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Writing Biosemiosis.org

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Origin Of Life
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In September of 2009 I started a new document on my computer entitled “A System of Symbols”, where I was going to write about the part of design theory that interested me the most – that is, the representations that are required for self-replication (von Neumann, Pattee). My goal was to inventory all the physical conditions necessary for one thing to represent another thing in a material universe. I wrote and rewrote that essay for more than four years — reading, learning, and sharing along the way. As it turns out, writing that essay was my way of coming to understand the issues, and I spent a great deal of that time trying to articulate things I had come to understand conceptually, but could not yet put into words. Eventually I came into contact with the types of scientists and researchers who had substantial experience with these issues, up to and including those who had spent their entire careers on the subject. It was a humbling experience to share my thoughts with people of that caliber, and have them respond by sending me papers of their own that reflected the same concepts.

Then In 2014, I retired that essay and began writing Biosemiosis.org in its place. Since that work is available to any reader, I won’t recapitulate it here, but there are a couple of concepts I’d like to highlight – particularly the discontinuity found in the translation of recorded information. Read More

[I’d like to thank Barry and Uncommon Descent for allowing me to publish this introduction to my two projects]

Comments
Thanks Joe. I am using the sense strand DNA table, as noted on my site. sense--> anti-sense--> mRNA--> tRNA CTA--> GAT--> CUA--> GAU--> tyrosineUpright BiPed
November 2, 2015
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Upright Biped, sir, I found a transcription error in your explanation of DNA. You say:
In order to encode this information, four different types of nucleic acids (adenine, thymine, guanine, and cytosine – A,T,G,C) are used to form individual representations called “codons”. A codon can be thought of as a "code word" inside the cell. Each of these code words is made up of three nucleic acids (triplets) which are read together as a single representation. For instance, the triplet TAC is translated by the cell to add an amino acid called tyrosine to a new protein being created. CTA means add leucine, GTC means add valine, CCG means add proline, GAC means add aspartic acid, and so on. This is how the cell builds every protein in the living world - it uses a code.
You are using DNA codons. Those are transcribed into mRNA anti-codons. That means the DNA triplet TAC would code for the mRNA codon AUG, which represents the amino acid methionine. CTA in DNA = GAU in mRNA which means add aspartate. You need to redo your list.Virgil Cain
November 2, 2015
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Upright BiPed @ 101. So true. Neither are living organisms the simplest possible self-replicator, which ought to tell Zachriel something. And von Neumann wasn't trying to model the simplest possible self-replicator, he was attempting to model a particular sort of self-replicator. So once again, Zachriel speaks a nugget of truth that tells us nothing at all interesting. It certainly isn't a refutation of anything. What is of interest is what was left unsaid.Mung
November 2, 2015
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Don't fret Zachriel, no one can take away your faith. But the physical realities remain.Upright BiPed
November 2, 2015
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Mung: That was also the conclusion reached by John von Neumann when he investigated the logic of self-replicating systems. A von Neumann machine is not the simplest possible self-replicator, e.g. template replication.Zachriel
November 2, 2015
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Zachriel:
From the diagram at the top of the post, with the indication of a “necessary discontinuity”, this seems to simply be a flavor of irreducible complexity.
Indeed. That was also the conclusion reached by John von Neumann when he investigated the logic of self-replicating systems.Mung
November 2, 2015
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I’m rather busy with more mundane but pressing issues at this time. The story of my life.Mung
November 2, 2015
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KF @86 Excellent point. Thank you. Problem is that some of your interlocutors won't get it, simply because don't want to. No matter how clear you explain it or how many times you repeat it. Pathetic reality we can't ignore.Dionisio
November 2, 2015
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I missed an earlier post at 69. Mapou, we can have that discussion when the time is right. Hopefully GP will be available to chime in.Upright BiPed
November 2, 2015
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Barry: 100 years of zapping fruit flies with radiation to scramble their genome and not a improvement. Yeah, but a million years of zapping it would produce astonishing effects. O ye of little faith! :Dmike1962
November 2, 2015
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Zachriel @ 92: Interesting observation. Any programmer here will tell you that "bugs" are bad things; if they have any effect at all, the effect is universally deleterious. What about the bugs that have been introduced into genomes (mostly of the fruit fly) over the last 100 years? Same thing. If they have any effect at all, the effect has been universally deleterious. Think about that Z. 100 years of zapping fruit flies with radiation to scramble their genome and not a improvement. Does that suggest that DNA is like or unlike human designed code?Barry Arrington
November 2, 2015
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Irony: Carp almost certainly sniggers, smirks and mocks the religious fundies who, in his view, clinch their teeth and dig in their heels in the face of evidence and logic.Barry Arrington
November 2, 2015
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From the diagram at the top of the post, with the indication of a "necessary discontinuity", this seems to simply be a flavor of irreducible complexity.Zachriel
November 2, 2015
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Based on several exchanges with Carp, I will answer UB's question to Carp at 49:
Can you do that Carp?
No.
Actually do it?
No.
Can you?
No. Which is not to say that exchanges with Carp do not serve a purpose. He is a valuable resource for us here at UD. He supplies us with an apparently inexhaustible fount of Darwinist talking points that we take apart at our leisure. Thanks Carp. And thanks to those, like UB, who have the patience to deal with him.Barry Arrington
