0
   

DNA and the 'Code of Life'

 
 
pagan
 
  1  
Reply Wed 13 Jan, 2010 11:10 am
@Zetherin,
Quote:
Aedes

The cosmos doesn't make statements. "1+1=2" is a statement that WE make. But whether it's true or not is not because of its natural cosmological truth, but only because that is how we've defined those symbols.


Are we outside the cosmos then?
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 11:15 am
@Aedes,
Aedes;119676 wrote:
First of all, if you got from that statement of mine to "you claimed that Philosophy invented language"


Yes I misread you. That's the beauty of language, we can ask for clarification. I did not want to assume. My problem is that I interchange "symbolic logic" and "language" and "code" synonymously. I should not suppose others do. That's why I asked.

Aedes;119676 wrote:
...then you have completely proven my point that language is imprecise, because I said absolutely nothing to even imply that.


Do we not use different languages for different purposes? The language of mathematics is extremely precise. It can tell me everything I need to know about the physics of why the plane crashed. But poetry is best suited to express how I feel about it. Different tools for different purposes. Both man-made tools of language.

Aedes;119676 wrote:
Symbolic logic is a formal domain of philosophy, developed by logicians like Frege and Russell, chiefly to express logical arguments using the most precise possible terminology. The only way to do that was to eliminate words and use agreed-upon symbols instead.


Yes, I misread you. But how is an "agreed-upon symbol" not a word? That's what words are... agreed upon symbols. And no matter what the symbol, it always represents the thought from a mind... does it not?

Aedes;119676 wrote:
I have no idea where you're going with this cosmos making statements. The cosmos doesn't make statements.


Then how could DNA have been encoded by the cosmos, or any other "natural" means? Coding requires a capacity for making statements.

Aedes;119676 wrote:
"1+1=2" is a statement that WE make. But whether it's true or not is not because of its natural cosmological truth, but only because that is how we've defined those symbols.


Yes for mathematics. But DNA/RNA has it's own definitions within a closed loop system. It didn't require us to define anything for it to function. In fact, one could argue, that we don't define it... it defines us. It's definition of us is extremely precise... More precise than Frege and Russell Philosophy of Symbolic Logic.

---------- Post added 01-13-2010 at 11:23 AM ----------

Zetherin;119678 wrote:
We understand that our numbers are abstractions, but that doesn't mean we can't make truth out of them, does it?


That's a point I was leading to. Every time we encode, we make truth. Even if what we have said is false, incorrect, or just plain deceptive. If that be the case, then it would be True that what we have said is Truly false, Truly incorrect, or just plain Truly deceptive.
0 Replies
 
pagan
 
  1  
Reply Wed 13 Jan, 2010 11:36 am
@pagan,
Quote:

QuinticNon

And I'm still confused as to your perspective of my views. You seem to determine me as thinking only with the "classical logic ice pick" of materialism. Yet my Info principle refutes the hard materialist. I don't get it. The "Laws of Logic" themselves are even immaterial.
uh well with respect you do seem to interpret peoples posts from your own ego centric and passionate perspective. (nothing wrong with that. it shows commitment) BUT if you really want to understand what people are 'intending' to say (information theory???) then try reading them within their own perspective in their own right. On several occasions (eg me and aedes) you have completely misinterpreted what we intended to communicate. Not least because you are so passionately committed to your own way of interpreting the world. (eg information is necessarily immaterial) that you 'read' us differently to how we intended.

This phenomenon incidentally is recognised as 'inevitable' within the philosophical movement of postmodernism ie happens in human communication all the time. To have any chance of moving outside your own narrative understanding and reading a post in a way such that it was intended, then you have to try and get into the narrative understanding of the writer. It isn't always easy, not least because as Aedes points out, one of the characteristics of common languages is the ambiguity of meaning in common words, phrases and grammatical structure. Hence the philosophical and scientific attempt to construct unambiguous language to use in their narratives.

I will give you an example that happened to me today. I woke up to a rare winter wonderland. Rare for my part of the world. Not only that but I have just taken care of a very beautiful house for some friends, rolling gardens, pristine snow lawn that extends into the countryside ....
So i take a walk and cant stop smiling. I am a pagan Smile I am so moved that i send the following text to a dozen pagan friends. "Sky god earth goddess, you are absolutely gorgeous!"

