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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
The question being discussed is not the origin of the system but whether it works.Petrushka
November 28, 2011
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One issue at a time.
lol Yeah, let us not talk about the physical evidence that allows the whole thing to operate.Upright BiPed
November 28, 2011
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I don't know where I said that I cannot support my position until ID supports its position. I thought this was an ID site. I don't subscribe to ID, so what's my position got to do with it?Timbo
November 28, 2011
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How I (and every other human) designs something is not the question. Taking the gratin example, I think of the end goal, work out how to achieve it, and implement the steps. But as Petrushka keeps pointing out, that approach is not possible in biology because it is not physically possible to maintain the database of combinations of what works and what doesn't. But in any case, as I said, how I design something is not the question. Unless you think the designer creates life by assembling ingredients and mixing them together?Timbo
November 28, 2011
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One issue at a time. That is why I stipulated that evolution can account for the changes in populations since the Cambrian.Petrushka
November 28, 2011
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2. I assert that the designer is evolution as described by mainstream biology.
Where has mainstream biology "observed and experimentally confirmed" the rise of the required formalities as they are demonstrated to exist in the storage and transfer of genetic information?Upright BiPed
November 28, 2011
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That’s false. It isn’t that we refuse to. It is that it is irrelevant to the design inference.
Well let's examine that line of reasoning: 1. We agree that living things are designed. 2. I assert that the designer is evolution as described by mainstream biology. 3. You assert that the designer is some other entity. 4. I assert that evolution has been observed and has been tested experimentally and is capable of making the changes in populations necessary to account at least for the history of life since the Cambrian. 5. You assert that your designer ... (well what do you assert about your designer?) See the problem. Two claims about the origin of design, only on of which has any testable attributes. When you claim evolution is insufficient you are making a claim about evolution as a designer. I accept your claim as relevant and in need of discussion. I claim you have no alternative candidate and have not put a team on the field. I will make an additional claim, and that is that when you look at the claims of dFSCI in coding sequences, it is impossible for any finite designer to produce such coding sequences without using some version or form of evolution.Petrushka
November 28, 2011
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It is not my fault that ID proponents refuse to speculate on the attributes of the designer.
ID proponents do not formally speculate on the designer because the physical evidence does not allow them to do so. In other words, they do not speculate past the point of having evidence to back up those speculations. You in turn fault them for following proper empirical practices, yet, you ignore the evidence that is there for all to see.
Evolution is a kind of intelligent design. That is true. It is a system that learns from feedback. That is a kind of intelligence.
According to you, the float valve in my toilet is intelligent.
Read Shapiro or Koonin (books recommended right here on UD) and tell me exactly what is required for evolution to work that has not been observed or experimentally confirmed.
What has not been confirmed? The establishment of the formalities required for the storage and transfer of genetic information, arising by purely unguided material processes.Upright BiPed
November 28, 2011
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Petrushka:
It is not my fault that ID proponents refuse to speculate on the attributes of the designer.
That's false. It isn't that we refuse to. It is that it is irrelevant to the design inference. The way to "know" the designer is through the design.
Evolution is a kind of intelligent design.
Well Intelligent Design evolution and front-loaded evolution are, but blind watchmaker evolution just breaks things.Joe
November 28, 2011
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This is getting old. Invisible? No attributes? How can anything have no attributes? You’re really stretching it to make it sound absurd.
It is not my fault that ID proponents refuse to speculate on the attributes of the designer. Evolution is a kind of intelligent design. That is true. It is a system that learns from feedback. That is a kind of intelligence. Read Shapiro or Koonin (books recommended right here on UD) and tell me exactly what is required for evolution to work that has not been observed or experimentally confirmed.Petrushka
November 28, 2011
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Petrushka, This is getting old. Invisible? No attributes? How can anything have no attributes? You're really stretching it to make it sound absurd. I don't need to do that. I can point out seafaring monkeys and it sounds stupid with no embellishment. Besides, your theory is identical to ID except without the I or the D. How is that better? No one cares how many mechanisms or processes you rattle off if you can't actually apply any of them or show that they do what you say they do. Take away all of the fluff with no concrete implementation and there's nothing left at all, not even an invisible designer with no attributes. Once upon a time something happened and then something else happened. Poof!ScottAndrews2
November 28, 2011
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This can change the perception of science in the heads of millions of people.
Yes, one certainly struggles uphill to promote the perception that an invisible agent having no attributes and no observed instances of action needs to be taken seriously. Can you name any science other than biology that invokes invisible intelligent agents as causes? Any incident in the history of science in which such a hypothesis was confirmed?Petrushka
November 28, 2011
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So what is Petrushka simply taking for granted?
Matter cannot learn by itself...
Any system that incorporates reproduction, fecundity, heritable variation and selection learns.
