Where's the Evidence??
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22-03-2012, 09:06 AM
Where's the Evidence??
Hello forum. I am a new member here who has been basically lurking for the past several days. As I stated on the Introductions page, I am a theist (and an empiricist) with no particular evangelical bent, and I have a couple of friends who are happy members here, and they’ve suggested I join in.

In lurking around, I have noticed several posts and threads about ID notions, which are (quite frankly) little more than caricatures of the actual disputes over evidence, without much to follow in the way of argument.

I wanted to make an offer. If anyone is interested, I will provide an actual ID argument here on this forum, and members would have an ample chance to attack its veracity directly. I am a generalist (and no expert) and occasionally my ability to participate becomes limited, but nonetheless, I will try to respond to any substantial rejoinders and will attempt to conduct the conversation to the best of my ability. On the other hand, if someone simply wants to close their minds to rational discourse, and vent their spleen over religion (man's relationship with God or Gods) then I have no interest.

Thoughts?
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22-03-2012, 09:28 AM
RE: Where's the Evidence??
Good luck to you.

The only thing I can say is you better have an iron will and not be offended easily.

I applaud theists who come here and actually want to have intelligent discourse (as that's rare) but I also do not envy them. It's very hard to keep these kinds of threads on any kind of track, and unfortunately a lot of the atheists on this forum have a hard time being civil with theists for long stretches of time due to history.

If you want to actually do something like this then be sure to prepare yourself. Remember your numbers are much less.

"I think of myself as an intelligent, sensitive human being with the soul of a clown which always forces me to blow it at the most important moments." -Jim Morrison
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22-03-2012, 09:36 AM
RE: Where's the Evidence??
Hi ludacris, thank you for the invitation and the warnings (I have my helmet at the ready).

The argument I am going to make deals with the semiotic nature of genetic translation during protein synthesis. I am fully aware that many people (theist and atheist alike) don’t follow these topics regularly enough to have a working understanding of them, so if it is okay with the forum, I will post two comments. The first will be just a bit of a modest backgrounder on protein synthesis taken from an essay on the subject. The second will then develop the semiotic argument.

If that is appropriate for this forum, then give me just a minute to make the posts.

(QUESTION: When I make two comments back-to-back, is there anyway for the system to not place them inside the sdame comment box? I noticed the system did that in the "Introductions" thread.)
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22-03-2012, 09:36 AM
RE: Where's the Evidence??
Well I'm intrigued enough to wonder what the argument could be in support of ID... Exclamation

Meaning no offence, but I have yet to observe any rational discourse on the subject.
Discussion usually descends into something akin to two children in the playground arguing about whose comic book hero has the bestest super powers. (AKA - The Batman kerb stomp conjecture).

If it's possible to define a common (mutually understood) definition of the words rational, design, and intelligent.

It would be interesting.

In life you can't have everything................. Where would you put it ?
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22-03-2012, 09:44 AM
RE: Where's the Evidence??
I'm hearing semiotic something something wha ???

I do believe we have a few biologists around here so they should be able to talk to you.
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22-03-2012, 09:48 AM
Photo RE: Where's the Evidence??
Protein Synthesis

As most people have come to know, DNA is at the center of all living things; it serves as a sort of "parts list and assembly instructions" for Life. Although the systems by which this happens are incredibly complex, to understand generally how it works is actually fairly simple:

Living things are made up of cells. Different types of cells make up the various parts of any organism (skin, nerves, organs, tissues, etc). The work of these different cells is performed by various proteins inside of each cell. These various proteins are created by attaching together a long series of 20 different kinds of amino acids. Some of these sequences have hundreds of amino acids, others have thousands. After all the amino acids are attached together in a long chain, the chain is then carefully folded up into a 3-dimensional protein. Each protein has a specific job to do, and if you change the order of those 20 different kinds of amino acids, then it changes the type of protein being created.

A living organism “knows how” to arrange these amino acids in the correct order by reading the information from its DNA.

