Where's the Evidence??
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23-03-2012, 09:34 PM
RE: Where's the Evidence??
Are you talking about DNA replication as you would find in a cell?. If we are talking about DNA replication, then the order is determined by the order of bases on the parent strand. The linear axis may be where the information is contained but its order is due the order of the complimentary bases in the original strand.
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23-03-2012, 09:58 PM
RE: Where's the Evidence??
Quote:Are you talking about DNA replication as you would find in a cell?. If we are talking about DNA replication, then the order is determined by the order of bases on the parent strand. The linear axis may be where the information is contained but its order is due the order of the complimentary bases in the original strand.


Hello Scot. I am sorry, I misunderstood you.

Let me say it again. There are no bonds between the nucleotides in DNA that determine their order. A base of cytosine does not have a bond with either the base before or after it (along the linear axis) which determines the sequence. One can simply say, "well, the order is established by the DNA that it was transcribed from", but that rather begs the question. At some point the order has to be established (and however it happened, it didn't happen because there are bonds between the nucleotides determining their order).

And as I said earlier, this is merely background info, and doesn't change the nature of the argument being made.
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23-03-2012, 10:06 PM
RE: Where's the Evidence??
Ah i see what you're saying now. Sorry i thought you were referring to replication instead of how DNA was first formed without a template.
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23-03-2012, 11:57 PM
RE: Where's the Evidence??
How many eons might it have taken for the first life to come into existence? (we don't have a universal scale due to our limited knowledge simply planetary) How many centuries has science existed? There are leaps and bounds in the understanding of things, but there is an extent to which these things simply must take time. You discuss that the process in question is perfectly understood, yet your question is about the fact that we don't know the process we simply observe it working. That all calculations simply factor it in.

Atoms were understood in a rudimentary way before they were ever observed, but after being observed the understanding of them became much more complex. Gravity was undestood long before Newton's theory was abandoned for Einstein's. Progress does happen in all fields of science, and a huge portion of this progress is that we do not need to understand why something works to first learn from it. You are saying that your process is observable and can be worked around, but is a bit perplexing if we try to describe it. That happens all of the time.

I don't know much of anything about most fields of science, but I know a bit about rationality. In order to understand how this process happened with the first lifeform which we aren't even sure whether it would have DNA or be RNA based we need this first life form to study. Otherwise we'll need to create our own lifeform out of similar processes which eventually will happen. The original lifeform all those years ago is undoubtedly lost, so the only way to get a serious answer to this question is to create life. You may say that the process is fully understood, but what you're asking demands much more than the field is capable of understanding at this point.

Your statement is that we've understood the processes of the copying of DNA, but how could this happen for the first? Those two things are completely seperate. I know you said you're not talking about copying, but your example has to do with the current model, yet you are trying to prescribe this system to the first. We can't currently know the workings of the first living organism since it does not currently exist in any sort of way outside of data that's been imprinted through all this time. That maze will take much much longer than the complete understanding of every neural pathway in the human brain. Perhaps the reason people kind of leave you to this argument is because, there is no way of currently answering it so they don't.

As far as your suggestion that this somehow has to do with ID, Denicio hit it spot on with his observation. You can call the progenitor anything you like, but your answer is the same as our non-answer you dont really know you're just guessing. Proof is a lot more than identifying an unknown process, Proof requires understanding something.

Every time there is something without a simple answer it is considered a gap and called god, going back to ancient times before things like storm patterns were understood, tectonic plates. All of these things were prescribed to the same exact thing you're prescribing this to, and so many of them were proven to be something completely different. Your argument is not new or complex, your argument is one of the oldest out there.

Cantor put it eloquently by discussing the fact that the tools man uses to understand the world are merely inventions of man. The actual process and creation did not use the tools we do to percieve it. The simplest bit of information you need to have in order to understand our limited knowledge is the fact that we weren't required to start everything we just came out of the whole process. We don't have to understand everything to do our part, but we're trying.

I'm not a non believer, I believe in the possibility of anything. I just don't let the actuality of something be determined by a 3rd party.
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24-03-2012, 09:50 AM
RE: Where's the Evidence??
(23-03-2012 07:52 PM)Upright BiPed Wrote:  SOL,



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)
Sorry UB, when I said gaps I meant elements that you had left out of your explanation. When you asked if it was factually correct, which wasn't possible to assess as you had missed out those pertinent details.


