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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
observed rates of mutation can provide the the rate of population change necessary to account for the differences between species.
That would mean something if all that was required was a rate of change. My car can consistently drive 100mph. That does not make driving to the moon a problem of distance/rate. Rate of change means nothing.ScottAndrews2
November 30, 2011
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Petrushka, That's not what I meant. You said:
Lenski and thornton are committed to demonstrating that evolution can traverse landscapes that include neutral or slightly detrimental mutations.
We already know that evolution can traverse landscapes consisting of neutral and detrimental mutations. It's such an obvious statement that I don't know why they would have to commit themselves to demonstrating it.ScottAndrews2
November 30, 2011
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Also because this kind of work provides a detailed account of the landscape and counters the argument that it cannot be traversed. And because Lenski's work in particular demonstrated that a small colony of bacteria can explore every possible point mutation in a couple of decades -- a confirmation that observed rates of mutation can provide the the rate of population change necessary to account for the differences between species.Petrushka
November 30, 2011
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Because Behe's Edge argues that three step adaptations are too improbable to occur without design. Evolution News and views specifically cited Thornton's reconstruction of a "gap" too improbable to occur in nature. Claims like that are tedious and time consuming to research. Lenski's work has taken decades.Petrushka
November 30, 2011
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Back up:
Lenski and thornton are committed to demonstrating that evolution can traverse landscapes that include neutral or slightly detrimental mutations.
Why are they committed to demonstrating what is observed with every successive generation of pretty much every living thing?ScottAndrews2
November 30, 2011
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people like Lenski and thornton are committed to demonstrating that evolution can traverse landscapes that include neutral or slightly detrimental mutations.
Research may as well come to a screeching halt if they are committed to the conclusion they are looking for.
What would bring research to a halt is if anyone took ID seriously.
I asked for an explanation for this reasoning, and you respond by saying it again. If all we're going to do is assert without explaining, I can do it too. Anyone taking ID seriously would not bring research to a screeching halt. Which research, by the way? Do you mean the collapse of science in general, or did you have something specific in mind?ScottAndrews2
November 30, 2011
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I hope I don’t need to point out the problem with your island and ocean metaphor.
If you understand that it's metaphor then why are you attempting to apply it literally? Nonetheless...
Islands are connected to the mainland, and water — even 500 miles of it — has not been an absolute barrier to the passage of living things.
The only evidence you have that monkeys ever sailed oceans is that the monkeys are there and the evolutionary timeline requires it. A glaring contradiction between the theory and the evidence is impossible to believe. Breeding pairs of monkeys doing a reverse Castaway? If that's what it takes, it must have happened. Theory first, evidence second.
Prove me wrong. Tell me how to interpret coding sequences, or tell me how to design a protein domain sequence.
Let's follow this where it leads. I'll just make something up. Sending people to Mars and returning them safely is impossible. It's a fact. And the only way for you to dispute that fact is to design the spacecraft and show me your mission plan. And if you won't, you must concede that it is impossible. Now that I've laid out my impeccable logic I'll sit back and watch for the layoffs at NASA. Let me save you the trouble of moving the goalposts. I'll do it for you: This is different! At least the people at NASA are working on it! (It just moves quicker this way.) So it was impossible until they started working on it and then became possible? You're building quite a bit on the foundation that if we don't know how to do something, it's impossible. It's such a fantastic assertion that I can't believe I spent a few paragraphs refuting it. But there it is. Will you continue to argue that deliberately designing functional protein folds without searching every combination is impossible?ScottAndrews2
November 30, 2011
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Research is not going to come to a screeching halt for the simple reason that people like Lenski and thornton are committed to demonstrating that evolution can traverse landscapes that include neutral or slightly detrimental mutations. What would bring research to a halt is if anyone took ID seriously. How many ID proponents are actively looking for gap fillers?Petrushka
November 30, 2011
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I hope I don't need to point out the problem with your island and ocean metaphor. Islands are connected to the mainland, and water -- even 500 miles of it -- has not been an absolute barrier to the passage of living things. Not knowing the exact history of the traversal does not imply that animals arrived by magic. And it is magic you are claiming. You cannot cite any instance of design nor can you describe how one would go about designing something as basic as a protein domain. The simple fact is that if design can't be incrementally modified by evolution, the only other option is magic. Prove me wrong. Tell me how to interpret coding sequences, or tell me how to design a protein domain sequence.Petrushka
November 30, 2011
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I have a simple microwave and a more complex one. I have a bicycle and a motorcycle. I have a calculator and a computer. Each is a simplified model followed by a more complex version with more functionality. Those are not incremental changes, and there is no reason to think that you could ever get one from the other if you could reproduce them with variation and apply a fitness function. You might actually optimize your bicycle. But a series of undirected, incremental changes will never invent a combustion engine or an ignition. There's that line again between improvement and invention. Many, many years ago we observed (I will oversimplify) that A exists and B exists, and someone proposed that B evolved from A. We then began debating it. We still are. You're simply pointing out that A exists as if it's some exciting new discovery. We already knew this. It's not new information. It sheds no light on anything.ScottAndrews2
November 29, 2011
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The genes have functions, just simpler functions. In this case, simpler versions of vision.Petrushka
November 29, 2011
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If incremental evolution of vision is impossible, why are there incremental versions of vision in existing things?