In essence, DNA is like a long computer tape which contains information an organism needs in order to build itself and regulate its internal systems. It is this information contained within DNA which ultimately organizes and animates non-living matter (carbon, nitrogen, hydrogen, etc) into living organisms. Also like a computer tape, the information within DNA is encoded in digital form. Whereas a computer (for instance) uses an iterative (repeating) series of 1’s and 0’s arranged in a specific sequence in order to encode information, DNA uses an iterative series of four chemicals to accomplish the exact same task. These four chemicals are known as nucleic acids (or nucleotides) and are commonly referred to by their initials A, G, T, and C (adenine, guanine, thymine, and cytosine).

   

In order to decode the information within DNA, these four chemicals are read off (transcribed) in a linear fashion just as the letters on this page are read in a linear fashion. For instance, in English text the arrangement of C-A-T spells the name of a feline animal with the sharp claws. In the genome, the arrangement of C-T-A is a code for an amino acid called Leucine. In other words, if the code C-T-A appears in the sequence when a protein is being created, then Leucine will be added to that protein (like a word being added to a sentence). Likewise, the sequence of A-G-T codes for an amino acid called Serine, T-A-T codes for Tyrosine, G-G-C codes for Glucine, and on and on throughout the twenty different amino acids that make up proteins.

These individual codes are fed into a molecular machine called a ribosome, and when they are read together in full sequences (in a similar way to letters being used to make words, and words being used to make sentences) proteins are constructed within the cell. It is those proteins that do the cellular work within all living organisms.

   

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.
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22-03-2012, 09:50 AM
RE: Where's the Evidence??
Oh I think, I see where this may be going......
irreducible complexity hmmm

edit: you beat me to the post.....

In life you can't have everything................. Where would you put it ?
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22-03-2012, 09:50 AM (This post was last modified: 22-03-2012 09:59 AM by Upright BiPed.)
RE: Where's the Evidence??
This second post is an argument I made to the Professor of Biochemistry at the University of Toronto, Dr Larry Moran; a very hardened materialist whom treasures any chance to beat his opponents down with his superior intellect. After all, he has eight collegiate-level textbooks on biochemistry to his credit. His response was direct – he immediately evacuated himself from the conversation. The same argument was presented to biologist and NCSE operative Nick Matzke. His response was just as direct, he immediately refused to engage the evidence, and tried repeatedly to change the conversation. Also in the chain was Dr Elizabeth Liddle, a Neuro-Scientist in the UK. She debated the topic for a period of several months, only to eventually retract her original claim (she claimed she could simulate the rise of recorded information like that in DNA), and ceased responding to the debate. Also there was Dr Robert Collins at the Department of Molecular Biophysics at Yale, who presented no contrary evidence, and ultimately, simply said anything in order to have anything to say. Others have given the same general response.


- - - - - - - - - - - - - - - - -


Dr Moran, sorry for the delay. Other responsibilities intervened for a bit.

Certainly the sequence in DNA is driving reactions. (And there are many varieties)

In your comments you refer to the use of the term “information” within nucleic sequences as a useful analogy, and you say that there is no expectation that it should “conform to the meanings of “information” in other disciplines.” I certainly agree with you that it conforming to other meanings would be a telling turn of events. And I assume your comment suggests that the nucleotide sequence isn’t expected to share any of the same physical characteristics as other forms of information – given that we live in a physical universe where information has physical effects. Ones which we can observe.

I think it makes an interesting comparison; the comparison between the physical characteristics of information transfer in the genome, versus information transfer in other forms. Just recently on this forum we were having a conversation about recorded information, and a question arose if a music box cylinder ‘contained information’. Speaking to its physical characteristics, the answer I gave was “yes”. Just like any other form of recorded information, the pins on a music box are an arrangement of matter to act as a representation within a system. No differently than ink on paper, or the state of a microprocessor, or the lines left on a recording tape, or an ant’s pheromones, or the tone of vibrations we make when we speak; they are all matter/energy arranged in order to represent an effect within a system.