I'm sure there are no gaps in understanding.

The point I was attempting to make was in the use of certain words, rather than the mild distinction of difference.

If you use the word translate, (rather than transfer) there is an intimation of an intermediate process, something that needs to do the translation, but which is not apparent or evident.
If you say transfer, there is no need for an intermediate process.

Also the word arbitrary would imply that some unknown force had to be in action for the arbitrary process to become an ordered form.

If you use the word iterative this would imply that the ordered form is conceivable, at some point, without outside intervention.

I feel the semantics (ie. precision of words) is important in describing a complex process.

In life you can't have everything................. Where would you put it ?
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24-03-2012, 12:41 PM
RE: Where's the Evidence??
(23-03-2012 11:57 PM)Lilith Pride Wrote:  How many eons might it have taken for the first life to come into existence? (we don't have a universal scale due to our limited knowledge simply planetary) How many centuries has science existed? There are leaps and bounds in the understanding of things, but there is an extent to which these things simply must take time. You discuss that the process in question is perfectly understood, yet your question is about the fact that we don't know the process we simply observe it working. That all calculations simply factor it in.

Atoms were understood in a rudimentary way before they were ever observed, but after being observed the understanding of them became much more complex. Gravity was undestood long before Newton's theory was abandoned for Einstein's. Progress does happen in all fields of science, and a huge portion of this progress is that we do not need to understand why something works to first learn from it. You are saying that your process is observable and can be worked around, but is a bit perplexing if we try to describe it. That happens all of the time.

I don't know much of anything about most fields of science, but I know a bit about rationality. In order to understand how this process happened with the first lifeform which we aren't even sure whether it would have DNA or be RNA based we need this first life form to study. Otherwise we'll need to create our own lifeform out of similar processes which eventually will happen. The original lifeform all those years ago is undoubtedly lost, so the only way to get a serious answer to this question is to create life. You may say that the process is fully understood, but what you're asking demands much more than the field is capable of understanding at this point.

Your statement is that we've understood the processes of the copying of DNA, but how could this happen for the first? Those two things are completely seperate. I know you said you're not talking about copying, but your example has to do with the current model, yet you are trying to prescribe this system to the first. We can't currently know the workings of the first living organism since it does not currently exist in any sort of way outside of data that's been imprinted through all this time. That maze will take much much longer than the complete understanding of every neural pathway in the human brain. Perhaps the reason people kind of leave you to this argument is because, there is no way of currently answering it so they don't.

As far as your suggestion that this somehow has to do with ID, Denicio hit it spot on with his observation. You can call the progenitor anything you like, but your answer is the same as our non-answer you dont really know you're just guessing. Proof is a lot more than identifying an unknown process, Proof requires understanding something.

Every time there is something without a simple answer it is considered a gap and called god, going back to ancient times before things like storm patterns were understood, tectonic plates. All of these things were prescribed to the same exact thing you're prescribing this to, and so many of them were proven to be something completely different. Your argument is not new or complex, your argument is one of the oldest out there.

Cantor put it eloquently by discussing the fact that the tools man uses to understand the world are merely inventions of man. The actual process and creation did not use the tools we do to percieve it. The simplest bit of information you need to have in order to understand our limited knowledge is the fact that we weren't required to start everything we just came out of the whole process. We don't have to understand everything to do our part, but we're trying.
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24-03-2012, 12:49 PM (This post was last modified: 24-03-2012 01:02 PM by Chas.)
RE: Where's the Evidence??
Quote:This all raises a very important question; how did these very special sequences come to exist?

Studies of DNA describe the chemical and physical bonds that form its famous helical structure. Those bonds create a stable backbone to which the individual nucleotides can be attached in the sequences described above. In other words, along this stable backbone are attachment points for each of the nucleotides (A, G, T, and C), and at each of these individual points any of the four nucleotides may be attached in order to form the encoded information.

Although the chemical bonds that actually form the backbone are well known, there is one set of bonds that are completely absent. Those 'missing' bonds are the ones between the nucleotides themselves which could determine their order within the sequence. 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). Those sequences are therefore referred to as "physico-dynamically inert" (meaning that the chemical bonds they are associated with do not determine the sequence in which they exist) and it is those sequences that create Life.

