DNA and the 'Code of Life'

@jeeprs,

The calculations concerning the spontaneous development of living cells from the fortuitous association of molecules rule out the idea that it is something that just happens - in the absence of some inherent tendency for it to happen, anyway. (See Life's Solution, by Simon Conway Morris. He presents a very detailed argument, far too complex to present here, which indicates that evolution unfolds in accordance with certain inherent tendencies rather than ad hoc. And indeed the examples given might also indicate an underlying order).

The number of potential (and mainly useless) ways in which the various ingredients of proteins, amino acids and enzymes might possibly be combined is a number greatly exceeding the number of stars in the universe. So I really don't buy the 'million monkey's' argument.

Here's a question: in what other scientific endeavour, other than that concerned with accounting for the nature of life, is the absence of a cause regarded as an hypothesis?

2 Replies

@pagan,

pagan;119215 wrote:

With respect.

Yes, respectfully, I'm simply asking you to explain why you believe as such. I've explained why I think info and code are seperate, drawing models of U2 and Computer Monitors. Where is the info represented by both our screens, on your screen or mine?

pagan;119215 wrote:

The word 'action' is charged though. I would distinguish between a machine action (reaction?) and a consciously willed action.

I've addressed this before as well. Do you have any issues with the notion I put forth explaining the differences between cause/reaction vs thought/action?

I do understand your thinking very clearly. I have no problem with us disagreeing. But since we disagree, I'm mostly concerned with understanding why you think the way you do. That's not an unreasonable request. You may illustrate something that I have not considered and sway my position. Please explain the logic behind your reasoning so I may understand where you're coming from better.

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@pagan,

You will have to excuse me again as I have difficulty with this separation from formula and code. For me the original formula required a certain medium , circumstance. Like all formulas it requires the right ingredients and the perfect circumstances. If the medium changed and it was not appropriate, then the formula would not be effective. This then, after the initial commencement of life, is where the formula becomes complex because it allows certain deviation from the initial requirements of medium. The medium can change when life becomes a viable, when it has past it initial creation. The formula to me writes the codes, as it records its progress , the formula is the author of the codes. This to me is the crucial question , the formula has that ability to write and rewrite the codes as circumstances change, but did it itself have an engineer that conceived of this complex but also simple formula. Its a simple question , is it just normal that an event needs a response and as the events become more complex the responses are no more complex , just simple reactions to the current event. Im sorry, I have given it much thought but Im not capable of describing my thoughts.

1 Reply

@jeeprs,

jeeprs;119225 wrote:

in what other scientific endeavour, other than that concerned with accounting for the nature of life, is the absence of a cause regarded as an hypothesis?

Oh that's ripe... the Absence of Cause Hypothesis.:brickwall:

---------- Post added 01-11-2010 at 03:28 PM ----------

xris;119229 wrote:

You will have to excuse me again as I have difficulty with this separation from formula and code.

No formula may exist without a code to formulate it upon.

xris;119229 wrote:

the formula is the author of the codes.

So to speak... the formula is the the thought. The thought is from mind. All immaterial and non physical. Just as the genome is non physical but the genetic code is physical.

The code is the mechanism that allows the thought to manifest physically. Without the code, the formula would just be a thought... pure information. With the code, the formula is expressed in our physical realm.

Code expresses thought into physicality.

---------- Post added 01-11-2010 at 03:40 PM ----------

jeeprs;119225 wrote:

which indicates that evolution unfolds in accordance with certain inherent tendencies rather than ad hoc. And indeed the examples given might also indicate an underlying order

Much like any language will have an underlying order of syntax and semantics that automatically arise.

1 Reply

@QuinticNon,

QuinticNon;119231 wrote:

Oh that's ripe... the Absence of Cause Hypothesis.:brickwall:

---------- Post added 01-11-2010 at 03:28 PM ----------

No formula may exist without a code to formulate it upon.

