DNA and the 'Code of Life'

It comes back to the analogy of a foot print in the sand, how many footprints do you need to find before you realise your not alone, on your desert island? It beggars belief that this formula has always existed with all its potential by mere chance of creation, at the BB. Its a bloody good reason to suspect.

Thanks for the close inspection of my comments. Communicating openly is good and helps everyone isolate points of disagreement. We may find that disagreement is actually misunderstanding one another. At the very least, we can detail the reasoning behind our positions.



I'm not picking... I promise. I only isolate this comment to illustrate what a hard linguist I truly am. This might help us understand one another better.

Science cannot describe. I know what you mean, but I refuse to allow myself to personify man made tools. Not science, math, or anything which is non-living. To personify tools is a form of dogma. Ultimately risking the elevation of any concept to deity. I am sometimes guilty of this myself but trying very hard not to do it. Yes this makes me difficult to communicate with. But knowing that might help us understand one another better.



Agreed. What man-made tool is? I have my problems with Shannon too. It was 50 years ago.



All codes are reducible to a factor of one bit. "Hey sexy!" becomes a wink. Where's the "wink" emoticon when you need one?



If we can agree that information is thought (both immaterial), then it most certainly is. Shannon and I disagree as to what information can be. He thinks entropy is a form of information. I reject that completely. Weiner coined the term "negentropy" to illustrate foreknowledge. I accept that. What do you suggest that "small talk" is?



"Information is information. Not energy and not matter. Any materialism that does not allow for this cannot survive in the present".
Norbert Weiner, Cybernetics p147



Boy we gotta slice this one up. Mathematics, as a concept of man, is indeed an immaterial thought. But those concepts are only perceptible with materialistic codes. Much like brainwaves are only perceptible with an electroencephalogram. But all of this is only possible by the mind of man. So yes, essentially we agree. The immaterial concept is modeling the immaterial equation with the usage of the materialistic codification tools of humans.



I'm glad we agree here. Many don't, instead seeing it as a foundational characteristic of the universe independent of man, almost godlike.

May we agree that mathematics is a descriptive language tool created by humans to objectively define what other languages can only describe subjectively?



Characteristics and variables that were also previously abstracted themselves. Observe and describe, observe and describe.



Defined by observation with the sentient created tools of man and described thus by the mind of man.



Observe and describe.



Express sentient intention, desire.



With a man made tool.



Yep. The final condition is expressed upon a codified description from a man made tool. That code allows us to predict an outcome. That's a nice function of code, to predict the future. Architectural plans do it the same as DNA does it. "I'm going to the store to get banana's" does it too.

The question is, did the final condition exist before mathematics and humans existed, or because we used a tool to author a code, manifesting it into physical reality? I believe both are possible. If the "final condition" was determined by an original observation, then it must have existed beforehand. But we can also author a physical building into existence without the need for an previous observation.



This is where we part ways. You say "Information can be abstracted into a mathematical model"... Well yes, but that's dependent upon it being genuine information to begin with. You suppose that the phenomenon is already information to begin with. Or that the pure act of observing it is already information, and then that pseudo info is somehow abstracted mathematically. Am I reading you correctly? Do you believe that observable phenomenon is information unto itself?

In honor of Dawkins use of the term "Apparent Design", I call this position "Apparent Information"... to see information where it is not.

My position posits that no information exists until an observable phenomenon has been described by a sentient mind. The codified description represents information (thought) of a mind, about the observation. Then and only then, may we apply mathematics to the description. But we can never apply mathematics to the phenomenal agent itself. Only to the description of it.



The mathematical abstraction is a physical medium used to represent the non-physical thought from a mind. They are not the same things. One represents the other.



From my position, do you think equations hold thoughts, or represent thoughts? From your position (if I read you right), do you think equations hold phenomenon or represent phenomenon?