This is a scientifically observable fact of DNA which is not even in question. It is not based upon what we don't know, but what we already know, and have demonstrated to be true.
The sequences that we see are the result of billions of years of evolution. The DNA sequences that work are the ones that create organisms that survive to reproduce, passing on those sequences.

There is no mystery and no meaning - no symbolism, no semiotics.

Skepticism is not a position; it is an approach to claims.
Science is not a subject, but a method.
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24-03-2012, 03:21 PM
RE: Where's the Evidence??
Stupid design
Neil Degrasse Tyson
http://www.youtube.com/watch?v=BbLDKLQYr...re=related
http://www.youtube.com/watch?v=oEl9kVl6K...re=related

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24-03-2012, 06:20 PM (This post was last modified: 24-03-2012 06:43 PM by Upright BiPed.)
RE: Where's the Evidence??
LILITH,

Thank You. I appreciate your thoughtful post, but I must simply disagree. Science (and knowledge itself) is not furthered by appealing to 'what we don't know', in order to dissuade the recognition of what we already know to be true. If that were our guide, then we'd still be in caves.

In 1959, a future Nobel laureate named Marshal Nirenberg set out with his colleague, Heinrich Matthaei, to finally uncover exactly how DNA encoded the information contained within it. They began their search for the keys to the code by controlling the nucleic sequences being input into the ribosome (the site of translation within the cell) and then used radioactive labeling to document the output being created. The first translation of the Genetic Code came from the input of a repeating sequence of uracil (UUU), which established that the code for the amino acid phenylalanine was a triplet of uracil, UUU. Later came the code for lysine (AAA), and then the code for proline (CCC). With these discoveries under their belts, they (and others) began the proccess of deciphering the entire remaining genetic protocol. For his work on the genetic code, Nirenberg became the first ever National Institute of Health (NIH) scientist to win the Nobel prize (1969). This research took place alongside experimental research by Mahlon Hoagland and Paul Zamecnik in the 50’s and 60’s which began to describe the tRNA molecule itself, and its unique function as the intermediary object in protein synthesis. Eventually, the molecular structures of the whole range of tRNA molecules were elucidated. Further, we have even gone to the extent of introducing man-made mutant tRNA molecules and aminoacyl synthetases (changing the actual protocols of translation) and thereby opening up the code to the expansion of novel proteins. What I am saying here is that we have demonstated knowledge of the translation apparatus; even though we don't know its history, nor do we know how to cure cancer, these facts of translation are already entirely known. That knowledge cannot be denied by appeals to the mysterious.

The history of scientific advancement is captured in the old yarn about “how to eat an elephant” - one bite at a time. This is all the semiotic argument attempts to accomplish; the recognition that translation during protein synthesis is materially semiotic. You will notice that nowhere in the argument does it attempt to assert any conclusions whatsoever (and certainly no “proof”) about how this semiotic state came into being. It merely suggests the logical conclusion: that to explain a semiotic state will require a mechanism capable of creating a semiotic state. This is the appropriately modest conclusion of the demonstrated facts, and it hardly constitutes any stretch of rationality in order to reach it.
SOL,

Again, thanks for the conversation. You say:

Quote:Sorry UB, when I said gaps I meant elements that you had left out of your explanation. When you asked if it was factually correct, which wasn't possible to assess as you had missed out those pertinent details.

The question I asked referred to the chain of material events: A DNA polymerase assembles an mRNA transcript from the DNA template. That transcript is used to order the anticodons of properly-charged tRNA within the ribosome. Those tRNA become properly charged in a materially isolated process where aminoacyl synthetases (aaRS) recognize both the anticodons of the tRNA and the correct amino acids in order to bind them.

Now certainly, there are a myriad of other helper elements to the story (eg. raw materials must be transported, energy must be distributed, also the end result of a peptide bond to the correct amino acid in the polypeptide, etc). But when I asked the question, I was casually assuming you would point out any problems with the key organization of the process. It's a little like asking if a person's car uses gas or diesel, and receiving somewhat of a reluctance to answer before we talk about the refining and transport of diesel.

