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Upright Biped Replies to Dr. Moran on “Information”

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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 expectations 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 the 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 makes 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 representative 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?

 

 

Comments
Merry Christmas... s/n: UBiped's post should link from resources.junkdnaforlife
December 25, 2011
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Merry C hristmas, UB and all!gpuccio
December 25, 2011
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Merry Christmas, UD.Upright BiPed
December 25, 2011
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lol It's pointed out to you that the argument does not use "semiosis" within the argument itself, but only concludes that translation is semiotic - after a review of the physical evidence. You read it, and ignored it. It's pointed out to you that the contemporary use of the term "semiosis" does not require an "observer" as a proximate entity in the process, and that this fact is demonstrated in real time by each of us in our everyday lives (ie computer systems). You read it, and ignored it. It was pointed out to you that the argument specifically makes no reference to a mind. You read it, and ignored it. It was pointed out to you that the argument uses the word "mechanism" as an appropriate alternate, since the origin of the semiosis would be (and is) in question. You read it, and ignored it. It was pointed out to you that there are already peer-reviewed journals dedicated to bio-semiotics, not to mention working biologists who regularly speak of semiotic systems in biology. You read it, and ignored it. It was pointed out to you that it is entirely illogical to call an argument "circular" just because it makes its case. You read it, and ignored it. And finally, it was pointed out to you that you keep simply asserting that the conclusion of semiosis in wrong, but that you steadfastly refuse to address the evidence and demonstrate how that conclusion is wrong. Your final response is to continue ignoring the evidence, and simply re-assert your claim instead. Consequently, you have demonstrated the perfect example of willfull ignorance on behalf of one's ideology, and you have shown no restraint in doing so. - - - - - - ...and you and I both know you are intelligent enough to realize that is exactly what you've done. The exchange is right in front of you.Upright BiPed
December 23, 2011
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1- Variation is part of natural selection 2- Neither natural selection nor genetic drift has been shown to construct new, useful and functional multi-part systems. Only designers are known to construct such systems.
If ID is right, then fully complex life should just suddenly appear.
Wrong again, as usual.
If you can show us bacteria suddenly appearing from dead rock, you’re going to convert scientists to ID theorists because evolution can’t do that.
How do you know "evolution" can't do that?Joe
December 23, 2011
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Where did the information in the designer(s) of Stonehenge come from Dave and HOW is that relevant to determining that Stonehenge was designed?
Stonehenge was designed by the humans who were known to live there at the time and they had tens of thousands of years to learn how to cut rock, transport it from the two quarries where it was cut and erect it.
Guess what Dave? We learned all of that by studying the design. And that means it was NOT relevant to determining whether or not it was designed. You lose, as usual.Joe
December 23, 2011
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dmuulenix:]
ID is TOTALLY anti-evolution.
Only an ignorant liar would say such a thing.
Every theory in ID first assumes that evolution can’t do the job.
Again, your ignorance is meaningless here. How are YOU defining "evolution" that makes ID anti-evolution? If we go by how the experts define evolution then ID is NOT anti-evolution And seeing that you are a nobody to science I will have to go with what science says. dmullenix:
Evolution and natural forces are both true and sufficient to explain life.