It was also pointed out that a physical arrangement of matter (like the pins on a music box cylinder) cannot by themselves convey information – they require a second coordinated physical object. This second object is easily referred to as a protocol, but physically its is a rule (a protocol) established in a material object. The necessity of this physical protocol is something easily understood; for one thing to represent another thing within a system, it must be separate from it, and if it is truly a separate thing, then there must be something to establish the relationship that exist between the representation and the effect it is to represent (within that system). That is what the second physical object accomplishes, it establishes the relationship between a representation and the effect it represents, which is a relationship that otherwise wouldn’t exist.

There have been examples of this dynamic given in previous conversations. For instance, an apple is an apple, but the word “apple” is a separate thing altogether. Being a separate thing from the apple, there must be something that establishes the relationship between the two. In the case of the word “apple” we as humans have learned the protocols of our individual languages, and they physically exist as neural patterns within our brains. These neural patterns are material things, and they establish the immaterial relationship between a physical representation and its physical effect. This same dynamic is found in all other cases of recorded information. I have previously used the example of a bee’s dance; a bee dancing in a particular way during flight is a separate thing than having the other bees fly off in a particular direction, and the relationship between the two is brought about by a protocol which physically exist in the sensory system of the bee.

In the dynamics of information transfer, the operative observation is that each of these physical things (the representations, the protocols, and their resulting effects) always remains discrete. This is one of the key observations that allows information to exist at all. The input of information is always discrete from the output effect, and the protocol that establishes the relationship between the two, remains discrete as well. They are three completely independent physical realities which share a relationship, with the protocol establishing the relationship between the representation and its effect within the system. In no case does the representation (or the protocol) ever become the effect.

This same dynamic is found in all forms of recorded information; including those used in the information processing systems created by intelligence. As an example, the first automated fabric looms used an arrangement of holes punched into paper cards (which acted as physical representations of the resulting effects within the fabric). Sensors and pins within the machine would sense where the holes were punched, and it would use that information to change and control the colors of threads being woven. In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to the specified effects. Each of these is physically discrete, while sharing the immaterial relationship established by the protocol.

So here we have a series of observations regarding the physicality of recorded information which repeat themselves throughout every form – no matter whether that information is bound to humans, or human intelligence, or other living things, or non-living machines. There is a list of physical entailments of recorded information that can therefore be generalized and compiled without regard to the source of the information. In other words, the list is only about the physical entailments of the information, not its source. I am using the word “entailment” in the standard sense – to impose as a necessary result (Merriam-Webster). These physical entailments are a necessary result of the existence of recorded information transfer. And they are observable.

That list includes the four material observations as discussed in the previous paragraphs: a) the existence of an arrangement of matter acting as a physical representation, b) the existence of an arrangement of matter to establish the relationship between a representation and the effect it represents within a system (the protocol), c) the existence of physical effects being driven by the input of the representations, and d) the dynamic property that they each remain discrete. Observations of systems that satisfy these four requirements confirms the existence of actual (not analogous) information transfer.

These same entailments are is found in the transfer of information from a nucleic sequence. During protein synthesis a selected sequence of nucleotides are copied, and the representations contained within that copy are fed into a ribosome. The output of that ribosome is a chain of amino acids which will then become the protein being prescribed by the input sequence. The input of information is therefore driving the output production. But the input and the output are physically discrete, as evidenced by the fact that they don’t directly interact, and that the material output is not assembled from the material input.