So to speak... the formula is the the thought. The thought is from mind. All immaterial and non physical. Just as the genome is non physical but the genetic code is physical.

The code is the mechanism that allows the thought to manifest physically. Without the code, the formula would just be a thought... pure information. With the code, the formula is expressed in our physical realm.

Code expresses thought into physicality.

I half agree, the formula has always existed but the manifestation of that formula, is life and life has a written code. We dont have to have thought, only to accept it always had that ability.

1 Reply

@xris,

Quote:

QuinticNon
What opening quote do you refer to? Where does the information of that quote reside, my computer screen or yours? Or do our monitors represent the same information that is immaterial?

The information resides potentially on both screens. The information is also a potential abstraction from either screen by the viewer. Our monitors are physical. We can use the term representation to represent a thing or a representation. ie van gogh can represent his chair in paint. I can represent his representation of the chair in a photograph. It may have been possible to represent the orginal chair in a photograph. All three are necessarily physical.

For me abstracted information from a physical code, is a representation. (it is still physical, because even an abstraction has to be held by a physical medium eg the brain.) That representation can be re-presented in another medium to the original code. Thus a cd may contain the digital code for this post. We may upon thinking about it, abstract in our minds the information part of the cd, and model it mathematically. But in order to transfer the information of the code of this post from a cd medium to your monitor medium, a physical process of copying the cd information to the physical monitor is required to recreate the code in the new medium. Physicality is always necessary and thus there is always a medium.

Quote:

QuinticNon

You said, "The laws of the universe as conceived by cause effect chains"

I call that Chaos. And if you speak of Patterns, you speak of a product of Chaos.

It is obvious to me now that we are not so distant in our thinking.

this was the quote referred to. For me there is a world of difference between pattern and chaos. If cause / effect chains reveal pattern then cause/effect is not chaos.

Quote:

I do understand your thinking very clearly. I have no problem with us disagreeing. But since we disagree, I'm mostly concerned with understanding why you think the way you do.

Maybe you didn't read my reply in the other thread where we first bumped? Evolutionary Philosophy and Reasons for Existence.

Anyway i am a multi narrative dude. For me science is a very particular narrative. Powerful but limited. When i examine the narrative of science i enter into the spirit of it. But i don't think the spirit of it is complete. That is why it is emminently sensible for me to ask a question of a non sentient thing. eg a narrative. I have already said all this. It is repetition.

I believe and use other narratives. In my spiritual narratives for example i can recognise that this world is not physical in a sense. But that sense is useless when talking about dna evolution theory, because science is materialistic. In art narrative there is for example the concept of a representation causing the thing in itself. eg a sculpture becomes the thing from an abstraction in the mind of the artist that represents say an emotion. or is it the thing in itself? It depends upon the narrative. and so on. Maybe looking at some other threads i have started like will help

susskind and the cosmological constant

the experimental evidence for 'now'

to be honest i feel like we are going around in ever decreasing circles.

---------- Post added 01-11-2010 at 10:32 PM ----------

jeeprs;119225 wrote:

Here's a question: in what other scientific endeavour, other than that concerned with accounting for the nature of life, is the absence of a cause regarded as an hypothesis?

but why do you suppose there is an absence of a cause? The dawkins crew believe there is a cause ...... biochemistry. It is yet to be mapped but they necessarily believe in it.

Also there is cosmology. There is no necessary cause postulated yet for the big bang. There are postulated causes such as multiverses.

1 Reply

@jeeprs,

Pagan - actually from my viewpoint, you and QN are not going around in circles, as such. There seems to be a fundamental disagreement between your positions viz-a-viz whether information can be said to exist apart from the medium in which it is embedded. QN is taking the positive position, arguing for the reality of information as a fundamental ontological category alongside energy and matter (please correct me if I am wrong). Whereas you are arguing the information cannot be meaningfully said to exist apart from the form of the message or communication in which it is embedded. I will declare I favour QuniticNon's argument because it certainly seems to me that such languages as mathematics are not at all explainable in terms of the operation of a subjective consciousness. Their meaning transcends individual consciousness, but is also not materially present.