I'm using the word "incremental" in the evolutionary sense - single genetic increments. I didn't think I needed to point that out since we're talking about evolution. This thing you linked to, what was the incremental step before it? What was the one after it? What comes three steps after it? Four? What in the world does the link you posted have to do with incremental change? I ask you to show me a traversable landscape and you point to a mountain 500 miles away in the middle of the ocean. ???ScottAndrews2
November 29, 2011
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We find genes for vision in organisms that don't have vision today, and never have had. We find genes for nerves in organisms that don't have nerves today, and never have had. Answer: Visual systems and nervous systems of organism with vision and nerves are so easily constructed that they don't even need to be selected for in order to appear. Poof. Now if we could just figure out how the observed immaterial formalities of information storage and translation (which make it all possible) came into being. Nahhhh, thats not important.Upright BiPed
November 29, 2011
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Great- how do we test the claim that "evolutiondidit"?Joe
November 29, 2011
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If incremental evolution of vision is impossible, why are there incremental versions of vision in existing things? http://www.nsf.gov/news/news_summ.jsp?cntn_id=110443 How much do you want to bet that we will not continue finding incremental versions of vision?Petrushka
November 29, 2011
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Following in Darwin's footsteps, you place the onus on me to state that something is impossible. Then you'll want to know why it's impossible. That's not how it works. It works like this: I'll give you an example, the evolution of complex vision. I happen to think that its evolution in increments of variation and selection is impossible. I'm not saying that in a very scientific manner. It just seems as preposterous as anything I've ever heard. The dog is more likely to eat your homework. But it's just an opinion. Your job, or someone's, is to demonstrate that it is possible. That's admittedly difficult. I can't reasonably expect you to evolve an eye or anything else. At the same time, the extrapolation just doesn't cut it. People, for example, get taller, shorter, wider, narrower, hairier, balder, lighter, darker, etc., etc. I can't extrapolate from that to think that they ever weren't human or ever won't be. In fact, the limited range of variation within that and other species somewhat confirms the notion that variation only goes so far. I would settle for a plausible, hypothetical pathway that goes one selected, beneficial increment at a time from an sightless creature to one with complex vision. Or a pathway to some other similar complex novel function. Maybe even a substantial fragment of a pathway. Isn't that reasonable? Isn't at least one piece of one hypothetical pathway the barest minimum for asserting that such pathways exist, are common, and that all living things have traversed countless numbers of them? Conversely, without even one what is the basis for accepting the explanation? Otherwise what you have is a hypothesis without a hypothesis. I wouldn't even rule out something truly impressive from a GA as evidence. But I've seen the lists, and there's way too much intelligent input, processing, and goal-setting involved. I don't expect to see any such things because they violate the non-scientific common-sense principle that stuff just doesn't start doing stuff and doing it better, climbing a million-rung ladder of increased and improved function, all by itself. Reproduction with variation can't circumvent that. If you or anyone else ever proves me wrong, I'll be surprised, disbelieving, skeptical, pick it to pieces because it's probably fabricated, and then I'll go sit in a corner somewhere in a fetal position throwing ashes on myself. I promise.ScottAndrews2
November 29, 2011
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You moved the smoke around, then simply took it for granted once again. This sleight-of-hand is evidenced by the fact that you refuse to acknowledge the observations against you. Your dismissive "we may never know" has a great history in the debate as well. It's a checkvalve that magically appears whenever a materialist gets cornered by the physical evidence. You are fooling no one but yourself.Upright BiPed
November 29, 2011
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You’re switching from the capabilities of evolutionary mechanisms to evidence of descent which cannot be reduced to those mechanisms.
That's what I'm asking for. An example of descent that is not possible via known mechanisms of variation.Petrushka
November 29, 2011
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The system that makes evolution possible is certainly not taken for granted. It is the central subject of study in biology. I think what you mean is that the origin of the system is unknown and may remain unknown.Petrushka
November 29, 2011
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Petrushka, it has been shown over and over again that you simply take the system (which makes evolution possible) for granted, then argue over evolution being causally adequate to explain what is found in biology. How does anything you said in your post at 27.1.2.1.6 change any of that? It doesn't. It is merely smoke and mirrors, and meaningless to the issue.Upright BiPed
November 29, 2011
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In other words, Petrushka simply takes the entire phenomena for granted, and then pretends it doesn’t matter.
