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The First Gene: An information theory look at the origin of life

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The First Gene: The Birth of Programming, Messaging and Formal Control

Here, edited by David Abel, The First Gene: The Birth of Programming, Messaging and Formal Control :

“The First Gene: The Birth of Programming, Messaging and Formal Control” is a peer-reviewed anthology of papers that focuses, for the first time, entirely on the following difficult scientific questions: *How did physics and chemistry write the first genetic instructions? *How could a prebiotic (pre-life, inanimate) environment consisting of nothing but chance and necessity have programmed logic gates, decision nodes, configurable-switch settings, and prescriptive information using a symbolic system of codons (three nucleotides per unit/block of code)? The codon table is formal, not physical. It has also been shown to be conceptually ideal. *How did primordial nature know how to write in redundancy codes that maximally protect information? *How did mere physics encode and decode linear digital instructions that are not determined by physical interactions? All known life is networked and cybernetic. “Cybernetics” is the study of various means of steering, organizing and controlling objects and events toward producing utility. The constraints of initial conditions and the physical laws themselves are blind and indifferent to functional success. Only controls, not constraints, steer events toward the goal of usefulness (e.g., becoming alive or staying alive). Life-origin science cannot advance until first answering these questions: *1-How does nonphysical programming arise out of physicality to then establish control over that physicality? *2-How did inanimate nature give rise to a formally-directed, linear, digital, symbol-based and cybernetic-rich life? *3-What are the necessary and sufficient conditions for turning physics and chemistry into formal controls, regulation, organization, engineering, and computational feats? “The First Gene” directly addresses these questions.

As we write, it is #2 in biophysics, and the trolls haven’t even got there yet.

Here’s Casey Luskin’s review:

Materialists Beware: The First Gene Defends a Strictly Scientific, Non-Materialist Conception of Biological Origins:

The First Gene investigates a number of different types of information that we find in nature, including prescriptive information, semantic information, and Shannon information. Prescriptive information is what directs our choices, and it is a form of semantic information — which is a type of functional information. In contrast, Shannon information, according to Abel, shouldn’t even be called “information” because it’s really a measure of a reduction in certainty, and by itself cannot do anything to “prescribe or generate formal function.” (p. 11) Making arguments similar to those embodied in Dembski’s law of conservation of information, Abel argues that “Shannon uncertainty cannot progress to becoming [Functional Information] without smuggling in positive information from an external source.” (p. 12) The highest form of information, however, is prescriptive information:

