Where's the Evidence??
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22-03-2012, 10:49 PM (This post was last modified: 22-03-2012 10:58 PM by Upright BiPed.)
RE: Where's the Evidence??
Hello House of Cantor,

Quote:“Geometry. It's not such an important question but rather reflects the self-importance of the observer.”

What is the geometric determinant between two objects which do not interact? And how does it determine it?

Smile

Hello again morondog,

Semiosis exist anytime one thing represents (means, stand for, is mapped to, symbolizes) something else, and is separate from it.

A bee's dance is representation of an effect within a system. That system is the communication behaviors of the bee. When the other bees see the dance, they respond to it based upon its pattern. They can map the correct response to the pattern because they have a physical protocol in their sensory systems for doing so. The pattern and the response have no material relationship to one another (meaning there is no physico-chemical cause that says a bee bopping up and down in a certain way must result in the other bees flying south), but that mapping exists, solely because the dance and the response operate within a system that has the required protocol to establish it.
Hello Bucky Ball,

Your thoughts regarding disease are understandable.

As understandable as such ultimate frustration can be for all of us, those feelings don't impact the material observations being made.
Sol,

Quote:“Thanks for the clarification, I needed that.”

Your welcome.

Quote:“I see from your responses you are more concerned with the philosophy of "information" transference rather than the Biological aspect.”

I think that, as in all other cases, finding answers will require both good observations and good rationale. In the transfer of information from the genome, there is an sequence of mRNA nucleotides which are assembled by an RNA polymerase from the DNA temple, and that mRNA transcript contains the sequence of codons required to order the anti-codons of charged tRNA within the ribosome. All of this is a chain of material events (bonding, breaking bonds, pairing, etc) leading up to the binding of codon and anticodon. But this chain of events does not translate the order (of the original sequence) into the binding of correct amino acids into polypeptides. That is translation is accomplished solely by the aminoacyl synthetases which charge the tRNAs with the correct amino acids, and operate completely isolated from this first material chain of events. Is there anything in this description that is factually incorrect?

Therefore the mapping of codons to amino acids is not a physical relationship based upon the material make-up of the two objects in question, but is observably determined by a separate object which doesn't interact with them. What principle is involved that suggests we should not recognize that this is precisely the same material dynamic as observed in any other form of recorded information transfer?

Quote:“If I may point out, without animosity... If you are to say that Pierce is anthropomorphic in his approach (which may be valid, although I would rather say anthropocentric.)

If you accuse an act of anthropomorphism, then it is somewhat invidious of you to use an anthropomorphic analogy ie, pheremones and text to humans, as a discount.

Simply as a matter of consistency, it may be best to avoid this type of thing.”

I have no issue with Pierce, but was simply responding to a question. And its hardly invidious to compare the physical process of information transfer in various domains. Far from avoiding the observations, it would be careless not recognize the objects and dynamics involved in the process.

Thanks for the conversation.







Chas,

Quote:“What evidence is convincing? There are no signs or symbols - they're just molecules”


Of course they are all material things. We live in material universe, what else would they be?

From the argument:

There has also been the profoundly illogical objection that because these things follow physical law (and can be understood), they cannot be considered symbols or symbolic representations. Not only does this deny the existence of any symbol in the extreme, it fails for the obvious reason that everything follows physical law. If something can’t be true because it follows the same laws as everything else, then we have entered the Twilight Zone.
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22-03-2012, 11:10 PM
RE: Where's the Evidence??
All those things you say are independent aren't so, they're interdependent: It's true that the patern of the bee's flight there's not direct causation for the other bees to behave in any particular way, this is A doesn't cause C.
But, because there's this thing you call the protocol, we can say A causes B (the protocol) that causes C, hence we have a causality relatioin between the pattern and the effect. The fact that we still don't understand the protocol doesn't mean anything. It's just like finding a new language, the last thing we learn is the protocol, we have the concepts and we have the symbols (words and letters) but the language is the hardest thing to learn, how to make our neurons to fire in a determined way to determined symbols so they connect to the neurons that encode the concepts.
But in the same way language evolves randomly and sometimes incoherently for some time, in the same way genetics can do it. But if you're a foreigner to that language and you grab a dictionary it seems like something organized and designed, but it's the other way around, the organization comes after the language exists, in the same way we could say that biologists had already found all the words (the genome) now are trying to find the meaning of each word, and others are trying to understand the "grammar rules" of the language.