All the more illustrative that information is independent of the medium that expresses it. But you seem to think that "sound" itself is information. Or that "dna" itself is information. That somehow the physical phenomenon is somehow information. How can this be? Information is not a medium. Information is not a code. Information is expressed and represented by mediums and codes. You know the old phrase... "The medium is not the message".



I could not agree more. And one must not confuse the medium with the message. The mathematical model is not the information. It represents it. And neither is the "thing" (observable phenomenon) information. Information exists only at the point where a sentient being has described the thing. We do not "read" the thing. We cannot. The thing doesn't have a code to read. It has no transmitter or any other of the many requirements to necessary. Chaos is not a code. They are complete opposites.



Yes, an image/object relationship must form for thinking to occur. This happens on many levels.



(youthinks incorrectly). We're getting into the necessary differences between patterns from chaos and code. They are complete opposites.

Fractal patterns may never be duplicated exactly. The reason (youthinks) a recreation of the thing itself is impossible is because you believe the phenomenon from nature is information when it is not. You succumb to the belief in "apparent information". Snowflakes may never be duplicated. Tornadoes, mudslides, hurricanes may never be duplicated exactly. They are fractal patterns and thus subject to the unpredictable irreducible complexity of chaos. They have no information. They have no code. They have no thoughts. They are not thoughts.

Codes can be duplicated exactly... I'd wager the code on my monitor is exactly the same as the code on yours. The PhotoShop you pirate is the exact same as the PhotoShop I pirate. Code represents information. Code is a physical object that can be duplicated exactly. Language could not exist otherwise.

Fractals are irreducible. Code is always reducible to a factor of one bit. There are 6 billion characters in every cell of your body and they all express the same exact information. They represent "pagan", and forensics will confirm that for you after your next crime spree.



You have misunderstood me sir. Your comment reveals that it is you who believe that "the thing in itself" is "ie information". The "thing" is not information. The "thing" is observable phenomenon. Information is a thought about the thing. The code is a physical representation of my thoughts. My thoughts are the information. Thoughtful information is authored from mind and nothing else.



No sir. You have simply misunderstood me. I've been very consistent with my presentation. I've debated and researched this subject to the extreme for the past 7 years. I know my **** very well. I am often accused of inconsistency by those who are new to this theory. It's such a dynamic shift from most clinging belief systems that it's very difficult to be heard clearly the first few times around. I repeat myself a lot out of necessity.



That is impossible in our physical realm. As I've always said, Code is a material lens that allows us to view the immaterial realm of Information. It's like asking to see a brainwave without an electroencephalogram. Or asking to see gravity without a ball to drop. Or asking to see dark matter without the mathematics to infer its existence. We cannot see these things even when we have these tools.

Why? Because...
Gravity is not the Ball
Brainwaves are not the Electroencephalogram
Dark Matter is not the Equation
Information is not the Code

One represents the other. And we infer their existence. By all the standards of inferring gravity, we must infer the existence of information when we see a code. Information comes from mind, so we must also infer a sentient author.



Information cannot be carried. It is immaterial. Nothing immaterial can be carried (in the physical sense). Sound doesn't weigh any more or less whether it represents Bohemian Rhapsody or a fart. A TV signal representing Gone with the Wind doesn't weigh any more or less than a signal representing the ShamWow.



Absolutely correct. The very same information can be represented upon infinite mediums. Sunday Bloody Sunday is the very same exact information independent of its representation on sheet music, DVD, CD, MP3, cover band, U2 live in concert electrified, or a drunken karaoke version. We could even codify it to smoke signals, color codes, or carve it in the hills of Zion. It is exactly the same information.

It is not thousands of different quantities of information. It is thousands of mediums all representing the very same information. They all represent the same single sentient authored thought of Bono.



How true.



Agreed.



So you agree DNA is a language... a genuine code? One that could not possibly have been created or encoded by humans?

Yes we can make exact copies of that code just like we can any other code. "see spot run" means exactly the same as "ver ejecutar in situ".



A telescope is not part of the stars. It only allows us to look at the stars. Code is a material lens that allows us to view the immaterial realm of information.