Comments
What does it mean if you say in once sentence that you can’t do something, and in the next that it might be possible? Doesn’t that negate the first statement that it can’t be done?
It means that I accept the conventional wisdom that faster than light travel is impossible, time travel to the past is impossible, ESP doesn't exist, UFOs are not alien spaceships, and so forth, but I am not emotionally attached to these beliefs and I read about counterclaims with interest. I have not said protein design is impossible. I have said it is not possible with the known resources of the universe to predict the utility of coding sequences. But I could be wrong. Feel free to demonstrate that you can take an existing coding string, make a point mutation, and predict the change in utility. This is what I would like to call the Douglas Axe conundrum. Most changes to coding strings are detrimental to utility. Tiny changes can have catastrophic effects. My point is that this makes evolution unlikely, but it makes design without evolution impossible. All the commercial molecule designers use directed evolution.Petrushka
December 2, 2011
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To explain the existence of recorded information, we need a mechanism to satisfy the observed physical consequences of recorded information
I read the post. You might note that my recent question quotes from it. But since the indenting on the forum can get confusing, let me repeat it. When you refer to “the rise of the recorded information in the genome” are you referring to each and every instance of information change or increase, or are you referring to the origin of the system, or are you referring to something like irreducible structures?Petrushka
December 2, 2011
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Petrushka, I am going to take you at face value. If this post is not something you can unserstand, then frankly, you have no business making the claims on this forum that you've made. As for Dr Liddle's Skeptical Zone, we are still awaiting her response. The dilly dallying of the commentors there exist not becuase they don't understanding the argument, but because they have no rebuttal to it.Upright BiPed
December 2, 2011
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Please humor me and try to answer a simple question. When you refer to "the rise of the recorded information in the genome" are you referring to each an every instance of information change or increase, or are you referring to the origin of the system, or are you referring to something like irreducible structures?Petrushka
December 2, 2011
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A lot hinges on this contradictory statement:
One reason the analogy with computer code fails is the problem of translation. Just as you can’t really translate poetry from one human language to another, you can’t translate DNA to computer simulations and design completely novel structures with complete accuracy. It might be possible, but not with our current understanding of physics.
What does it mean if you say in once sentence that you can't do something, and in the next that it might be possible? Doesn't that negate the first statement that it can't be done? You're relying a lot on this "it can't be done" argument, and by your own words you don't believe it yourself. I've lost count of how many times you've repeated it, and now you've unraveled it. Doesn't that negate every single post in which you've said it's impossible?ScottAndrews2
December 2, 2011
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You are correct to assume I don't follow your argument. Most importantly, I can't tell whether it applies to the origin of life or to evolution, or to some ongoing feature of life. I have read through the thread at Skeptical Zone several time in hopes that someone could clarify your position or offer an alternative explanation of it, but I didn't see anyone there who understood it. You have posted a lot of words, but I think you begin to make your point here:
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.
That seems to be an origins question.Petrushka
December 2, 2011
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Information is a label used to describe a process. The process is chemical. If you are into dictionary definitions, look up reification.
The definition of information that I operate under is the standard, dictionary sense (from the latin verb informare: to give form to, to in-form). Sorry, but I really have no interest in now playing a game of definiton derby, particularly since the dynamics of the phenomena are already understood and coherently described. Such games become evident when someone objects to the use of a term, but fails to demonstrate that the term was misused. Moreover, after reading your posts this morning, it becomes clear to me that you really have not quite conceptualized what is at issue. Perhaps the best response is to back out and allow you a chance to process the information. I can tell you that protein folds, computer simulations, and the differing rhythms of human speech have nothing whatsoever to do with it. later...Upright BiPed
December 2, 2011
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One reason the analogy with computer code fails is the problem of translation. Just as you can't really translate poetry from one human language to another, you can't translate DNA to computer simulations and design completely novel structures with complete accuracy. It might be possible, but not with our current understanding of physics. Check gpuccio's link. In human language, deep translation fails because you can't simultaneously translate rhythm, connotation, denotation, melody and phrasing. I'm not enough of a physicist to know why chemistry can't be completely simulated. I just both that the people attempting it fall back to chemistry and directed evolution for industrial design.Petrushka
December 2, 2011
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In any case, biologists (as demonstrated by Larry Moran himself) routinely view the information transfer in the genome as only being analogous to semiotic transfer.
Information is a label used to describe a process. The process is chemical. If you are into dictionary definitions, look up reification. Take a look at gpuccio's discussion and link regarding protein design. Chemistry does stuff that can't be abstracted and can't be modeled completely with our current knowledge of quantum mechanics. Chemistry is faster than computation, and our best efforts to predict chemistry are both painfully slow and inaccurate. I grant that DNA embodies a code, but it is a code that defies abstraction. Look at gpuccio's link. Our best efforts to design completely novel proteins using atom by atom simulation and quantum theory are both slow and inaccurate. We can't read the code except by running the chemistry. We can't design it except by running the chemistry, using cut and try.Petrushka
December 2, 2011
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Aside from the big words you have restated what biologists have known since about 1968, that DNA embodies a code that is interpreted by the cellular machinery.
Being a follower of biology, surely you can point me to a paper where these particular physical observations are being advanced, or even discussed. A semiotic genome would virtually falsify materialism, so I bet you won't find much. In any case, biologists (as demonstrated by Larry Moran himself) routinely view the information transfer in the genome as only being analogous to semiotic transfer. He and they are wrong. It's semiotic state has physical entailments which can be coherently observed.
No one really knows if the system evolved or was poofed into existence. reasonable people can believe it was poofed, and reasonable people can research the problem under the assumption it might have a natural origin.
You are correct, a research program to study the possible unguided origin of Life is perfectly acceptible, and by logical extention, so is a program to study a possible guided origin of Life. But what science cannot do (from the level of peer-reviewed publishing, up through the public domain) is ignore that the information transfer in the genome is semiotic; it very observably is. We know this is true, and we know why it is true. It's a system that demonstrates the same dynamic entailments as any other semiotic information system. Those entailments have been observed and understood, and those observations stand unrefuted.