Quote:I'm sure there are no gaps in understanding.

On that process, agreed.

Quote:The point I was attempting to make was in the use of certain words, rather than the mild distinction of difference.

If you use the word translate, (rather than transfer) there is an intimation of an intermediate process, something that needs to do the translation, but which is not apparent or evident.

Of course, here I must completely disagree. And I believe that virtually all of the biological sciences would as well. A quick search of Google Scholar returns something over 1.25 million references for the search string “DNA translation”. It is the fact of this 'translation' (and not merely 'transfer') that is centerstage in the argument I presented. If I may, I'll ask you to look at the issue from the standpoint of “inventorying” the key interactions during translation (and here we can consider the process to begin when the DNA strand is exposed for copying, and end when the correct amino acid is bound to the polypeptide). From the point that the sequence in DNA is copied into mRNA, to the point where that mRNA transcript is used to bind to the anticodons of charged tRNA, you could refer to that entire process as “transfer”. A sequence is being transferred from a template to a mobile messenger, and that messenger is then transported to the site of the ribosome, and in that ribosome the sequence is then transferred to a sequence of anticodons. Throughout that entire process, the material control of maintaining the original sequence is based solely upon the complementarity of nucleic acids; transferred first from DNA, then between RNAs. But from that point forward, the transfer becomes a translation. In “Nature”, they describe it thus:

“During transcription, the DNA of a gene serves as a template for complementary base-pairing, and an enzyme called RNA polymerase III catalyzes the formation of a pre-mRNA molecule, which is then processed to form mature mRNA (Figure 1). The resulting mRNA is a single-stranded copy of the gene, which next must be translated into a protein molecule.”

Three nucleotides will be translated into a single amino acid, but those three nucleotides will have no material interaction with it whatsoever. The sequence is no longer solely controlling which amino acid will be bound to the polypeptide, that is now determined by the physical protocol established in the aminoacyl synthetases (in other words, the result is therefore not inherent to the sequence, but is arbitrary and must be established instead). Remember, the system functions by means of the sequence itself varying in order to specify different proteins, while the aaRS remains constant in maintaining the protocol (a change in the protocol would be a catastrophic end of function). With a level of certainty that can only come upon massive observation, both objects have an irreducible role to play in a formal system. Why formal? Because the mapping is not inherent, but must be established.

These are representations and protocols specifying effects within a semiotic system. Not only have we never seen a system of transferring information that operated in any other way, we cannot even conceive of one. We can conceive of squares and we can conceive of circles, but not square circles. Therefore, we have no justifiable grounds to believe it's even possible.


CHAS,

Quote:The sequences that we see are the result of billions of years of evolution.

The existence of Darwinian evolution is entirely dependent upon the existence of recorded information (the sequence) being passed from parent to daughter. It is the information that is evolving. So to say that the cause of the information is a process that requires it in order to exist, is saying that a process that doesn't exist can cause something to happen.

Quote:The DNA sequences that work are the ones that create organisms that survive to reproduce, passing on those sequences.

The question is not the content of the sequence in terms of results, the question is the existence and transfer of the sequence itself. I can grant you that the content of the sequence today is the accumulated result of evolution over time, but that is not the issue at hand. That sequence exists and is transferred by a semiotic system, with representations and protocols demonstrating the same physical entailments as any other form of recorded information transfer. The semiotic argument was posted on this thread, If you have any evidence that suggests the descriptions of the system are materially incorrect, then I'd be happy to respond.

Quote:There is no mystery and no meaning - no symbolism, no semiotics.

If that is the case, then you'll certainly be able to answer the challenge given in the argument: If in one system we have a genuine representation, and in another system we have something that just acts like a representation, then surely you can look at the material evidence and point out the distinction.


BUCKY BALL,

Quote:“Stupid design”

That is a theological response to a purely material observation. The issue of suffering and loss among the living is not answered in the actions of aminoacyl synthetases.
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24-03-2012, 07:27 PM
RE: Where's the Evidence??
So yer half-stepping; the stairway to heaven has a platform at semiotics. Perhaps the science makes no conclusions, but you began with one. Wink

Thus the suspicion of Denico; yet another conclusion or but anticipation? The science does not have an agenda. Tongue

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