One reply was from a dude. "Cheers mate. Didn't know you cared :-)"

Another from a dudette. A picture of herself naked in the mirror.

get it?
Zetherin
 
  1  
Reply Wed 13 Jan, 2010 11:56 am
@jeeprs,
QuinticNon wrote:
Yes I misread you. That's the beauty of language, we can ask for clarification. I did not want to assume. My problem is that I interchange "symbolic logic" and "language" and "code" synonymously. I should not suppose others do. That's why I asked.

Just to clarify, I believe he was speaking of logic formalizations, which utilize logic symbols.

Quote:

Yes, I misread you. But how is an "agreed-upon symbol" not a word? That's what words are... agreed upon symbols. And no matter what the symbol, it always represents the thought from a mind... does it not?


Right. But the purpose is to cut down the level of ambiguity. And it accomplishes this task. Just like mathematics does.

Quote:

That's a point I was leading to. Every time we encode, we make truth. Even if what we have said is false, incorrect, or just plain deceptive. If that be the case, then it would be True that what we have said is Truly false, Truly incorrect, or just plain Truly deceptive.


You're using two different senses of the word "true" here. If I say a statement it true, it is different than if I say someone is truly X. Don't confuse the two. Every thing we speak in language is not always true, even if we're truly speaking in language.
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 12:48 pm
@Zetherin,
Zetherin;119692 wrote:
Every thing we speak in language is not always true, even if we're truly speaking in language.


You are correct. Is it not True, that Truly statements are ultimately supportable by Truth statements?

---------- Post added 01-13-2010 at 12:51 PM ----------

Zetherin;119692 wrote:
...the purpose is to cut down the level of ambiguity. And it accomplishes this task. Just like mathematics does.


Yes and as poetry cannot. Yet poetry accomplishes tasks that symbolic logic and mathematics could not hope to achieve.

Are they all not tools of human?
0 Replies
 
Zetherin
 
  1  
Reply Wed 13 Jan, 2010 01:05 pm
@jeeprs,
QuinticNon wrote:
You are correct. Is it not True, that Truly statements are ultimately supportable by Truth statements?

True statements are true, but something which is truly a statement, need not be true. It is truly a statement that, "The moon is made of jello", but it is not a true statement.

I don't know what else you would have in mind by "Truly statement". All I can think of is that you are using truly as a synonym for "genuine" or "sincere" or "honest".

"Did he truly state that the moon is made of jello?". Here we are not evaluating the truth of the claim, but the honesty of the person. Isn't this right?

Quote:

Yes and as poetry cannot. Yet poetry accomplishes tasks that symbolic logic and mathematics could not hope to achieve.

Are they all not tools of human?


Who ever said one was better than the other? I sure didn't. But when attempting to see if a conclusion is a valid, I suppose it's better to formalize, and when attempting to express your feelings and delve into the 'human condition', I suppose it's better to be poetic. Do you disagree?
0 Replies
 
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 01:12 pm
@pagan,
pagan;119687 wrote:
get it?


Yes. A form of affirmation of expression. "Nature loves courage". Why would she not love courage on her behalf? You spoke upon her behalf, and from her behalf, she returned your invitation with the affirmation of others who... got it.

A tickle and a laugh. What could be better?

pagan;119687 wrote:
you do seem to interpret peoples posts from your own ego centric and passionate perspective.


Peoples posts from passionate perspectives present potholes in the pursuit of perfection. Best not get stuck there. Thanks for the helping hand out.

pagan;119687 wrote:
if you really want to understand what people are 'intending' to say (information theory???) then try reading them within their own perspective in their own right.


A good reason for a worthy goal. Thank you for suggesting.

pagan;119687 wrote:
On several occasions (eg me and aedes) you have completely misinterpreted what we intended to communicate.