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23-03-2012, 04:03 AM (This post was last modified: 23-03-2012 04:07 AM by Sol.)
RE: Where's the Evidence??
(22-03-2012 10:49 PM)Upright BiPed Wrote:  All of this is a chain of material events (bonding, breaking bonds, pairing, etc) leading up to the binding of codon and anticodon.[ .....Gap A.....]

But this chain of events does not translate the order (of the original sequence) into the binding of correct amino acids into polypeptides.[ .....Gap B.....]

That is translation is accomplished solely by the aminoacyl synthetases which charge the tRNAs with the correct amino acids, and operate completely isolated [ .....Gap C.....] from this first material chain of events.

Is there anything in this description that is factually incorrect?

factually incorrect is debatable, due to the gaps,
Gap A - the "chain of material events" is not arbitrary it is iterative toward stability.
Gap B - The process does not translate it transfers, a subtle distinction but important.
Gap C - See Gap A, they are not isolated as a process, there isn't a stop codon in the tRNA and the anticodon loop has complementary bases for the stable (DNA) code.

Quote:Therefore the mapping of codons to amino acids is not a physical relationship based upon the material make-up of the two objects in question, but is observably determined by a separate object which doesn't interact with them.

This bolded part has me confused (my comprehension skills may be lacking).
Observably determined.........m'kay
By a separate object ..... I think it is observed to be more than one interactive process.
Doesn't interact with them - Begs the question, how can it be determined by them without any interaction from them.

Quote:I have no issue with Pierce, but was simply responding to a question. And its hardly invidious to compare the physical process of information transfer in various domains. Far from avoiding the observations, it would be careless not recognize the objects and dynamics involved in the process.

I meant invidious in the sense that it is unfair or unjust to negate something like anthropomorphism and then use the same thing in an analogy to support your proposition.

As others, I am having difficulty discerning what exactly it is that you find unanswerable.

In life you can't have everything................. Where would you put it ?
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23-03-2012, 04:30 AM
RE: Where's the Evidence??
(22-03-2012 10:38 PM)Upright BiPed Wrote:  Hello Craniumonempty,

I think you are generally correct in your understanding of the bonds in DNA, but then you say: “The orders are determined by the RNA and other DNA strands (or whatever that's called)”. The paired strand of DNA does not determine the sequence it contains, and neither is that sequence determined by RNA. The ordering of messenger RNA (mRNA) during transcription is determined by the sequence instead.

“However, you aren't questioning that, you are questioning where did the sequences come from, correct? Basically, how did life come from non-life. If you are looking where it started, then you need to look in abiogenensis as that is what they study in that field.”

The question of how the sequence (the information) came to exist is certainly one of the unanswered question in abiogenesis, but the observations I made are about the objects and dynamics of a transfer of information as we already know it to exist. In other words, one is a valid open question, and the other is what we already know.

“As far as sometime after the first life form was stable (or stable enough) and able to reproduce (because there may have been many, but only one was able to multiply and go one until today), then from there you have the beginning of evolution by natural selection.”

I have no particular response to make, other than to say that Darwinian evolution requires recorded information to exist (in order to function), so the observations I made are a requirement for evolution to exist, and therefore must either precede it or be congruent with it.

“... BTW, do you have a hypothesis for ID abiogenesis (as that's what it sounds like you are trying to get at) or is this simply trying to argue against current theories? I'm not sure I see an argument for anything, just against.”

No, I am not trying to get at a theory of ID abiogenesis. My argument is that the transfer of information from the genome demonstrates a semiotic state. This isn't an argument against something, so much, but an argument for something based upon they way in which we find it. In all of the material observations I made in the argument, none of them are even controversial. The argument, is nothing more than recognizing something for what it materially demonstrates itself to be.

Ok, I might be a little unclear what you are trying to argue exactly (for or against) or trying to understand. I've read your two large posts and quite a few others. I'm under the impression currently that you are talking about maintaining the information?

When I spoke of abiogenesis, it was because there was a rudimentary DNA strand that was made (or at least before life forms that start current natural selection data). They are still working on that... you know that though.

However that strand had to be reproduced otherwise, the organism wouldn't last long. Well, it might, but the species would die with it.

Yeah, you are right about the RNA. Goes to show how long I've been out of school

Currently DNA is recreated via DNA replication. Is this what we are speaking of?