QuniticNon - I am interested in your response to my 'absence of cause hypothesis'. Is this a regular line of argument? Even a 'chestnut', perhaps?I hadn't encountered it previously.

---------- Post added 01-12-2010 at 09:38 AM ----------

pagan;119242 wrote:

but why do you suppose there is an absence of a cause? The dawkins crew believe there is a cause ...... biochemistry. It is yet to be mapped but they necessarily believe in it.

But they don't. They explicitly reject it. There is only a sequence of events, which are shaped by adaptive necessity. This is different to a cause in the sense understood by any formal pre-modern philosophy. Etienne Gilson has argued in Aristotle to Darwin and Back Again that science has deliberatly rejected the idea of formal and final causes, ergo there are only material causes. Dawkins always ridicules the idea of telos in the sense of any over-arching cause. As he must. It is almost more basic to the spiritual outlook that the idea of deity.

2 Replies

@xris,

xris;119236 wrote:

...the formula has always existed...We dont have to have thought, only to accept it always had that ability.

How can a formula form without thought. How can a formula be expressed without code?

1 Reply

@jeeprs,

Quote:

jeeprs
Whereas you are arguing the information cannot be meaningfully said to exist apart from the form of the message or communication in which it is embedded.

no it is very meaningful to me to conceive of information in that way. Its just that i can't see the point of adopting such an attitude when considering concepts within the narrative of science ...... unless you intend to take a philosophical position against materialistic science itself. (which i do myself on occasions). When we do that we just don't cross over with the science. Its a rejection of science itself.

Now having said that there are other conceptual schemes for doing 'science'. ie Different narrative structures that would concievably yield a history of science and experiments that could even yield the same theories (though unlikely in the same order). But information as immaterial is 'unscientific' as far as i can tell. (i realise that QM verges upon this but QM is pushing the scientific narrative to its limits).

Information abstracted mathematically as if immaterial, is potentially useful scientifically. The reason being that science itself is the development of a text, and the medium of that text is declared by science to be irrelevant. Necessarily a medium, but the text is of a form such that its meaning is independent of the medium. This is possible for certain types of text in a material world. ie universal texts. eg mathematics. Universality is also intrinsic to human science (at the moment). The text must be true for all space time and circumstance. Such a project would require that the text is not medium dependent in the sense that a medium cannot alter its meaning. But it remains medium dependent in a general sense because for science everything is medium dependent. Now such types of text (ie the scientific restrictions placed upon them) is itself a way of deconstructing science, because other types of text can be conceived. ie medium dependent texts. Notice also that a text is a medium category in itself. I flagged the difference re speech and writing. In fact it may be that dna/rna is itself necessarily posited by science as a medium dependent text. But that does not necessarily contradict the description of it in the scientific text, which is a medium independent text. ie science would be a medium independent text that describes dna/rna as a medium dependent text.

By physical i really mean substance such that energy is included as well as space time. The relationship between energy and matter and space time is complex in science. This is no surprise. If you push an incomplete narrative to its limits then it will come up with some very strange sentences. You might also flag up the rather obvious philosophical point that how can the meaning of the scientific text be independent of the medium unless the meaning is understood by a being that is able to read it out from any medium? In other words you are flagging another deconstruction of science re objectivity versus subjectivity. I agree.

Does this mean that science has contradictions in it. Yes. It is fairly easy to deconstruct science. But so what? All narratives can be deconstructed.

Quote:

But they don't. They explicitly reject it. There is only a sequence of events, which are shaped by adaptive necessity.

well ok if your definition of cause won't include that, then fair enough they have rejected a cause, under your scheme. But thats not the scheme they take.

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@pagan,

pagan;119242 wrote:

For me abstracted information from a physical code, is a representation.