Not the first time that's happened. The only way I know to avoid that is to ask many questions. But now I have your suggestion to approach the subject from the other perspective. Another tool in the toolbox!

pagan;119687 wrote:
Not least because you are so passionately committed to your own way of interpreting the world. (eg information is necessarily immaterial) that you 'read' us differently to how we intended.


I was an only child set far away who never developed interpersonal skills. I became the Devil and the World became mine! I'll try to get over it.

pagan;119687 wrote:
This phenomenon incidentally is recognised as 'inevitable' within the philosophical movement of postmodernism ie happens in human communication all the time.


Fascinating connection.

pagan;119687 wrote:
To have any chance of moving outside your own narrative understanding and reading a post in a way such that it was intended, then you have to try and get into the narrative understanding of the writer.


I suppose so even more now so in the age of Tweet. Inflection, expression, even pun must be engaged in different ways than ever before.:eek:

Not keeping up with the evolution of language and communication sure can make a guy feel old real fast.:Not-Impressed:

---------- Post added 01-13-2010 at 01:16 PM ----------

Zetherin;119709 wrote:
Isn't this right?


Truly I believe this is right.

Zetherin;119709 wrote:
Do you disagree?


Truly I agree.
0 Replies
 
Aedes
 
  1  
Reply Wed 13 Jan, 2010 01:17 pm
@Zetherin,
Zetherin;119678 wrote:
You mean it has no direct correspondance with reality. Such as the truth that water is composed of H2O does, right?
Right.

Zetherin;119678 wrote:
But does that make it not a truth? It is still true that 1+1=2, is it not? We understand that our numbers are abstractions, but that doesn't mean we can't make truth out of them, does it?
Here's a truth for you:

{$}# + ^^$%} = $RQ$@#$

That is because I have defined this as a true statement. It's just as true as 1+1=2, only the message hasn't caught on quite so well.

---------- Post added 01-13-2010 at 02:23 PM ----------

QuinticNon;119681 wrote:
But how is an "agreed-upon symbol" not a word?
In the case of symbolic logic, these are technical words with restricted meaning meant to expunge propositions of linguistic ambiguity. It's a practical difference, not a metaphysical one.

QuinticNon;119681 wrote:
Then how could DNA have been encoded by the cosmos, or any other "natural" means?
DNA just is. So are rocks. That's how we know about DNA -- we looked for it and we found it. You can't say the same thing about something metaphysical.

QuinticNon;119681 wrote:
Coding requires a capacity for making statements.
Heh, human coding does. Show me the proof that that is true for nucleic acids.

QuinticNon;119681 wrote:
But DNA/RNA has it's own definitions within a closed loop system.
I do not agree that it is closed. It is factually incorrect to speak of DNA's sequence as somehow divorced from the regulatory things that govern if and how its language is even read at all.
Zetherin
 
  1  
Reply Wed 13 Jan, 2010 01:26 pm
@jeeprs,
Aedes wrote:

Here's a truth for you:

{$}# + ^^$%} = $RQ$@#$

That is because I have defined this as a true statement. It's just as true as 1+1=2, only the message hasn't caught on quite so well.


Right, but just because you devised the system, it does not mean that the truth here is any less of a truth than anything else you discover is true. Imagine language as a devised system, and "H", "O", and the number "2" as devised symbols. If I say water is composed of H2O, isn't this true, and not less of a truth, just because I'm using a system of communication?

You're not the creator of that truth, you see. The truth was already there. You just discovered it by a devising of symbols.
pagan
 
  1  
Reply Wed 13 Jan, 2010 01:46 pm
@Aedes,
Smile QuinticNon
Quote:

Yes. A form of affirmation of expression. "Nature loves courage". Why would she not love courage on her behalf? You spoke upon her behalf, and from her behalf, she returned your invitation with the affirmation of others who... got it.

A tickle and a laugh. What could be better?
Superb! Well now i am left wondering how you could possibly get much simpler interpretations so off center, 'apparently'. Dunno lol life is strange.
0 Replies
 
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 01:48 pm
@Aedes,
Aedes;119719 wrote:
{$}# + ^^$%} = $RQ$@#$


Set apart against the white pixels of my monitor {$}# + ^^$%} = $RQ$@#$ may stand out but tucked within an entire line of code it doesn't raise an eyebrow so much. Especially if it doesn't have any meaning to me. In fact, if I did see such an unrecognizable scramble, I may believe it was a mistake. Could {$}# + ^^$%} = $RQ$@#$ be the invisible boat in Botany Bay? It means something to you, the sailor. But to me it's just the flotsam and jetsam floating in the cove.