November 2, 2015
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C'mon Carp, don't quit. We can drive this bus together right to the font door. You are not hitting on anything that hasn't been thrown up and worked through thousands upon tens of thousands of times in the history of thought on this subject. You'll end up right were the evidence universally takes you. All this nonsense about ocean waves could have been avoided if you would just quiet yourself long enough to uptake the observations, but you don't seem to be that kind of person. So, we can go through all your counter-examples if you wish. They will all fade away unless you demand them against evidence to the contrary, but if that is your goal, nothing can be done for you anyway. After all, we are not discussing how to be a better dancer or how much spice to add in a recipe, we are discussing universal material facts.Upright BiPed
November 2, 2015
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Carpathian:
1) The ID designer designs nature. 2) Nature, without the reintervention of the ID designer, designs life.
Great, find a way to test it.Virgil Cain
November 2, 2015
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Carpathian- You ignored the argument- try again: 1- Experiences and observations say that all codes come from intelligent agencies 2- No one even knows how to model physicochemical processes producing a code. Such a thing flies in the face of our experiences and observations 3- And because of that it is safe to infer that an intelligent agency designed the code even though we did not observe it happening, as is the case with the genetic code. Science 101. And yes that inference, as with all scientific inferences, can be refuted by demonstrating that physicochemical processes can produce the genetic code. Again, science 101 Our opponents whine about that because they know they could never demonstrate such a thing. The only thing assumed is that our knowledge, based on our experiences and observations, is correct.Virgil Cain
November 2, 2015
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KF: Thank you for bringing other important points to the discussion. Equivocating between deterministic patterns, which are only the result of the forces which create them, and symbolic representations, like modulated radio waves expressing language or music, or, even more evidently, digital codes where definite numeric states correspond to symbolic meanings, is really a poor argument.gpuccio
November 2, 2015
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Folks, ocean waves are a dynamic system, not symbolic discrete state codes, they are not even a case of analogue modulation. The objections are being stretched to the point of reductio, inadvertently underscoring the force of the point. KFkairosfocus
November 2, 2015
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Ocean waves unintentionally encode local weather or distant seismic activity.
Okay. I'll play along. What is required for an ocean wave to serve as a representation of the weather beyond the horizon?Upright BiPed
November 2, 2015
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Upright BiPed:
My previous question: What is required for a representation to be a representation? Have you clarified this in your mind yet?
Yes and I thought I explained it. A representation is dependent on the observer. AM radio waves intentionally encode a song. Ocean waves unintentionally encode local weather or distant seismic activity. Your task is to prove intelligent intent for your representations. You haven't tried to do that. Connect life with the intent of an ID designer.Carpathian
November 2, 2015
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Carp,
In the case of ocean waves, period and amplitude. In the case of AM radio waves, period and amplitude. One has intent, the other doesn’t.
Please focus on the actual argument Carp.Upright BiPed
November 2, 2015
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Thank you computerist. Please help me the foster dialogue when you can.Upright BiPed
November 2, 2015
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Carpathian: Ah, OK, are you a Theistic Evolutionist? That would explain much. Going to your point. If the system is nature, then you must show that nature has the power to generate symbolic codes. Please, do that. You ask: "Do you think God is not powerful enough to do what I have just suggested?" I do not think anything like that. I just observe that nature cannot generate symbolic codes. that's it. Observation, not thinking. Regarding God, I could well answer: "Do you think God is not powerful enough to intervene and design biological objects in time and space?" But, frankly, I am not interested to discussions about how powerful God should be according to our narrow ideas about Him.gpuccio
November 2, 2015
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Upright BiPed:
Ocean waves Carp, ocean waves.
No, UB, waves and the patterns groups of waves make. In the case of ocean waves, period and amplitude. In the case of AM radio waves, period and amplitude. One has intent, the other doesn't.Carpathian
November 2, 2015
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Carp, please try to focus on the actual argument.Upright BiPed
November 2, 2015
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BTW, great work UBP. It will be interesting to see where ID research such as this will influence science for the foreseeable future.computerist
November 2, 2015
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gpuccio:
And it is not true that the system works “without the designer’s help”. The system works because of the designer’s help (the intelligent complex functions implemented in it by the designer), even if no reintervention is needed.
I'll give you that for the sake of argument. 1) The ID designer designs nature. 2) Nature, without the reintervention of the ID designer, designs life.Carpathian
November 2, 2015
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#72 Ocean waves Carp, ocean waves. Your own counter-example, remember? - - - - - - - - - - My previous question to you: What is required for a representation to be a representation? Have you clarified this in your mind yet? I am trying to get you to focus on actual material observations.Upright BiPed
November 2, 2015
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Carpathian: "An AM radio converts waves into audio that drives a speaker." An AM radio is designed, I suppose. As the radio transmitter. Translation systems are complex and designed.gpuccio
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