But the code is not the sentient being. It only represents the thoughts of the sentient being.



I make no claims as to the nature or characteristics of the required author for DNA. Only that there must be one. It could be extraterrestrial aliens for all I know... it could be time travelers... who knows?




Since this theory challenges commonly held notions of what physicality even is, I make no claims as to what the requirements are for sentient authorship. If A.I. ever wakes up on the net, would that be considered a physical being? If quantum physics ever opens a portal to another dimension, finding intelligence, would they be considered physical beings?

What do we say to this Russian research of the holographic nature of DNA and the phantom existence it exhibits? Is this phantom a physical object?
Gariaev 06 Scroll down to see the phantom effect. Is this physical or not?



Is not sentience dependent upon thought capacity? Is not thought capacity dependent upon the abstract reasoning of language capacity? A wolf more sentient than a bumble bee... A whale more sentient than a wolf... A man more sentient than a whale... In this manner, yes, sentience is an immaterial quality for all of us. Touching my physical body is not touching my sentient capacity.



No we don't. Is this even knowable? Should progress stop because of what we don't know, or should it move forward by what we do know?



Shall hope for a black swan slow the progress of science? Shall hope for a promised god slow the intellect of humanity?

Here's why it concerns me. What could be learned about genetics if we did conclude there must have been an original author? Perhaps nothing good at all... but perhaps, if we treat that notion as an archeology discovery some clues would begin to surface.

What's the first thing we do when we find an ancient manuscript? After decoding it, we pursue learning more about the one who wrote it. We often find a great deal and come closer to the true characteristic nature of the author. Shall we stare at a manuscript and leave it at that? Or shall we use it as an excuse to get to know Socrates better, Nostradamus better, Confucius better. Could we possibly get to know a creator better? To learn how it thinks? Is this not a worthy quest?

---------- Post added 01-10-2010 at 07:56 PM ----------



That's absolutely right. That's all anyone can hope for. All theory should be suspect, even the Authorship Theory of Intelligent Evolution.

What pleases me in this particular discussion, is that nowhere was God or a particular religion invoked. It's just science.

Although... my studies have presented quite a number of correlations to many world religions. I don't mean anything by this, only that I find it interesting.

"In the beginning was the Word. And the Word was God and the Word was with God. And the Word became flesh."

A two thousand year old scripture depicting the word of DNA becoming flesh. Astounding to speculate upon.

A note from your friendly local esotericist.

This perspective can be interpreted from viewpoints other than the strictly Christian, as QuinticNon says. This is important. So it is not a covert argument for biblical literalism or anything like that. It provides scope for the Christian perspective. But there are many other metaphorical allusions to the idea of the 'great mind' or the 'divine intellect' in traditions other than strictly Christian, for example, Platonic, Neo-platonic, Hermetic, Islamic, Hindu and Buddhist.

The quoted verse 'in the beginning, was the Word', has always been of special significance to the esoteric and gnostic aspects of the Christian path, if interpreted symbollically in the way that is being suggested. It also provides many 'integration points' between the Christian faith and other cultural traditions.

Absolutely. When considering teachings of the Way and Bhartrihari... it's absolutely fascinating to see the connections. Even Judaism when they claim God speaking the universe into existence... "And God said, Let there be..."

I also find the psychedelic teachings of McKenna right in line with all of this... but that's another story altogether.

hi QuinticNon

ok first off i haven't got time at the moment to reply in detail to your post. tis late, i have been snowed in for a week and tomorrow i plan to escape ....... not least to get some food

But i will quickly try to clarify some points. We do differ, i find your conceptual framework interesting, but because our narrative understanding of science, perception language and thought are different we are bound to misinterpret each other.