Aedes;119719 wrote:
DNA just is. So are rocks. That's how we know about DNA -- we looked for it and we found it. You can't say the same thing about something metaphysical.


What do you mean that we "looked" for it? Did we not discover it? Did someone presuppose it existed before it was discovered? If so, during that time of "looking", would it not be held as a purely metaphysical notion until the molecule we were "looking" for was actually found to exist in physicality and beyond hypothesis?

Aedes;119719 wrote:
Show me the proof that that is true for nucleic acids.


If necleic acid is encoded, then a statement has been made. Nothing can be said without intending to say it. The necleic acid is not an undefined statement of{$}# + ^^$%} = $RQ$@#$. Though it may be a defined but confined to one mind {$}# + ^^$%} = $RQ$@#$. But if {$}# + ^^$%} = $RQ$@#$ is really an encoded message, then author of {$}# + ^^$%} = $RQ$@#$ must have the capacity to make a statement.

Aedes;119719 wrote:
I do not agree that it is closed. It is factually incorrect to speak of DNA's sequence as somehow divorced from the regulatory things that govern if and how its language is even read at all.


From the Double Helix through to the Protein, the entire genetic mechanism is a closed loop communication protocol. One could even say it produces its own power if not for the food, water, oxygen and sunlight required by the host. When speaking of a closed loop system, I include the regulatory things that govern.

All previous known examples of closed loop communication systems that we know of were programed to function this way by a sentient author.
0 Replies
 
Aedes
 
  1  
Reply Wed 13 Jan, 2010 02:11 pm
@Zetherin,
Zetherin;119725 wrote:
Right, but just because you devised the system, it does not mean that the truth here is any less of a truth than anything else you discover is true. Imagine language as a devised system, and "H", "O", and the number "2" as devised symbols. If I say water is composed of H2O, isn't this true, and not less of a truth, just because I'm using a system of communication?
But in the case of H and O, it can be demonstrated without those symbols. There are ways to demonstrate that there is such a thing as that which we call H and that which we call O; and it can be demonstrated that the substance we refer to as water is composed of molecules that have two represenatives of that which we call H bound to that which we call O.

Zetherin;119725 wrote:
You're not the creator of that truth, you see. The truth was already there. You just discovered it by a devising of symbols.
In that case, let me be the first to announce that I've discovered the truth that 1+1 =/= 2, and I have discovered this pre-existing truth by a devising of symbols.

---------- Post added 01-13-2010 at 03:20 PM ----------

QuinticNon;119730 wrote:
Did someone presuppose it existed before it was discovered?
It was known that traits can be inherited. It was known that this is true for cells, and that the conveyor of heritable traits is subcellular. DNA as a molecule was known to exist before it was known to be the genetic element. Most people actually presupposed that proteins were the genetic element before this was disproved by one of the best experiments in the history of biology.

QuinticNon;119730 wrote:
If so, during that time of "looking", would it not be held as a purely metaphysical notion until the molecule we were "looking" for was actually found to exist in physicality and beyond hypothesis?
Hypothetical is not metaphysical. It's a propositional physical entity, which subject to physical investigations will be accepted or rejected.

QuinticNon;119730 wrote:
If necleic acid is encoded, then a statement has been made.
I think this is a ridiculous assumption that speaks only of how you are completely unwilling to look at DNA and only willing to look at your chosen labels for it.

QuinticNon;119730 wrote:
From the Double Helix through to the Protein, the entire genetic mechanism is a closed loop communication protocol.
Wrong!!!
jeeprs
 
  1  
Reply Wed 13 Jan, 2010 02:50 pm
@jeeprs,
The central contention still remains the fact that RNA/DNA was said to encode information by Crick and Watson, who discovered it, and made it part of the so-called 'central dogma of molecular biology'. If the counter-argument is that biological systems don't contain information, and that therefore are not explicable in terms of information systems theory, then let's debate that. Debates about 'the meaning of meaning' per se rarely advance beyond the 'what do you mean by meaning' stage.....