Reproduction and Fecundity requires functional organization to already exist. Heritable variation requires the establishment of formalities in order to transfer information from parent to daughter. Selection is simply the end result of these requirements being in place. - - - - - - - - - In other words, Petrushka simply takes the entire phenomena for granted, and then pretends it doesn't matter.Upright BiPed
November 28, 2011
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Joe, I think I understand what Petrushka is saying. E.g. it is possible to create composite materials that 'remember' their state. This property of matter is actually exploited in space exploration. As far as I know one such use is spacecraft aerials unfolding under certain conditions almost to their previous twisted shape. However this does not remove the principal hurdle for materialism, the origin of control. It is intelligence that can exploit those properties of matter. And we cannot take it out of the equation.Eugene S
November 28, 2011
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Both are explanatory. The comparison with darwinism is what? Again, uncertainty, contradiction, and revision are often attributes of valid theories. You seem to think they are the criteria. The reason GR and quantum theory aren't footnotes is because they both hold up under the weight of scrutiny and are subject to falsification. Darwinism is not. The transitions aren't gradual as predicted? Scratch that, transitions are punctuated. Darwin's own lenient standard for falsification, the inability to even imagine variations in incremental steps, is met 1,000 times over? Let's just put that on the back burner and come back to it later. Forget about traversing fitness landscapes - let's talk literal landscapes. Monkeys can't traverse the landscape because there's an ocean in the middle of it? No problem - Kong Tiki and the Mrs. just catch a floating branch to the next continent. Over and over and over. And then we're supposed to believe that if they can fudge this, we can trust them when it comes to the abstract concept of fitness landscapes? Once Curious George gets his own sub-theory, anything goes. That you can and do always make up something new to keep the theory afloat is not a strength. It demonstrates a commitment to the theory first and reality second. Confirming evidence is good while contradictory evidence disappears into this week's latest sub-theory. Would you buy a Yugo that goes to the shop every other week and reason that's a good thing because even a Toyota breaks down once in a while? If you did, one might reasonably conclude that owning a Yugo was most important and reliable transportation was second.ScottAndrews2
November 28, 2011
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Your examples are invalid in the absence of intelligence as a means that enables learning. Matter cannot learn by itself (without human intervention).
Any system that incorporates reproduction, fecundity, heritable variation and selection learns. As far as I know everyone here accepts microevolution, so the principle that populations learn is not in dispute. ID proponents seem to believe that a system that can learn one thing is somehow blocked from learning another. Behe's Edge, whatever that means.Petrushka
November 28, 2011
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Strings- GR and Q are OK wrt strings...Joe
November 28, 2011
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You are again alluding to something like vitalism. No, you missed again. All I am saying is that physics and chemistry are simply not enough (mathematically, if you like) to explain the phenomenon of life simply because life is about fine tuned control. Physics and chemistry provide the material substrate while life remains irreducible to either or both, sort of like NP-complete problems are (suspected to be) polynomially irreducible to problems in the complexity class P. Hence the impotence of chance/necessity as explanatory means of the origin of control. Your examples are invalid in the absence of intelligence as a means that enables learning. Matter cannot learn by itself (without human intervention). Of course, I am not speaking about violations of the 2nd law. But such a process as life emerging spontaneously is extremely highly unlikely. There is no evidence whatsoever that can support the counter-intuitive assertion that matter without intelligence is capable of being the origin of control.Eugene S
November 28, 2011
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Actually General Relativity and Quantum theory are absolutely contradictory at the particle level. Does that mean astronomers should hold off in describing the orbits of planets?Petrushka
November 28, 2011
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What's interesting, Timbo, is that your argument requires some pretty big leaps. First, because I'm convinced that design can be detected apart from its implementation or process, that I have no interest in that implementation. Is that really logical? That I don't quit my job and go back to school for biology seems to reinforce it. Here's the smokescreen, and I don't even think you realize the diversion you're creating. Read back and notice that while I'm attempting to evaluate the evidence for design and for darwinism, you are only attempting to evaluate me. (Not that I've never done it.) Perhaps without even meaning to you're trying to change the subject from a comparative look at the evidence to me and what I do or don't want to know. But that doesn't matter. What if you're right and all I want to know is whether life was designed and I don't care one bit how? How would that make a difference or change the underlying evidence. It's valid to examine the other person when they show signs of bias, perhaps asserting logic and applying it selectively. But this tangent of telling me what does or doesn't interest me leads nowhere.ScottAndrews2
November 28, 2011
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Science requires revisions and reexamination of evidence. But it doesn't follow that revising and altering something is what makes it good science. Physics confirms numerous predictions while leaving unanswered questions and maybe a few contradictions. Darwinism opens its gaping maw to swallow every contradiction until confirming the theory is more important than explaining anything. No longer the theory of X, it has become the vague, ineffectual theory of 'not Y.' Physics and darwinism both get revised. But physics flies you to the moon while darwinism exists only to confirm darwinism.ScottAndrews2
November 28, 2011
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That's what I was asking for.ScottAndrews2
November 28, 2011
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Geez my baseball is a material object- do you think it can learn?Joe
November 28, 2011
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Petrushka, Your continued equivocation is nauseating. The point of ID is that "evolution" is directed- ie it has a goal/ target. That said there still isn't any evidence that the immune system evolved via accumulations of random variations- there isn't any way to even test that premise. So when you say "evolution" you need to be more specific as there are several types- for example there is blind watchmaker evolution, intelligent design evolution and front-loaded evolution. So enough with your equivocating and it is time you buy a vowel. Thanks.Joe
November 28, 2011
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Inanimate matter cannot spontaneously generate meaning. Inanimate matter can be used as a substrate to carry semantics by something/somebody imparting meaning to it.