"Information is information. Not energy and not matter. Any materialism that does not allow for this cannot survive in the present".
Norbert Weiner, Cybernetics p147

i agree with Weiner's statement.
I think that equations can represent phenomenon to the reader/writer of equations. Since thought is a phenomenon i suppose equations could represent them. But remember i do not believe any representation is complete. Its in the nature of language and narrative. I don't believe in the grand narrative, that describes everything accurately and completely. This is not least because a representation for me is necessarily not the thing in itself, therefore it doesn't make sense that a respresentation can be complete. Further, by deconstruction, we can find 'contradictory points' in a narrative that demonstrates its incompleteness ........ while languages by having characteristics of their own, show limitations also.

Quote:
Originally Posted by pagan
A representation is not a respresentation if it is a complete representation. It then becomes a clone. A recreation of the thing in itself. (this is impossible methinks)

yes this is where we differ......

I do not believe a code is immaterial, though often as shorthand we speak as if they are. A code is information (which can be abstracted from the material medium) written on the medium. The reason therefore a code cannot be cloned is because not only would it have to clone the exact material composition of the medium, but also because it would have to occupy the same space and time. Thats why it is impossible. If we conceive of a timeless, spaceless, immaterial medium for holding abstracted information ..... then it is possible to conceive of the clone of a code. However, i do not conceive of such a medium as having any evidence for existence (if the word existence has any meaning in such a context). Moreover, if i did, then the representation of a 'thing' in such a medium could be complete! After all in such a strange place a clone would be a complete representation. In such a strange place therefore, a representation of a thing could actually be the thing in itself, and we agree that that is not possible. Thus such a place is not consistent with the necessary difference between the representation of a thing and the thing in itself. (which as i understand it is crucial to your conceptual scheme as well as mine.)

Thus when you say the code on your monitor is the same as that on mine, in my terminology it may be that the abstracted code is the same, but not the actual existence of the code. They are written on different monitors. (we have to be careful here though because code can also mean encoding. ie an equation applied to a language, where the equation and the language may be defined in the abstracted sense, ie divorced from a medium. eg mathematically)

Quote:
Originally Posted by pagan
Whether it is returned to the original medium (eg sound - transfer - sound) or another (eg rna - transfer - dna).

In my scheme of course the information is never independent of a medium, while also is not dependent on any particular medium. Thus i was illustrating the latter characteristic, while simultaneously refuting your understanding with the first characteristic. (nb i mean this in the context where information theory is useful as compared to small talk, see below.)

And it is for that reason that i draw your attention to the famous phrase ....

"The medium is the message" a phrase coined by Marshall McLuhan

The reason can be illustrated by the example of small talk. One of the characteristics of small talk is that people often speak at the same time. This falls outside information theory. Information theory is applicable to writing as we are doing now. Why? Because the medium of writing on a forum does not permit interruption or simultaneity. Sound can. That is not to say that information theory is not applicable to speech, because in serious well behaved speech, people wait for the other to finish talking before responding. In that instance information theory is useful. But in small talk it breaks down when small talk actually incorporates (on occassion) the ability to speak simultaneously as part of the skill of small talk. eg mimickry of another as they speak, to have a laugh.

If you study the nature of media in this way then that is when you can see that the medium is the message. If president bush makes a speech on tv .... it will have a completely different communication effect to if he attempted to do it down my local pub. There is a power structure written into media. Modern politicians know this well. The public very rarely interrupt them on telly. (occassionally you get a flying shoe ) Similarly its difficult for politicians to convey their ability to small talk on tv which they would like to do. When they attempt it we usually smell a false performance with the interviewer, and by default us the viewers.

I know that that seems a long way away from evolution, but i felt it necessary to illustrate why not all communication is consistent with information theory. (incidentally the structuralist's attempt to describe language failed catastrophically and this is not unrelated since theirs was a logico rationalist attempt to describe language and communication.)

In conclusion

"Information is information. Not energy and not matter. Any materialism that does not allow for this cannot survive in the present".
Norbert Weiner

to which i would add ...... "any theory of information that does not allow for the characteristics of media, will not survive either."

and now it is very late. lol

Oh man it's got a fun dark side too... biblically at least. Claude Shannon worked for Bell Labs, owned by Lucent Technologies. Lucent (Lucifer Enterprises - false bearer of light). They're the largest communications company on the planet and probably have their chip sets in nearly every computer ever made. Their address is 666 Fifth avenue and their logo illustrates the dragon eating its tail.

