
Reply to: Message 23 by mark24
05-26-2009 7:33 PM


Mark,
And the only "known" examples of a code are man-made, thus removing god from the equation.
Oops...Back to the drawing board.
Precisely. But man didn't make the coded information in DNA, thereby removing man also! Now, what's left? Intelligence, as the only known available explanation.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 28 of 334 (510022)
05-26-2009 7:57 PM
Reply to: Message 24 by Dr Adequate
05-26-2009 7:34 PM


... and no miraculous events were involved at any point. Nor did his parents use their minds to design his genome. It happened naturally and without the application of intelligence.
When my computer logs on for automatic updates, all by itself, is this by intelligent design or just natural? What is ultimately acting itself out, be it unobsevable and without direct intervention? Thought.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 30 of 334 (510024)
05-26-2009 8:17 PM
Reply to: Message 26 by Dr Adequate
05-26-2009 7:42 PM


Dr,
Which demonstrates that your mode of reasoning is fallacious, since it breaks down when we can test it.
Agree, so when can we observe the origin of the coded information in DNA? Postulate all we want. But until then, we are left with only one known observable explanation, thought. Unless you can provide one without it.
How about the beneficial mutations that we can observe happening today. Were they produced by a mind? If so, why does this happen more frequently in the presence of mutagens?
I believe in intelligent evolution.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 31 of 334 (510025)
05-26-2009 8:21 PM
Reply to: Message 29 by mark24
05-26-2009 8:17 PM


mark,
But he must of, your logic requires that conclusion.
But we can exclude man, therefore we are left with "other-intelligence." This argument can not identify the intelligence. Only that it is the only known available explanation.

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 47 of 334 (510342)
05-30-2009 7:00 AM


Hey guys, sorry for the delay....
mark24 writes:
Nope, it could have evolved.
The problem with that is that for anything to evolve according to Darwinian evolution it must be able to reproduce to make copies of itself. John Von Neumann determined almost 50 years ago that any self-replicating machine must first have a code to represent the structure to be built. Without a code, there is no evolution.
No code, equals no replication, which equals nothing to select, which equals no evolution. 'Evolution" is a non-answer to the origin of life question.
Hey onifre,
Now, wouldn't you agree that nucleosynthesis, which is how these elements come to exist, fits quite well within your definition of coded information?
I'm afraid not. Please remember the original definition. "Coded information = a system of symbols used by an encoding / decoding mechanism that transmits a message which is seperate from the communication medium itself."
Hi Dr,
Well, we can watch mutations producing new information.
The evolution of codes does not in any way explain the origin of them.
Hi RAZD,
The same way we account for the coded symbolic information in H20, atoms, salt crystals, and snowflake..."
They contain no coded information, only information of themselves. You can have a box of square wooden blocks, and if you tilt the box towards one corner and shake it, they will naturally line up in lattices. But none of those blocks contains instructions to assemble a lattice. They're just blocks.
Likewise, the edges of crystals are boundaries, but they are not codes. Whatever molecule is next to a boundary is next to a boundary, but there is no symbolic relationship. A water molecule all by itself contains no plan or instructions to build a specific structure or a particular molecule, but DNA does.
There are no DNA molecules that do not follow these basic patterns of combination.
Correct, but just because a process obeys known scientific laws does not mean the coded information is derivable from those laws. Computer programs for example. The operation of biological processes is explainable by purely natural processes, but the origin of codes is not. The molecule itself is the medium, the ordering of the base pairs defines the code. The question that naturalism can’t answer is where the code came from.
Hi Michamus,
We have already demonstrated that the Genetic Code is no more special a molecule than water.
Please see above responses.
Hi Mr Jack,
If I take a cube of ice and then hit it with a hammer, is there more or less information afterwards?
It never had coded information as has been defined...." a system of symbols used by a encoding/decoding mechanism that transmits a message independent of communication medium."
Anyway, gotta run for now guys. Peace.
For the correct understanding of this argument, see here. He's advanced it over at infidels for 3 years and counting.
Information Theory and DNA
"The Atheist's Riddle: 30+ Skeptics Attempt To Solve It
For Three Years and counting, I have successfully advanced the Information Theory argument for Intelligent Design on Infidels, the world’s largest Atheist discussion forum."