DNA is reproduced by itself. That sequence is split when the cells split and they create more.

And? I'm not entirely sure I know what your question is?

"no-one in the field thinks they'll re-write the process of protein synthesis."

That might be true, but they would still change given enough evidence. That's why I'm wondering what the replacement is also.

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theist: "See! There is a heaven."
atheist: "So, you consider heaven a joke too?"
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23-03-2012, 05:22 AM
RE: Where's the Evidence??
(22-03-2012 10:49 PM)Upright BiPed Wrote:  Hello House of Cantor,

What is the geometric determinant between two objects which do not interact? And how does it determine it?

I see a relationship between geometry and abiogenesis. I don't know what you're seeing. Tongue

Perhaps the only nature the protocol exists in is our nature. We have devised tools for our use, with one technology built upon another to the extent that it is forgotten what is natural. Words and identities conspire to make us believe things must be the way we see them through our tooled-up glasses.

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23-03-2012, 07:48 AM
 
RE: Where's the Evidence??
Oh my....when this guy types..this is all i hear.....

http://www.youtube.com/watch?v=B5Slxr_JwEA


If ALL his science and all his arguments lead back to GOD then its creation 101.

He managed to speak to my post but failed to answer a single question.

The video i posted pretty much sums it up.

D
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23-03-2012, 07:52 PM (This post was last modified: 23-03-2012 08:13 PM by Upright BiPed.)
RE: Where's the Evidence??
NACH

Quote:All those things you say are independent aren't so, they're interdependent

The fact that the transfer of information requires an organized multi-part system is not being denied. That does not change the fact that the relationship of the codons to their resulting effects is a non-material relationship, one that is established by a physically isolated object. Those physical dynamics are the same as any other form of recorded information transfer, and they demonstrate that the transfer is semiotic.

Quote:A causes B (the protocol) that causes C, hence we have a causality relation between the pattern and the effect

I might choose slightly different words, but your point is more than clear. The problem is this: A is the codon. B is the aminoacyl synthetase. C is the binding of the proper amino acid to the growing polypeptide chain.

But A does not physically interact with B, and B does not physically interact with C. In order to establish the relationship between A and C, the actions of B are isolated from both A and C - as they must be. This is a lesson we learn from observing any other form of recorded information transfer, and when we look inside the cell, lo and behold, we find exactly the same thing there are well. The amino acid synthetases bind the correct amino acids to the correct tRNA both spatially and temporally isolated from the ribosome, where the input of the codons and the binding of the polypeptides take place. The observations made in the semiotic argument are completely demonstrated by the evidence.

Your comment about interdependence also raises another point which I have yet to mention, but is itself demonstrated as clearly as it could possibly be. It’s an interesting side issue to the main point of the semiotic argument, and it needs neither to be accepted nor denied on order for the semiotic argument to stand validated. That is, a representation is an arrangement of matter which is completely useless without a protocol to decode it (into an effect). I cannot imagine anyone earnestly challenging that statement. On the other hand, a protocol is an arrangement of matter that is completely useless without a representation to decode. These two physical objects – in whatever form the transfer of information may take place – absolutely require the existence of other object in order to function. That would make the information transfer in the genome the most prevalent form of irreducible complexity on the surface of the planet.

Thanks for the conversation Nach. I have no illusions of changing anyone’s mind; I simply wanted to demonstrate that materially valid arguments exist. There are many of them.

SOL,

Quote: factually incorrect is debatable, due to the gaps,
Gap A - the "chain of material events" is not arbitrary it is iterative toward stability.
Gap B - The process does not translate it transfers, a subtle distinction but important.
Gap C - See Gap A, they are not isolated as a process, there isn't a stop codon in the tRNA and the anticodon loop has complementary bases for the stable (DNA) code.

There are no fundamental gaps in our understanding of the how DNA, DNA polymerase, mRNA, tRNA, amino acids, aminoacyl synthetase, and the ribosome are used during protein synthesis. The rather mild semantic distinction between you saying “transfer” and me saying “translate” does not constitute a gap in our knowledge of the system, yet you posed it as such. To say that “the chain of material events” is not arbitrary is merely an assertion against observable evidence to the contrary. It's also a slight misrepresentation of the argument. The chain of events I described was never represented as being anything other than a material process. Finally, to note that the stop codon binds with a release factor instead of a tRNA (in order to terminate the translation) is nothing more than to acknowledge another integral part of the system (and that acknowledgment does nothing whatsoever to change the observations being made). And the anticodon loop you mention only binds with the mRNA codon, it plays no active role in the binding of the correct amino acid to that tRNA. That binding is established by the aaRS (the only molecules in biology that establish the genetic code).