I'm not sure what you mean by inanimate matter. Is this a reference to vitalism? Matter itself has proved too complex to understand completely, so I'm not sure why "materialism" is considered a disparaging word. But material objects can certainly learn. Computerized robots can explore an environment and learn to traverse it. Learning doesn't violate any laws of entropy. Nor does evolution, which is a form of learning.Petrushka
November 28, 2011
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We have a wonderful model of intelligent selection in the immune system.
You and I have somewhat different definition of intelligent selection. I think of intelligent selection as synonymous withe selective breeding -- something people have been doing for thousands of years with plants and animals. The breeder has no control over what variations occur, just which ones get to pass on their genes. It's interesting that you discuss the immune system. Shapiro devotes a lot of time to it. I'm sure that everyone at UD too advantage of the free book offer when it was announced here. What more could anyone in the ID movement want than a free major book by a mainstream scientist who has struggled for years under accusations of being ID friendly. Shapiro doesn't come out and say the immune system itself is designed. Nor does he assert that the variants produced by it are targeted in the sense that they anticipate which variant will be useful. He just notes that in time of need the production of variants is ramped up, increasing the likelihood of finding something useful. He asserts that evolution itself works this way, and that stress triggers increases rates of mutation production -- particularly production of large genomic mutations, such as duplications and transpositions. He doesn't claim that any of these anticipate specific need, but that increasing their frequency increases the probability that something useful will turn up. He, along with most mainstream biologists, note that most of this kind of evolution happens in microbes. Which is why most protein domains have originated in microbes.Petrushka
November 28, 2011
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That conclusion, with all of its unanswered questions, is preferable to a theory that endlessly adds new mechanisms, never applies them in any specific manner to what it proposes to explain...
Sort of like physics. Actually sort of like all sciences. Particularly like gravity, which has had all kind of do-dads added on over the centuries without explaining anything about its ultimate source. Despite Einstein's efforts, the equations still don't work at all scales, indicating the theory is incomplete or flawed. So do we conclude Intelligent Falling? Do we conclude, as Newton was tempted to do, that demiurges put the planets into their orbits and keep them there? I'm really curious if you think this is how science should work?Petrushka
November 28, 2011
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Petrushka, I think it was you who corrected me earlier on when we were talking about cryptography by saying that specificity depended on meaning. That was a very good point, for which I am grateful. So meaning should come first. What brings it about in neo-darwinism? IOW, why should I care about GAs producing 10 letter words when they are designed to produce those given the language, the alphabet and the semantics? Yes, they do produce 10-letter words, so what? The most important thing is the meaning and that is taken for granted. Inanimate matter cannot spontaneously generate meaning. Inanimate matter can be used as a substrate to carry semantics by something/somebody imparting meaning to it. In no experiments up to date, did they demonstrate that organisation per se (whereby complex structure would appear along with control) emerged spontaneously.Eugene S
November 28, 2011
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Something funny on the subject of ID inference and possible practical implications. I was driving yesterday with one of my sons in the car. To our left on the grass, we saw an overturned ad poster. It was fine but quite windy so I immediately hypothesised that it might have been the wind that overturned it. My son said, yes but there was another identical one standing upright next to it, so, he said, it might as well have been done on purpose. I retorted by further supposing that it still might have been the wind, because the one that remained upright was probably in a more stable position than the first initially (maybe the patch of ground had a bit less of a slope). Then my son said that it was exactly the opposite and the one which was standing upright was in fact put on a visible slope whereas the other one was lying in a level place. I gave it up and said, a nice example of inference to intelligent agency. Of course, in this case we were far from exhausting all possibilities for natural cause, but I think the owner of a place may be better off installing a cctv camera, regardless of who did it and how they did it.Eugene S
November 28, 2011
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Timbo:
I can’t say life wasn’t designed until a model of how that process might have worked is put up.
Evos say the stupidest things. Timbo sez he cannot support his position until ID supports its position. Timbo doesn't just have an empty plate, it appears it also has an empty head...Joe
November 28, 2011
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