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 51 of 334 (510370)
05-30-2009 1:03 PM


Gentlemen,
As has been said, we must agree on the definition of coded information.
"How do you define information?
Code is defined as communication between an encoder (a writer or speaker) and a decoder (a reader or listener) using agreed upon symbols. DNA's definition as a literal code (and not a figurative one) is nearly universal in the entire body of biological literature since the 1960's. DNA code has much in common with human language and computer languages DNA transcription is an encoding / decoding mechanism isomorphic with Claude Shannon's 1948 model: The sequence of base pairs is encoded into messenger RNA which is decoded into proteins. Information theory terms and ideas applied to DNA are not metaphorical, but in fact quite literal in every way. In other words, the information theory argument for design is not based on analogy at all. It is direct application of mathematics to DNA, which by definition is a code.
The book Information Theory, Evolution and the Origin of Life is written by Hubert Yockey, the foremost living specialist in bioinformatics. The publisher is Cambridge University press. Yockey rigorously demonstrates that the coding process in DNA is identical to the coding process and mathematical definitions used in Electrical Engineering. This is not subjective, it is not debatable or even controversial. It is a brute fact:
Information, transcription, translation, code, redundancy, synonymous, messenger, editing, and proofreading are all appropriate terms in biology. They take their meaning from information theory (Shannon, 1948) and are not synonyms, metaphors, or analogies. (Hubert P. Yockey, Information Theory, Evolution, and the Origin of Life, Cambridge University Press, 2005)
A: The dictionary definition (computer science case in particular) will suffice: "Processed, stored or transmitted data."
From Wikipedia:
Information is a message, something to be communicated from the sender to the receiver, as opposed to noise, which is something that inhibits the flow of communication or creates misunderstanding. If information is viewed merely as a message, it does not have to be accurate. It may be a lie, or just a sound of a kiss. This model assumes a sender and a receiver, and does not attach any significance to the idea that information is something that can be extracted from an environment, e.g., through observation or measurement. Information in this sense is simply any message the sender chooses to create.
This view assumes neither accuracy nor directly communicating parties, but instead assumes a separation between an object and its representation, as well as the involvement of someone capable of understanding this relationship. This view seems therefore to require a conscious mind.
information is dependent upon, but usually unrelated to and separate from, the medium or media used to express it. In other words, the position of a theoretical series of bits, or even the output once interpreted by a computer or similar device, is unimportant, except when someone or something is present to interpret the information. Therefore, a quantity of information is totally distinct from its medium.
What's important here is 1) information always involves a sender and a receiver; 2) an encoding / decoding mechanism; 3) a convention of symbols ("code") which represent something distinct from what those symbols are made of. A paragraph in a newspaper is made of ink and paper, but the sentence itself may say nothing about ink or paper.
It may be very helpful here to point out the difference between a pattern and a code. Patterns (snowflakes, crystals, hurricanes, tornados, rivers, coastlines) occur in nature all the time.
A code is "A system of signals used to represent letters or numbers in transmitting messages." Examples of code include English, Chinese, computer languages, music, mating calls and radio signals. Codes always involve a system of symbols that represent ideas or plans.
All codes contain patterns, but not all patterns contain codes. Naturally occurring patterns do not contain code.
Q: But information CAN arise naturally - the gravitational constant, Pi, the speed of light, or strings of molecules like C 7 H 5 NO 4 (Benzine).
A: None of these things contain coded information (see above for definition of information). Gravity is gravity. It is a force. But it contains no code or symbols. When we measure it and quantify it (or even speak of it) we assign code and symbols so we can understand it, but in and of itself, it contains no information.
Pi is a relationship between the diameter of a circle and the circumfrence. The number 3.14159 is a way of expressing Pi, based on a human-designed encoding/decoding system (numbers, base ten) but the relationship between the diameter of a circle and the circumfrence itself is not coded information. The same can be said of the speed of light. The speed of light is the speed of light, it represents nothing other than itself.
A molecule, such as Benzine, is just a molecule. When we describe it with symbols like C 7 H 5 NO 4 we are using an encoding / decoding mechanism to describe it, but Benzine itself contains no code, and it is not an encoding / decoding mechanism. It represents nothing other than itself. Information is different from benzine because it represents something OTHER than itself.
If I arrange pebbles on the driveway to spell your name, those pebbles represent you. As such they now encode information, and possess a property they did not possess before I spelled your name with them. They now contain information.
Q: DNA is not a code, DNA is just a molecule
A: Francis Crick received the Nobel prize for discovering DNA. The following is from the first paragraph of Francis Crick's Nobel lecture on October 11, 1962. Note his use of the word "code" and "information," emphasis mine:
"Part of the work covered by the Nobel citation, that on the structure and replication of DNA, has been described by Wilkins in his Nobel Lecture this year... I shall discuss here the present state of a related problem in information transfer in living material - that of the genetic CODE - which has long interested me, and on which my colleagues and I, among many others, have recently been doing some experimental work..."
The following quotes are from atheist Richard Dawkins' book The Blind Watchmaker:
"Every single one of more than a trillion cells in the body contains about a thousand times as much precisely-coded digital information as my entire computer.
"Each nucleus, as we shall see in Chapter 5, contains a digitally coded database larger, in information content, than all 30 volumes of the Encyclopaedia Britannica put together. And this figure is for each cell, not all the cells of a body put together."
Having quoted Dawkins here, it's interesting to note that neither he, nor any materialist has ever provided any scientific (i.e. empirical, testable, falsifiable) explanation for the origin of information. For a very interesting and extensive read on this subject, read "The Problem of Information For The Theory of Evolution" by Royal Truman. If you carefully trace every reference and rebuttal to this article on the internet, you'll discover that not one person has ever supplied a scientific response to the questions raised here, nor provided any examples of materialistic processes that produce coded information.
No naturally occuring molcule possesses the properties of information. Nature does not produce any kind of code, encoding/decoding mechanism or symbolic relationships at all; everything in nature represents only itself.
DNA, on the other hand, represents a complete plan for a living organism. DNA is an encoding / decoding mechanism that contains code, or language, representing the organism."
Would we all agree with the above then??