Well yes, evolution is a description of how living populations change over times. It is not a final cause. Intelligence is not a final cause either. It does not explain it's own existence. Does it matter? Not for describing population change over time.Petrushka
November 29, 2011
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Modern cyphers are an example of a class of problems that yield only to brute force.
Cyphers and encryption are intelligent, purposeful solutions. You don't use one unless you have a message, a purpose to communicate it, and foresight to determine that it should remain confidential. Then the design of the encryption/decryption process to meet that need is purely intelligent. As for breaking one, I'm sure that highly-paid, very intelligent cryptographers are thrilled to hear of their work being called "brute force." When you apply that term to sophisticated software running on designed computers it loses its meaning. Not to mention, what prompts someone to attempt decryption on a sea of seemingly random characters? What makes them think there is a message in there at all? Sounds like design and design detection. How do you look at something that is deliberate, purposeful, and intelligent at every last step and see nothing but evolution? You've got evolution-colored glasses on. Take them off and look around.
Give me an example of something in the plant or animal kingdom that appears to have no cousins. Or a structure that does not appear to be incrementally different from ancestral structures.
I'm incrementally different from my father, which supports your case how? You're switching from the capabilities of evolutionary mechanisms to evidence of descent which cannot be reduced to those mechanisms. In the examples you cite, can you elaborate on how evolution produced them - the incremental genetic changes and why each was selected? That's exactly what you need to cite them as evidence of darwinian evolution, and I'm pretty sure you don't have it.ScottAndrews2
November 28, 2011
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You’re still arguing that designing functional proteins is impossible without searching every possible combination.
I'm taking the word of Douglas Axe, who has published on this very subject. But not his word alone. There are hard problems that don't have formulas for solutions. Modern cyphers are an example of a class of problems that yield only to brute force. There are many people looking for a shortcut for protein folding. Such a shortcut would be a prerequisite for biological design, assuming you are not going to allow some form of evolution. I'm not saying design is another word for cause. I'm saying that evolution designs. Pretty much the way many R&D programs design, by systematically trying and testing possibilities. Give me an example of something in the plant or animal kingdom that appears to have no cousins. Or a structure that does not appear to be incrementally different from ancestral structures.Petrushka
November 28, 2011
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Well Timbo, the way to the design inference is THROUGH materialism, ie the premise that living organisms and the universe are reducible to matter and energy. Therefor the PROPER way to refute ID is to produce positive evidence for said materialism. And the proper way to criticize ID is to show how said materialism does it.Joe
November 28, 2011
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Petrushka, Please get off the dope. Intelligent Design is NOT anti-evolution. Also there isn't anything in the observed processes of evolution that can be extrapolated to infer universal common descent. That means either there are or have been some unobserved processes or universal common descent is bogus.Joe
November 28, 2011
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We agree that living things are designed. 2. I assert that the designer is evolution as described by mainstream biology.
Redefining "design" to include "not design" accomplishes nothing. So every effect is "designed" by its cause. Now design is another word for cause. Ripples in a puddle are designed by raindrops. You can call it whatever you want, and I'm not going to play dictionary games, but all you've done is add your own bizarre definition for the word in the hope that it will catch on. It won't. You are not talking about design. You're still arguing that designing functional proteins is impossible without searching every possible combination. By that reasoning, every post we type is impossible because we must search every possible combination of words. And yet I find myself matching words to a target, the thought I wish to express, without an iterative process that begins with a single word and evolves in functional, incremental steps, each compared against a target that doesn't exist. And it only took a minute. It's impossible. How did I do that? And what's with origami? Testing every imaginable crease in a piece of paper to reach a result that resembles an animal would take longer than a life span. How do they do that? You're creating a false choice between evolution and a random search, and it's a bad once since neither is capable.ScottAndrews2
November 28, 2011
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The question being discussed is not the origin of the system but whether it works.
Okay I get it now...you want to know the designer's hair color and favorite boy band before you'll acknowledge the design inference, but when it comes to the system itself, 'how' and 'why' it works is discounted as being irrelevant to the conversation. Check. You are an outstanding empiricist.Upright BiPed
November 28, 2011
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Give me an example of a specific structure that, new since the Cambrian, that requires some special explanation.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.
So if I speculated that would be better? Why? Speculation + $.99 gets a you small fries and the theory of evolution.ScottAndrews2
November 28, 2011
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tell me exactly what is required for evolution to work that has not been observed or experimentally confirmed.
Now you're asking me to formulate your hypothesis for you. This isn't my idea. Why don't you tell me how this intelligent evolution designs biological innovation designs things. An example would be especially helpful. To call evolution "intelligent" is just another way of begging the question. I have no reason to think that it is intelligent or does what an intelligent agent can.ScottAndrews2
November 28, 2011
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