So... biblically of course, what this invites is for us to view Lucifer sitting with Eve under the Tree of Knowledge of good and evil. He invites her to taste the fruit claiming her eyes would be opened to see as God sees. Supposedly this happened around 8,000 years ago. Written language is thought to have formed approximately 8,000 years ago.

Shall we thank Lucifer and Bell Labs (info co) for allowing us to see as God sees... for allowing us the ability to author code ourselves? Just for fun I assure you.


---------- Post added 01-10-2010 at 08:32 PM ----------



Neither do I. Code is material. Information is immaterial.

TNT...til next time (boom!):whistling:

---------- Post added 01-10-2010 at 08:34 PM ----------

Oh yes and let's not forget that Hebrew has no numbering system. They use the letter W to represent the number 6. So.... everytime we log on to the web with www do we take the mark of the beast?
Is the codification of information actually the work of Satan? Hahahahahahaaaa!!! :devilish:

In what way is DNA different than a mold used to make horseshoes or hammers?

It specifies the construction of material things that has a certain function. Is this how loosely we're defining codes and information??

I can't see how this is a 'loose definition'. As mentioned above, the transmission of information is central to the theory of how DNA works. Even the Wikipedia definition of DNA says:



That is not a 'loose definition'. That is a definition.

Wikipedia's use of 'information' is quite colloquial in this case.

I think the information content of DNA is impressive only by virtue of its scale. I mean come on, it's a four letter alphabet that contains 64 three-letter words that is decoded by ribosomes to make a twenty letter alphabet. So fine, I can use DNA to encode "alanine" or "glycine". I can use DNA in the form of genes to encode "insulin" or "glucose 6-phosphate dehydrogenase" or "myosin". But again, we're talking about a series of molds into which I can make horseshoes, hammers, anvils, and die-cast cars.

So are we to call the mold for a horseshoe 'information'?

The genetic code is the rule for translating the instructions for building huge protein molecules from 20 basic amino acids. The instructions are sequences written using a four-letter alphabet.

A point that I was going to try and lead Jeeprs to is that to reduce DNA to a code is extremely reductionist. DNA is nothing without regulation, and in multicellular organisms different cells and organ systems that all originate from the same DNA regulate one another. The 'code' in DNA is the simple part. It's the physiology of DNA that is the remarkable part.

You're much deeper than I am. I just flip open an intro book and try to understand some of the amazing wealth of material accumulated the past few decades.

Hi Bluemist,

Everything has its deep levels, of course, but the regulation of DNA should be accessible to anyone curious about it.

Just think about it -- not all cells are doing the same thing. Your neurons are not doing the same thing as the cells that line your stomach. But their DNA is the same. Clearly the DNA is being 'used' differently, i.e. different gene products are being expressed, at different amounts, in response to different signals...

But I think that is a separate argument. I understand there are many factors involved in the regulation of the development of individuals, like master genes and the like (which in some ways just replaces one mystery with another, anyway). There was a fair amount of detail on that in the book I have just finished.

But I don't see how it can be denied that DNA contains information. I don't see how evolution can be concieved without the idea that biological information is transmitted via reproduction.

"That's the problem hard materialists are having a difficult time with. That word "formula"... You cannot have a formula without a code to formulate it upon. The hard materialist believes that information and code are everywhere and nothing separates a rock from living entities. They think a random assemblage of molecules is somehow qualified to be called a "formula". This is false and errant thinking.".....QN

but i am as far from a hard materialist as anyone can get. i suspect that there is the same thing behind the existence of life and nonlife, this architect if one must use a human term, hoping it does not take on the form of something created in the image of mankind.

so there may be a difference between life and nonlife-yet they could both have been authored and it may be possible some day to find evidence of it once someone tries to look for it. there may be some elusive quality (chi or prana if it be named) that exists in what we designate as living and not elsewhere.

if you want to cite the scriptures, it would be that which was 'breathed' into man after his creation. there are also correlations between the expansion/contraction of the universe to the 'breath of god'. i believe there is a wealth of information there that is waited to be correctly interpreted.