To be very clear about my position, it seems unarguable to me that (1) Crick and Watson do make this claim and (2) that therefore, information systems theory can be applied to living systems.

Besides, even leaving aside all the philosophy, I would have thought that the application of information systems to molecular biology might be a very fascinating new field of endeavour.
0 Replies
 
Zetherin
 
  1  
Reply Wed 13 Jan, 2010 02:50 pm
@jeeprs,
Aedes wrote:
But in the case of H and O, it can be demonstrated without those symbols. There are ways to demonstrate that there is such a thing as that which we call H and that which we call O; and it can be demonstrated that the substance we refer to as water is composed of molecules that have two represenatives of that which we call H bound to that which we call O.


And can't you demonstrate what you just devised otherwise? You could.

Quote:

In that case, let me be the first to announce that I've discovered the truth that 1+1 =/= 2, and I have discovered this pre-existing truth by a devising of symbols.


I don't understand. If you mean that 1+1 does not equal 2, then you'd be wrong.

Or do you mean you are using the symbol "1" to mean something else? In this case, it could be true that "1" + "1" does not equal 2. Of course, you could and should demonstrate to those you are speaking with just what it is you mean by "1" and "2" (if you are deviating from how they are commonly used), then.

What about this doesn't seem right to you?
0 Replies
 
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 02:57 pm
@Aedes,
Aedes;119738 wrote:
a ridiculous assumption


I certainly don't want to believe or spread ridiculous assumptions. So please correct me as to how the process of code (mapping probability space A to probability space B) is not a process of making a statement. Instructions cannot be given unless a statement is made. Are there instructions given or not?

Aedes;119738 wrote:
Wrong!!!


How is DNA/RNA transcription not a closed loop communication protocol?

http://www.ctphotographx.com/clients/infotheory/YockeyComModel.jpghttp://www.ctphotographx.com/clients/infotheory/YockeyComModel.jpg
Aedes
 
  1  
Reply Wed 13 Jan, 2010 03:02 pm
@QuinticNon,
QuinticNon;119756 wrote:
I certainly don't want to believe or spread ridiculous assumptions. So please correct me as to how the process of code (mapping probability space A to probability space B) is not a process of making a statement.
"Making a statement" is a phrase that I have never before seen used without preconceived reference to a human's intentions. So why on earth should I assume this about DNA?

QuinticNon;119756 wrote:
How is DNA/RNA transcription not a closed loop communication protocol?
Because if, when, how, and under what circumstances it happens is subject to innumerable external direct influences.
pagan
 
  1  
Reply Wed 13 Jan, 2010 03:10 pm
@QuinticNon,
Quote:
jeeprs

To be very clear about my position, it seems unarguable to me that (1) Crick and Watson do make this claim and (2) that therefore, information systems theory can be applied to living systems.

Besides, even leaving aside all the philosophy, I would have thought that the application of information systems to molecular biology might be a very fascinating new field of endeavour.
i agree it is potentially fascinating, but information theory was developed from communication theory. It is mathematics and engineering based. Therein those terms is shown a potential narrative bias. ie communication and engineering. Thus, applied to molecular genetics on a metaphysical level, dna is evidence of 'communication' and 'engineering'. One implies more than one sentient being (re wittgenstein), the other implies at least one sentient being (intelligent design). The other bias is that information theory is independent of the medium.
QuinticNon
 
  1  
Reply Wed 13 Jan, 2010 03:38 pm
@Aedes,
Aedes;119758 wrote:
"Making a statement" is a phrase that I have never before seen used without preconceived reference to a human's intentions. So why on earth should I assume this about DNA?


All codes make statements. It's not just limited to human communication. The figure 8 waggle dance of the bee, whale song, wolf howls... all intended to make statements. The process of encoding/decoding is a process of communicating information. Something has to be said. Some(one) must make a statement, or design a mechanism that can.