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WordBeLogos
Member (Idle past 5393 days)
Posts: 103
From: Ohio
Joined: 05-25-2009


Message 54 of 334 (510388)
05-30-2009 5:54 PM


pmarshall writes:
It doesn't even matter how we define "codes" as long as we don't change definitions in mid syllogism."
"The definition of code I have provided is sufficient and applies whether the code is arbitrary or not. Again, I define "Coded Information" as a system of symbols used by an encoding and decoding mechanism, which transmits a message representing an idea or plan.
If there are pebbles below a rapids, there are pebbles below a rapids. There is no coded information associated with them - unless you measure their size, in which case you have created information to describe the pebbles, based on your chosen symbols and units of measurement. Same with orientation of sand dunes, layers of hailstone. Those objects represent only themselves; there is no encoding and decoding mechanism within these material objects, such as there is in DNA. If someone says the layers of a hailstone are an encoding mechanism, I reply that there is no convention of symbols, nor is there a decoding mechanism.
The information in DNA is independent of the communication medium insofar as every strand of DNA in your body represents a complete plan for your body; even though the DNA strand itself is only a sequence of symbols made up of chemicals (A, G, C, T). We could store a CAD drawing of a hard drive on the same model of hard drive, but the medium and the message are two distinctly different things. Such symbolic relationships only exist within the realm of living things; they do not occur naturally. As a result we observe that, so far as anyone knows, coded information only exists in the realm of conscious minds and living things; there is no purely materialistic explanation for its origin.
If you disagree, all you need is one example."
Now, before we go any further, can we agree with this?

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