Perhaps I was unclear then -- if you're going to call its contents information, then you MUST include its regulation in your conceptual definition. A dead gene with no promoter or a noncoding sequence has nucleotides in sequence -- but it's never expressed, never does anything, it's just a polymer of nucleotides and not a code. The expression of DNA is what is required to think of its contents as information at all, and what is conveyed in a gene product is conveyed not just by what it is (and DNA only directly specifies the amino acid sequence, it does NOT specify folding of said polypeptide!!!), but also WHEN it is expressed, HOW MUCH of it is expressed, UNDER WHAT CONDITIONS, etc!

By the way, I'm not really willing to confirm or deny the thesis that it is information -- I'm just saying that it's a departure from virtually all other uses of the term 'information', and I don't think you can get around that without a terminally circular argument.

So is the famous 'central dogma of molecular biology' incorrect in saying that DNA and RNA encode biological information? Or are you obfuscating because you don't like the implications of the argument?:bigsmile:

You are absolutely correct. The regulation that RNA programs into the protein is fascinating. And why does Uracil replace T? And how does the mRNA call for exact tRNA needed? What mechanism initiates the ribosome to form? What instructs the amino acid to separate from the RNA? How does the RNA know to travel to the outer part of the cell after separation? How do the transfer molecules know which specific amino acids to bring to the ribosome?

This cannot all be explained by chemical reactions. There are very specific timed instructions being given.

I believe a clue would be found somewhere in the quaternary logic of the DNA and/or the ternary logic of the RNA. Perhaps both codes combined, who knows. But the LifeOS is being instructed by something. It's just fascinating.

Everyone should see it happen. Best vids I've found...
http://www.youtube.com/watch?v=41_Ne5mS2ls&NR=1
http://www.youtube.com/watch?v=4PKjF7OumYo

---------- Post added 01-11-2010 at 12:59 AM ----------



Sorry, that comment was a generalization and not specifically directed at you. Sorry.



I believe you are correct. Somethings up. Other confirmations are pouring in from knowledge gained in robotics, cybernetics, A.I. and all information sciences.

Even this atheist programmer must question where the author is...
"The source code is here. This not a joke. We can wonder about the license though".
DNA seen through the eyes of a coder

He wonders who owns the license to DNA and yet still sells Dawkins books on his website. Evrbody funnay... now you funnaytoo.

does this somehow negate the possibility of there having been an author involved in its beginning? and does it prove whatever happened after the beginning is going on in a random way among chaotic circumstance?

of course it is being used differently-and it is being used correctly, no? as a matter of fact, how could it possibly be working that way without intelligence and premeditation not only certainly preceding it but even as part of an ongoing process at its core?

---------- Post added 01-11-2010 at 02:38 PM ----------

Quote:
Originally Posted by salima
but i am as far from a hard materialist as anyone can get.

"Sorry, that comment was a generalization and not specifically directed at you. Sorry."...QN


that's ok, i didnt really think so-but i did want to point out that the same views can be held both by materialistic and spiritualistically minded thinkers.

Salima I mention a formula, why should that make me a hard realist. All formulas could by your interpretation, have the smell of an engineer. If you can imagine an engineer for life, the same engineer must have engineered the circumstance and the building blocks. How can you divorce one from the other?

My only problem with all of this talk of DNA etc is why look at the final outcome , we must look for the original simple formula that made it all possible. The building blocks of life must have started very simply but the progress of life must still have been written into that original formula. Who writes the formula? does it require an author. For me its very hard not to see an author. Would a simple code develop by its circumstance?