And here is where I think we agree... until...

pagan;119242 wrote:

(it is still physical, because even an abstraction has to be held by a physical medium eg the brain.)

You're still only able to point to the medium. Where is the info? How can it be physical if it cannot be isolated and observed? You're still talking about two separate things but only able to physically observe one of them. Do you not distinguish between a physical brain vs a non physical mind?

pagan;119242 wrote:

That representation can be re-presented in another medium to the original code.

Yes, physical copies of copies all representing the very same non physical agent. Van Gogh, U2, Computer Monitors... we're talking about the same thing... "representation"... But where is the what that is being represented?

That's one of the crucial differences between patterns and code.

Patterns always and only represent themselves.

Code always and only represent something other than itself.

Any info produced from observing the pattern of a tornado is always and only about the tornado. The tornado is the pattern. A pattern produced by cause/reaction. Cause/reaction that functions under the mechanism of Chaos.

Any info produced from reading a code is never about the code. It's about what the code represents. My code, "hot air + cold air + wind + pressure + time" is not about the word "cold" or the letter "p". My code represents my observation about a tornado. The tornado didn't give me that code. I wrote that code to describe it. Just like DNA is a code that describes Pagan. Who wrote it?

Observing and reading are different activities. Patterns are observed. Code is read.

---------- Post added 01-11-2010 at 06:07 PM ----------

pagan;119251 wrote:

But information as immaterial is 'unscientific' as far as i can tell.

"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

1 Reply

@QuinticNon,

Quote:

"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

oh for goodness sake i have very clearly responded to that quote. I know you think information is immaterial. Repeating it over and over again wont change my opinion. WE JUST DISAGREE IN THE CONTEXT OF THIS DEBATE! block capitals doesn't alter a thing. Constant repetition of statements doesn't change anything. WE DISAGREE. thats it! The points of difference between us have been identified and dissected. What more is there to say?

0 Replies

@jeeprs,

jeeprs;119245 wrote:

'absence of cause hypothesis'. Is this a regular line of argument? Even a 'chestnut', perhaps?

No I've never heard of that. But I think of "cause" in a different manner than most. "Cause" is usually sufficient for the hard materialist. They mistake "cause" for "reason". I don't allow that. Cause and reason are different things. Yet even the Creationist is fond to claim a "First UnCaused Cause".

Reason requires reasoning. Cause requires Chaos. That's why I so adamantly distinguish between Cause/Reaction vs Thought/Action. Only Thought/Action is reasoned. The only way we can know the Thought/Action Reasoning of another is with Code.
But this certainly is not to suggest that the Code IS the thought/action reasoning. It only represents it.

---------- Post added 01-11-2010 at 06:33 PM ----------

pagan;119258 wrote:

What more is there to say?

You said that "information is immaterial" was unscientific. I presented you a scientist that says otherwise. One of the most respected scientists in all of history. A quote you previously agreed with.

Yet you still claim that "information is immaterial" is unscientific. It seems very contradictory to me.

0 Replies

@jeeprs,

pagan;119223 wrote:

but don't you agree that analogy when it comes to dna/rna and such may be missing a crucial point simply because it is an

I wasn't the one who brought up that analogy. The fact of the matter is that adenine and thymine form two electron bonds with one another and guanine and cytosine form three -- and this is THE basis of RNA-DNA complementarity. It's basic chemistry.

Quote:

Where if any do you see the relevance of media, especially dna/rna etc?

The "medium" is the chemical properties of the constituent molecules, their concentration, the presence of catalytic or otherwise essential cofactors (like inorganic phosphate), and a suitable energetic environment.

jeeprs;119225 wrote:

The calculations concerning the spontaneous development of living cells from the fortuitous association of molecules rule out the idea that it is something that just happens - in the absence of some inherent tendency for it to happen, anyway.