That is the propaganda yet there still isn;t any evidence to support it.Joe
December 23, 2011
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DMullenix, And thanks for the award as well :) I just could not resist it and proved the rule of thumb. That was amusing.Eugene S
December 23, 2011
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Petrushka, Sorry I did not get the message. How is that link relevant to the particular question of self-replicators not being around in astronomical numbers for continuous billions of years to make spontaneous life origin a statistical plausibility?Eugene S
December 23, 2011
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Merry Christmas, DMullenix! Best wishes for the New Year to all of us. No, I do not think that ID is the big lie. I am convinced that materialistic naturalism is inadequate in tackling the problem of life origin. A lot of great minds agree with me on this issue :) Moreover, I think that its explanation of the current state of life is also inadequate. Apologies for posting 11.2.1 in the wrong place.Eugene S
December 23, 2011
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That’s just guesswork, not empirical science. Such guesswork could be called naive if we did not know what philosophical commitments caused it. If we don’t know something, we must explicitly say so without prevarication. However what we hear materialistic naturalism say is nowhere near. It says, it must be so. Full stop. The sheer lack of empirical observation of such self-replicators convincingly tells us that the beginning of life on our planet was a unique event which in addition was highly implausible if explained only by chance and necessity.Eugene S
December 23, 2011
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That's just guesswork, not empirical science. Such guesswork could be called naive if we did not know what philosophical commitments caused it. If we don't know something, we must explicitly say so without prevarication. However what we hear materialistic naturalism say is nowhere near. It says, it must be so. Full stop. The sheer lack of empirical observation of such self-replicators convincingly tells us that the beginning of life on our planet was a unique event which in addition was highly implausible if explained only by chance and necessity.Eugene S
December 23, 2011
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We can't give you an explict model because nobody, science or ID, has any samples of how DNA was developed. Give us some fossils spanning the period where DNA was being developed and we'll be happy to answer that question. Without fossils to show how it was done, we're left with the observation that the result is entirely materialistic in nature and the knowledge that evolutionary processes can produce the information needed to create what we see incrementally. ID, on the other hand, seems to have no choice but to kick JoeG's fabled Newton's First Rule out the window and invent an Intelligent Designer containing billions of times more information than is found in the DNA system it's trying to explain in the first place. And ID has no idea of where that astonishingly improbable amount of information could possibly come from. Wait ... maybe you could become Mormons. I think they claim that the Gods sort of evolved. Maybe that would work. Except it would still violate Newton's First Rule because if evolution could explain a Designer, it could explain DNA too, so the Designer would be superfluous.dmullenix
December 23, 2011
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As Chas D told you in reponse 7, "semiotic" refers to human (that is, intelligent) use of symbols. It's circular reasoning / begging the question to use the term when you're trying to argue that the DNA system is the product of intelligent design.dmullenix
December 23, 2011
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How is that relevant? Because you're not going to build anything unless you know how to build it and that "know how" IS "information". No "information", no "know how". ID is TOTALLY anti-evolution. ID was killed a century and a half ago by evolution. If evolution is true, ID is not needed. Every theory in ID first assumes that evolution can't do the job. Newton's first rule is, "We ought to admit no more causes of natural phenomena than such as are both true and sufficient to explain their appearance." Evolution and natural forces are both true and sufficient to explain life. An Intelligent Designer necessarily contains enormously more information than the life it is trying to explain. It's not necessary, so Newton's first rule rejects it.dmullenix
December 23, 2011
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Stonehenge was designed by the humans who were known to live there at the time and they had tens of thousands of years to learn how to cut rock, transport it from the two quarries where it was cut and erect it. http://www.history.com/news/2010/12/13/solving-the-riddle-of-stonehenges-construction/ They missed being around when the first life appeared by several billion years and molecular construction would have been way beyond their capabilities if they were.dmullenix
December 23, 2011
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Me in 2.2.1.2.4: "Evidence! You know, the stuff you’re demanding from us. Let’s see samples of the first life and later life. Show us the whole DNA/RNA/tRNA/protein synthesis system coming into existence overnight and you’ll have good evidence supporting your claim. If it develops slowly and step by step we’ll have good evidence for our claim. But nobody has such evidence because whatever happened, it happened billions of years ago at a sub-microscopic scale and we haven’t found any fossils yet. Neither side has such evidence, but you’re declaring victory because you’ve defined your answer into the question. “It was semiotics.” Sorry, that doesn’t work. Meanwhile, science has a process, variation and natural selection, that is known to exist, is observable in the real world and the lab and generates information incrementally. Your side has a claim “supported” by circular reasoning." Show us some samples of first life. If science is right, then it would have started out very simply and grew gradually more complex, probably over a period of millions of years, until it reached today's levels of complexity. If ID is right, then fully complex life should just suddenly appear. We should go from dead rocks to fully modern bacteria with no intermediate steps. If you can show us bacteria suddenly appearing from dead rock, you're going to convert scientists to ID theorists because evolution can't do that. But I'll bet you $10,000.00 that even if the samples showed that life appeared slowly it wouldn't convince an ID theorist that his theory was wrong. You'd just claim that it was The Designer that produced the first self reproducing molecule and The Designer sho produced all of the intermediate steps that eventually produced modern life. Or maybe front loading and fine tuning. Because ID just has to be right. Meanwhile, just keep demanding evidence without ever admitting that ID has none to support its theory of abiogenesis either.dmullenix