The exchange of information (from input to output) is facilitated by a set of special physical objects – the protocols – tRNA and its entourage of aminoacyl synthetase. Acting together they make it possible for the input to alter the output, and they do so by allowing them to remain separate. The tRNA physically bridges the gap between the input and the output, acting as a passive carrier of the physical protocol. It accomplishes this by being charged with the correct amino acid by the synthetases (the only molecules in biology which actually hold the rules to the genetic code). The synthetases accomplish their tasks by being able to physically recognize both the tRNAs and the amino acids. They charge the tRNAs with their correct amino acids before they ever enter the ribosome. The actions of the synthetases are therefore completely isolated from both the input and output. In other words, the only molecules in biology that can set the rule that “this maps to that” are physically isolated from both the input and output, while the input and output remain isolated themselves.

These observations establish that the entailed objects (and dynamic relationships) exist the same in the translation of genetic information as they do in any other type of recorded information (in every example from human language, to computer and machine code, to a bee’s dance). These observations have been attacked as being as a misuse of the definition of words (a semantic word game, as you call it). But I have already produced the definitions of the words from a standard dictionary; I’ve restated the observations using those definitions in place of the words themselves; and I have asked the question: “If in one instance we have a thing that actually is a symbolic representation, and in another we have something that just acts like a symbolic representation – then someone can surely look at the physical evidence and point to the distinction between the two. There is also the simple fact that there is nothing about the attachment of cytosine to thymine to adenine that intrinsically means “bind leucine to a nearby polypeptide” as an inherent property of its matter. That is a quality beyond its mere materiality, one it takes on by being in a system with the correct protocol to cause that effect from that arrangement of matter.

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.

So going back to your comment, a fair reading suggests that the information transfer in the genome shouldn’t be expected to adhere to the qualities of other forms of information transfer. But as it turns out, it faithfully follows the same physical dynamics as any other form of recorded information. As for “disciplines”, you will notice that these observations are very much in the domain of semiotics. Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments make no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery. It must be acknowledged; human beings did not invent iterative representational systems, or recorded information. We came along later and discovered they already existed.

Therefore, the search for an answer to the rise of the recorded information in the genome needs to focus on mechanisms that can give rise to a semiotic state, since that is the way we find it. We need a mechanism that can cause an arrangement of matter to serve as a physical representation. We need a mechanism that can establish within a physical object a relationship between two discrete things. To explain the existence of recorded information, we need a mechanism to satisfy the observed physical consequences of recorded information

Do you agree, or do you have evidence that attaching adenine to thymine to guanine is mapped to “start a new protein” in any physical context?


So…

The argument given above is based solely on material evidence; the objects and dynamic relationships observed within the translation apparatus. The conclusion of the semiotic argument is both limited and simple. It attempts no more than to establish by material observation that the translation of recorded information from the genome during protein synthesis is semiotic in nature.

I would be happy an engage any responses on that material evidence. I understand that many will want to change the subject to other issues, so I will observe my right to leave those concerns for others to address in an effort to keep the engagement focused on the material evidence.

Thanks!
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22-03-2012, 09:56 AM (This post was last modified: 22-03-2012 09:58 AM by morondog.)
RE: Where's the Evidence??
(22-03-2012 09:48 AM)Upright BiPed Wrote:  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.

Could you expand on this paragraph? The rest was well written but I'm having trouble following this. I get that the spiral is where we hook the nucleotides on, that the order of the nucleotides determines the info that's encoded. What you're saying is that a C can be next to a T or G or U and it's not a problem?
Oh woopsie, I see by your second post that this stuff is gonna be waaaaay out of my comfort zone. Are you in fact a biologist yourself then?
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22-03-2012, 10:05 AM (This post was last modified: 22-03-2012 10:10 AM by Upright BiPed.)
RE: Where's the Evidence??
Hi morondog, thanks for the question.

You are correct, there arre bonds to attach the nucleotides (AGTC) to the backbone, but there are no bonds between the nucleotides that establish their order along that backbone.

No, I'm not an expert, just a generalist (a research director in a completely unrelated field) with a healthy curiosity.
By the way morondog, the fact that the bonds in DNA do not determine the order of nucleotides is a well understood idea - and is merely a background tidbit of information, so there's no need to get hung up on it.
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