I don't know how much more clearly I can say it -- no one contends that cells just fortuitously popped up from nothingness. There were many intermediate subcellular chemical events that happened first, like the development of organic molecules and later organic polymers.

jeeprs;119225 wrote:

indicates that evolution unfolds in accordance with certain inherent tendencies rather than ad hoc. And indeed the examples given might also indicate an underlying order

The order is chemical and physical. The materials that constitute a living cell have chemical properties that persist whether or not they're inside a living cell.

jeeprs;119225 wrote:

The number of potential (and mainly useless) ways in which the various ingredients of proteins, amino acids and enzymes might possibly be combined is a number greatly exceeding the number of stars in the universe.

And the useless ones do not persist.

The HIV virus produces only one viable virus for every 10,000 that result from its replication -- simply because its 'fidelity' to its genetic program is highly flawed. And the dead ones don't go on.

jeeprs;119225 wrote:

So I really don't buy the 'million monkey's' argument.

Good thing that no one argues it!

jeeprs;119225 wrote:

Here's a question: in what other scientific endeavour, other than that concerned with accounting for the nature of life, is the absence of a cause regarded as an hypothesis?

Just because Creationists argue that there MUST be a cause does not mean that "absence of a cause" is a scientific hypothesis.

But to answer your question about demonstrability of ultimate causes, the following fields of science are just as incapable of that demonstration as evolution:

1. Geology

2. Linguistics

3. Astronomy

4. Physics

5. Chemistry

6. Mathematics

1 Reply

@Aedes,

Aedes;119266 wrote:

Just because Creationists argue...

A personal question from me to you Aedes. Do you consider me a Creationist or a proponent of Intelligent Design?

1 Reply

@jeeprs,

I don't consider you either, mainly because I don't know your beliefs and arguments well enough to pass judgment. The comment was not directed at you or anyone else in particular, though it was indeed deliberately chosen.

And what do you consider me? If the answer is a hardcore materialist, then you're wrong.

1 Reply

@Aedes,

Aedes;119185 wrote:

When people invoke the conundrum "what are the odds that life would just randomly form from chemicals in a primordial soup", they are talking about STATISTICAL randomness. Quite specifically! They're making an argument about likelihood and unlikelihood in the absence of a guiding hand.

But just because it's unfathomable doesn't make it random. In actuality the formation of organic macromolecules might have been exceedingly likely simply based on chemistry and abundance of substrate. The formation of early cells might have been exceedingly likely. This is not randomness -- but it sure is chaotic and it sure is unfathomable to us.

i am definitely getting entangled in the different definitions people are using for words in this thread.

the word immaterial is being used a lot and in my history that always meant 'insignificant' which is not its use here at all. now i wonder how is there a statistical randonness that would be different from a randonness that wasnt statistical? unless it means that the statistics arent possible to follow for long enough until the randonness would appear? like the monkey typing shakespeare?

also, is there a way events can be chaotics but not random? it is all getting unfathomable to me now...

2 Replies

@jeeprs,

Well I won't repeat here the arguments covered in the other current thread, Evolutionary Philosophy and Reasons for Existence. Suffice it to say that I believe the scientific account of evolution does not come to terms with the idea of causality in the sense that this is understood in any traditional metaphysic. The Gilson text I referred to states that:

Quote:

final causality or purposiveness is an inevitable idea for those who think hard and carefully about the world, including the world of biology. Gilson insists that a completely rational understanding of organisms and biological systems requires the philosophical notion of teleology, the idea that certain kinds of things exist and have ends or purposes the fulfillment of which is linked to their natures. In other words, final causes.

So the idea that life is 'self generating' is, according to traditional philosophy, irrational, on the grounds that nothing appears which does not have a cause. Therefore to say that life began to exist without a cause is not an argument, nor an hypothesis. It is an irrational supposition.