Did you see my link of Yockey's mapping the transcription process here?
http://www.ctphotographx.com/clients/infotheory/YockeyComModel.jpg

This is a closed loop communication system. See where they say "message" or "genetic message". Those are statements being made. So either Nature is making a statement or it isn't.

It is modeled directly from Claude Shannon's communication model here:
http://www.ctphotographx.com/clients/infotheory/ShannonComModel.jpg


Aedes;119758 wrote:
Because if, when, how, and under what circumstances it happens is subject to innumerable external direct influences.


Just like radio and television transmission. Transcription is no different.
0 Replies
 
jeeprs
 
  1  
Reply Wed 13 Jan, 2010 04:41 pm
@pagan,
pagan;119761 wrote:
i agree it is potentially fascinating, but information theory was developed from communication theory. It is mathematics and engineering based. Therein those terms is shown a potential narrative bias. ie communication and engineering. Thus, applied to molecular genetics on a metaphysical level, dna is evidence of 'communication' and 'engineering'. One implies more than one sentient being (re wittgenstein), the other implies at least one sentient being (intelligent design). The other bias is that information theory is independent of the medium.


Bear with me here while I try and articulate the 'story so far' in this thread, from my viewpoint.

I have also thought that it might be the case that this argument mis-applies the analogy from electronic to biological systems, but I don't think so any more. The argument is saying information is information, whether it is electronic or biological. Before we try and distinguish between electrical and biological information, consider the difference between 'information' on the one hand, and 'energy and matter' on the other.

The laws describing the interaction of mass and energy are described by physics. The laws describing the interactions of substances are described by chemistry (including biochemistry and organic chemistry.)

A basic premise in the argument is that, were there no life forms in the cosmos - were it possible to conceive a universe in which there was no living matter - there would be no encoded information. You could even say there would be no information of any kind (because there would be no observer to perceive or 'make sense' of the matter and energy that existed - no-one to 'be informed' about it.)

So the first thing to notice about anything organic is that it transmits form (morphe). This is of the very essence of life. If there is no continuity of form, in this sense, life cannot be said to exist, surely. And this capacity is not described by the laws of physics and chemistry. (It might be described by organic chemistry but this is on the basis of observing how life-forms work.)

To the laws of chemistry and physics, we now have the theory of evolution by natural selection.

I would have thought that the view of mainstream science would be that the laws of physics, chemistry and evolution are sufficient to explain the existence of life on earth (and elsewhere, should we discover it.)

But I think this argument casts doubt on this conclusion by saying that (1) information is irreducible to the laws of physics and chemistry and (2) the capture, storage and transmission of information is indispensable for the existence of life.

This is starting to make sense to me, and note I haven't brought 'a designer' into the picture. It is more a matter of understanding the principles. To observe that the capture, storage and transmission of information cannot be explained on the basis of existing scientific laws does not amount to any kind of religious assertion (although it does leave the door open to those who would make these assertions.)

My philosophical view is that reality is heirarchical, with matter at the lowest level, and intelligence at the highest level, an outlook which is common to nearly all the 'traditional philosophies'. So without introducing theistic arguments, this approach does lend weight to my outlook.
0 Replies
 
NeitherExtreme
 
  1  
Reply Wed 13 Jan, 2010 05:23 pm
@jeeprs,
Hi all! First I'll admit that I did not read this entire thread... If I'm repeating what's been said already, I honestly apologize.

I personally question whether DNA/RNA should be classified as "information", simply because (as I understand it) they are functional pieces of the system, not non-functional representations of a system.

Analogy: Does a key hold "information"? I would say not. Although its exact shape allows it to turn the lock, if a million randomly shaped keys were used, one of them might turn the lock without any intelligent key-cutting involved. (Of course a person can design a key to fit the lock, which would introduce "intelligent design", which in day to day life is what actually happens, but I don't think that qualifies a key as "information".)

I would think that in the evolutionary model, each individual organism, and the DNA which "built" it, could be seen as random keys each trying to turn the "lock" (reproduce in it's environment). The DNA would not be seen as encoded information, but more like a random iteration of a functional part of a machine, like a key and a lock.
 

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