I fail to see the source of your hostility toward me.
Please don't conflate directness for hostility, after all, this is a competition of ideas, and you have been no less strident in defending yours and attacking mine. To this very moment you haven't actually engaged the content of the argument being made, yet you are quick to demean ID with repeated little quips of "magic" and "poof". I have not reacted to any of them. But having said that, if you feel I have overstepped into hostility, then I do apologize. Rest assured, any hostility is directed at your argument.Upright BiPed
December 1, 2011
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Aside from the big words you have restated what biologists have known since about 1968, that DNA embodies a code that is interpreted by the cellular machinery. No one really knows if the system evolved or was poofed into existence. reasonable people can believe it was poofed, and reasonable people can research the problem under the assumption it might have a natural origin. A third, but not exhaustive possibility is that the universe is rigged to make it happen without additional intervention. If this is the case, research will show that a natural origin is possible. I fail to see the source of your hostility toward me.Petrushka
December 1, 2011
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Properties are immaterial or abstract by definition.
Magnets of opposing charges will repel each other regardless of an observer. That quality is a part of their material properties. The only immaterial thing connected to that reaction is if I observe it and record the information, but whether that happens or not, it would not alter the reaction itself. However, if I take those magnets and use them to spell my name across the refrigerator door, then they have taken on an immaterial quality that they themselves can never attain from their physical make-up. They signify something that they have absolutely no material connection to, and therefore a physical protocol is required in order for that immaterial relationship to be realized. It's a relationship that otherwise wouldn't exist. So let's not equivocate on definitons, it is a waste of time.
What I’m asking is the nature of the event in which molecules were arranged in a way that enabled them to reproduce and evolve.
Because we weren't there when it happened, and because we try to be careful not to make unsupported assumptions, we are left to a rational observtion of the physical dynamics themselves in action. Without the slightest equivocation, the information storage and transfer system in the genome displays the same physical objects and physical dynamics as any other form of recorded information transfer ever observed. By satisfying each of the physical entailments of recorded information transfer, it demonstrates that its nature is semiotic. The coherent observation of its semiotic state must be the guide for any claims made with material integrity.Upright BiPed
December 1, 2011
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Properties are immaterial or abstract by definition. What I'm asking is the nature of the event in which molecules were arranged in a way that enabled them to reproduce and evolve. When did this happen? Did it happen more than once? Was it updated repeatedly? I promise not to ask by whom. I just want to know where the natural formation of organic molecules left off and the designed molecules began.Petrushka
December 1, 2011
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Petrushka, you have already been given the evidence of immaterial properties observed to exist in the translation system. Time to spin again.Upright BiPed
December 1, 2011
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Quite frankly, the only opponent on this forum that has shown any guts (any intellectual stomach at all) has been Dr Elizabeth Liddle.Upright BiPed
December 1, 2011
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I'm not aware of any properties of anything that are not instantiated. Perhaps if you would identify the event or events you are referring to, with a before and after snapshot of the relevant system.Petrushka
December 1, 2011
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How does an immaterial property become instantiated into a physical object Petrushka??Upright BiPed
December 1, 2011
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…and yet you still haven’t acknowledged the [observable] evidence. You simply can't do it in earnest. Your ideology doesn't leave you the empirical sovereingty to do so.Upright BiPed
December 1, 2011
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Protein assembly is chemistry. The code that specifies them evolves. The origin of the cellular machinery is a mystery. I suspect the origin is closer to that described by Michael Denton in Nature's Destiny than it is to intervention by unnamed demiurges, but I have no great emotional attachment to hypothetical causes. I do have an attachment to ways of researching mysteries, and I am more impressed by Szostak than by anyone in the ID movement. But I have not personal commitment to Szostak being correct. We might never solve the mystery. I would place a small bet it will remain a mystery for my lifetime. I have lots of conjectures without deep emotional ties. I suspect that strong AI is possible, but I see nothing on the horizon that will lead to it in my lifetime. I think faster than light travel is impossible, but I watch with curiosity the recent experiments.Petrushka
December 1, 2011
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…and you still haven’t acknowledged the evidence.Upright BiPed
December 1, 2011
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Petrushka, you have made dozens of remarks that proteins cannot be the result of design. Yet, proteins are assembled as the result of processing semiotic information. This is an observed fact. You now want to equivocate and play the ridiculous school-yard suggestion that "OH YES, the information processing system required for protein synthesis may show evidence of design, but I am not talking about that, I am only talking about the proteins themselves..." Very convincing.Upright BiPed
December 1, 2011
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If your evidence doesn't dispute common descent, I see no reason to be interested in it.Petrushka
December 1, 2011
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Where Have I said it was? Link to a post of mine where I make claims about the origin of life.Petrushka
December 1, 2011
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...and you still haven't acknowledged the evidence.Upright BiPed
December 1, 2011
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The evidence falsifies the claim that Life is the result of unguided chemical origins.Upright BiPed
December 1, 2011
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If it's not anti-evolution, it's not against me. What is it you think I am that the evidence is against?Petrushka
December 1, 2011
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ID is not anti-evolution Petrushka, and its not anti-common descent either. You already know this. Yet, at the same time, you haven't even acknowledged the evidence against you.Upright BiPed
December 1, 2011
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Interesting claim. I was just reading a November article that describes 60 genes new to humans that have clear sequence similarities to non-coding sequences in chimps. Indicating that new gene formation via mutation is not rare. The new genes appear to have low functionality, which is what you would expect if they haven't been refined over time. http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002379Petrushka
December 1, 2011
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That's right Petrushka, your ideology has been blown up by modern molecular science. The best thing to do is not notice.Upright BiPed
December 1, 2011
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I suppose we are deadlocked then. You accept that evolution happens, but don't think it can produce anything useful. I have seen not seen any design events nor any sightings of the designer. Nor has anyone demonstrated that it is feasible to design living things from scratch without using evolutionary processes.Petrushka
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