I think that many scientific philosophers say that life began 'without cause' because (1) causality as it is understood in the traditional sense is out-of-scope for science and maybe even for the 'modern outlook', and (2) because the scientific view has been shaped by opposition to the previous religious and mythological accounts which did provide a causal account(namely, the divine will). So the modern account is based on the denial of cause, in this specific sense. If traditional metaphysic asserts there is a final cause, then its modern critics will say, well, no there isn't.

It amounts to saying 'while the specifics of what actually happened are unknown, it is our belief that it did not occur as an act of divine will'. Faith in the divine will is now replaced by faith in will in another sense, namely, we will find out how it happened, one day.

In the course of time, this attitude has actually reified the absence of cause into a cause. In other words, the fact that life is uncaused has become foundational to the modern outlook.

The idea of causality, in this sense, was one topic in a famous 1948 BBC radio debate between Bertrand Russell and Father Frederick C. Copleston on the existence of God.

1 Reply

@QuinticNon,

QuinticNon;119197 wrote:

in number 3, wouldnt you say that the unpredictability in weather is more an apparent unpredictability? i dont care for that definition...in fact i dont like any of them.

wouldnt chaos more aptly be described as a lack of cause and effect, or perhaps contradictory effects from identical causes regardless of circumstance? chaos can be predictable in fact...another chaotic mind can predict what a chaotic person might do next...but not always of course!
i also think order within chaos is entirely possible...or perhaps i mean utility within disorder? chaos is not necessarily 'bad' (and i realize you never said it was, but many people interpret it so)

0 Replies

@salima,

salima;119271 wrote:

i wonder how is there a statistical randonness that would be different from a randonness that wasnt statistical?

Statistically random (the formal use of the word) means that all possibilities are equal. But in colloquial use, people use the word random to mean unpredictability. In this conversation it makes a difference, because the unpredictability does not mean that all possibilities were equal.

salima;119271 wrote:

like the monkey typing shakespeare?

But this is not an applicable analogy. In the English language, the letters A and X are not used with the same frequency, for instance. There are frequencies of letter usage in every language. This is important because the primordial soup had rules -- it was beholden to certain chemical and physical properties. In fact carbon chemistry and the chemistry of water are extremely important and very unique -- and this imposes a strict set of rules. So you have to start imposing rules on the monkey -- letters must be used with the right frequency; consonants and vowels have certain relationships, etc.

The vast majority of a cell is made out of Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, and Sulfur. These chemicals were abundant in the early earth, and they all have particular properties - they exist in a restricted number of ionic states, they have a certain amount of electronegativity, etc. And people HAVE made organic molecules out of just this stuff just in a lab.

salima;119271 wrote:

is there a way events can be chaotics but not random?

Yes. Take a coin and weight it so that it's 2/3 as likely to land on heads as tails. Take another coin that is 7/8 as likely to land on tails as heads. Now take 2562562457 of coin 1 and 34902374098 of coin 2 and throw them 1 trillion times.

How many heads do you get and how many tails do you get?

That is a highly chaotic scenario. It's not random at all. In fact a computer algorithm could probably easily make a prediction. But throw in more and more and more and more and more variables, all with different probabilities, and have the outcomes interact, and you develop a situation with so much chaos that it is beyond any reasonable prediction.

But it is still not random.

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@QuinticNon,

thanks for your reply Aedes

what i find interesting is that we can read the genetic code in one relatively simple representation (a sequence of paired bonds) and identify general characteristics of a life form. eg brown eyes. But it takes a much more sophisticated chemical modelling to even begin to understand the incredible complexity of the physical behaviour of the molecules. This in turn will be required to physically model a cell, and then again another level of reading to understand how a cell will react to its cellular environment.

Does it follow from this that there is likely to be new ways of 'reading' the genome in the future. By this I mean that the physical form of the dna/rna molecules (eg their twisting folding) will potentially provide information within information.

as a very crude analogy ....

Green
Eyes Large
Nose hyetr
Optic nerve lppku
Mouth Lips
Ears

0 Replies

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