Quote: This bolded part has me confused (my comprehension skills may be lacking). Observably determined.........m'kay

I apologize for being clumsy. Allow me to clarify… ‘it has been demonstrated by observation that the relationship is set by an object which does not interact with either the codon or its resulting effect’.

Quote: Doesn't interact with them - Begs the question, how can it be determined by them without any interaction from them.


What is being determined is the arbitrary relationship between the codon and its effect within the system (the binding of the correct amino acid to the polypeptide). The aminoacyl synthetase accomplish this be being able to physically recognize the amino acid and the codon; charging the tRNA with the correct amino acid prior to it ever entering the ribosome. That charging process is therefore spatially and temporally isolated from both a) the presentation of a codon in the ribosome, and b) the binding of the correct amino acid to the polypeptide. Here is a short, rather descriptive explanation from the RCSB Protein database:

“When a ribosome pairs a [certain] tRNA with [certain] codon, it expects to find a [certain] amino acid carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases” (emphasis added)

Quote:I meant invidious in the sense that it is unfair or unjust to negate something like anthropomorphism and then use the same thing in an analogy to support your proposition.

Again, I have no issue with Peirce, and therefore I do not negate his ideas. However, his ideas were generally isolated to human communication. Others (such as Charles Morris) then expanded his concepts to animal communication systems. And in the age of information-driven machinery, we see these same concepts repeated once again. Representations and protocols are not only the single conceivable method to physically record and transfer information, they are the only method we have ever found. This is an observation without contradiction anywhere in the cosmos. And, it is demonstrated in its earliest possible form as the very thing that organizes a living cell. It is hardly anthropocentric to recognize that it did not originate with mankind. That recognition is an act to remove anthropomorphisms from the equation altogether – and appropriately so. The only thing being observed is the material itself.


CRANIUMONEMPTY,

Thank you for the conversation. Your response looks a little like the responses I’ve had when becoming familiar with the physics of the matter. I get the feeling that your position boils down to “what are you talking about, where’s the issue?”.

I will attempt to spell it out. Again, thanks.


HOUSE OF CANTOR,

Quote:I see a relationship between geometry and abiogenesis.

I understand you see a relationship between abiogenesis and geometry. That is why I asked you to explain it, so that we can determine if it has any impact of the observations being made.
DENICIO

You began your post with three questions that demanded a level of proof that no theory - of any kind - will ever be able to provide. It was an act to insulate yourself.

To willfully ignore material evidence is one thing (and a very poor thing at that). To do so by demanding the physically impossible – is simply irrational.

It’s anti-science.
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23-03-2012, 08:33 PM
RE: Where's the Evidence??
(23-03-2012 07:52 PM)Upright BiPed Wrote:  I understand you see a relationship between abiogenesis and geometry. That is why I asked you to explain it, so that we can determine if it has any impact of the observations being made.

What's this we shit? Big Grin

Geometry trumps ID; I see it, you acknowledge that I see it... my job is done. Tongue

Numbers make shapes that naturally fit together, we are but derivative of shape shifting. Lycanthropes, the lot of us... Angel

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23-03-2012, 08:36 PM
RE: Where's the Evidence??
Quote:. In other words, there are no physical or chemical bonds between the nucleotides that determine their order along the linear axis of DNA (where the information is).

I may be misunderstanding what you are saying here, but as far as i know the order of the nucleotides is due to matching the original 'parent strand' by the base pair rule C-G, A-T. Its a case of mirroring the parent strand during replication and not due to a chemical bond determining what base pairs with what in a set order.
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23-03-2012, 09:11 PM (This post was last modified: 23-03-2012 09:17 PM by Upright BiPed.)
RE: Where's the Evidence??
HOUSE,

Quote:Geometry trumps ID; I see it, you acknowledge that I see it... my job is done.


he he. you've got me there.
Hi Scot,

The complimentarity of the bases does not determine their order. If there are no bonds between the nucleotides on one strand (along the linear axis) determining their order, then there are no bonds between them determining their order on the other side either. The pair bonds are across the linear axis, not along it. The linear axis is where the information is.
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