December 23, 2011
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Merry Christmas, Eugene S! For Christmas, I'm giving you the Godwin Award and kairosfocus gets one too for supporting you. I don't suppose that either of you have even considered the possibility that ID is the big lie? Nah. Merry Christmas anyway.dmullenix
December 23, 2011
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Maybe it's because we don't know where to look for a self reproducing molecule that's too small to be seen in a microscope and which would probably last about one minute before it got eaten?dmullenix
December 23, 2011
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When the truth becomes your enemy, watch out!kairosfocus
December 22, 2011
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http://www.sutter.com/PDF/RP0028_King-2.pdf And I guess all those people conceived via in vitro fertilization don't exist.Petrushka
December 22, 2011
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I can't refrain from citing somebody famous. I hope it is not an off-topic because we can apply this to evolutionism as an ideology. The name of this man is Dr Goebbels. If you tell a lie big enough and keep repeating it, people will eventually come to believe it. The lie can be maintained only for such time as the State can shield the people from the political, economic and/or military consequences of the lie. It thus becomes vitally important for the State to use all of its powers to repress dissent, for the truth is the mortal enemy of the lie, and thus by extension, the truth is the greatest enemy of the State.Eugene S
December 22, 2011
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dmullenix, you've gone from ignoring physical evidence, to ignoring my posts. Your abbreviated reply at 2.2.1.2.8 is the third time you have simply refused to address the content of my posts. The reason for this should now be obvious to any fair reader; you cannot argue your case against either the evidence, or the rationale. Otherwise, you would have already done so. Physical evidence and reason are rightfully promoted to the height of empiricism and materialism by its adherents. The very last thing one should expect a materialist to do is avoid the observations of physical evidence. One should not expect a materialist to make a game of it. Yet, both observable physical evidence and coherent reasoning have been provided to you to affirm the claim that protein synthesis demonstrates a semiotic state. But you ignore both the evidence and reasoning outright. And you do so willfully. When an ideologue ignores physical evidence and clings instead to the claim that the existence of a designer is impossible, then he has shown his cards. - - - - - - - - - In your post to GP you disregard all observations to the contrary, and simply re-assert (once again) that the system is not semiotic. If that is true, then it must be true at an observational level. In other words, you can point to the physical evidence and show the distinction between something that is a symbol and something that just acts like a symbol. Why have you repeatedly refused to do this?Upright BiPed
December 22, 2011
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"This does not mean that all symbolic representations must necessarily be intentionally generated." Perhaps you could provide us with a single counter-example.Eugene S
December 22, 2011
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By the way, a living cell cannot even reintegrate itself if its membrane is pierced with a needle. It dies as a consequence of this even though all other things are perfectly okay for it to live (temperature, acidity of the environment, presence of food, etc.). So what spontaneous emergence are we talking about?! Is that science?Eugene S
December 22, 2011
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Are you referring to his hypothetic assumption that any newly appeared primitive life would have been instantly devoured by more advanced life? I guess contemporary science would have been able to detect that anyway.Eugene S
December 22, 2011
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Darwin gave a pretty good reason for that in Origin.Petrushka
December 22, 2011
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Plausible events occur plausibly. Implausible events do not occur in practice. There is simply no empirical evidence of that. If life had been able to spontaneously self-organise at some distant point in the past, we would have seen it happening today also simply because the conditions on our planet are life-friendly. But for some stupid reason we don't see it. Why would that be the case?Eugene S
December 22, 2011
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LoL! Just because Dave sez it isdn't irrelevant makes it so! No Dave if YOU say it is relevant it is up to YOU to make YOUR case. But you don't have a case so you just spew nonsense. Where did the information in the designer(s) of Stonehenge come from Dave and HOW is that relevant to determining that Stonehenge was designed?Joe
December 22, 2011
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Tell you what dmullenix, to refute the design inference all YOU have to do is actually step up and produce positive evidence for YOUR position. Then Newton’s First Rule applies and ID is refuted. Strange that you choose to whine as opposed to actually putting up…Joe
December 22, 2011
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