Uncommon Descent Serving The Intelligent Design Community

Writing Biosemiosis.org

Share
Facebook
Twitter
LinkedIn
Flipboard
Print
Email

 

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
gpuccio:
Then, you must observe an intelligently designed, complex system which generates codes. Where is this system in nature?
The system is nature. 1) God designs nature. 2) Nature designs life. Do you think God is not powerful enough to do what I have just suggested?Carpathian
November 2, 2015
November
11
Nov
2
02
2015
10:09 AM
10
10
09
AM
PDT
Dionisio: Chicken-egg, absolutely! :)gpuccio
November 2, 2015
November
11
Nov
2
02
2015
10:06 AM
10
10
06
AM
PDT
Upright BiPed:
Waves are not translated into physical effects that I am aware of. If you know differently, then explain.
An AM radio converts waves into audio that drives a speaker. A very physical effect.Carpathian
November 2, 2015
November
11
Nov
2
02
2015
10:03 AM
10
10
03
AM
PDT
computerist, That is the meat of the OP with regard to the additional utility of spatially-oriented representations, (dimensional semiosis) and the material requirements to implement them into a physical system. Dimensional semiosis enables combinatorial utility and efficient transcribability, but can only be enabled by additional organization.Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
10:02 AM
10
10
02
AM
PDT
The way I see it and have always argued, code alone is not what is so interesting, what is interesting is universal code flexible enough to be used for building and maintaining higher order functional systems. The binary system (1's and 0's representing electrical states) was chosen for its simplicity in implementation and potential. So the code is derived from its potential, top-down, that is the primary reason I would infer design as opposed to merely arbitrary symbolic labeling (object->symbol mapping).computerist
November 2, 2015
November
11
Nov
2
02
2015
09:55 AM
9
09
55
AM
PDT
U.B. I'm rather busy with more mundane but pressing issues at this time. But, as soon as I get some free time to think, I do plan to look deeper into your ideas and react to them accordingly.Mapou
November 2, 2015
November
11
Nov
2
02
2015
09:52 AM
9
09
52
AM
PDT
gpuccio @50
[...] the implementation of the code is extremely complex, and requires long and big proteins which can only be synthetized by the code itself.?
Did you just describe a case of chicken-egg dilemma? Or maybe I misunderstood what you wrote?Dionisio
November 2, 2015
November
11
Nov
2
02
2015
09:49 AM
9
09
49
AM
PDT
Carpathian: "Without that connection, the genetic “code” is simply a pattern we observe." Ah, something resembling an argument. Well, that's an improvement. The point is, a pattern is not a code. A code is a pattern which represents symbolically something else. The sequence of nucleotides in DNA is not just a pattern, like the waves of the ocean. It is a pattern which obeys strict symbolic rules, so that each word of 3 nucleotides, when interacting with the translation system, generates a specific aminoacid, and the resulting protein is the functional proteins. So, it is similar to the radiowave patterns which transmit language, or a piece of music. Could you please answer that, instead of confounding patterns with codes? Thank you.gpuccio
November 2, 2015
November
11
Nov
2
02
2015
09:47 AM
9
09
47
AM
PDT
Carpathian at #59: ???? What do you mean? "The intelligent designer could have designed a means by which coding and decoding systems could have arisen without the need of any intelligence guiding it." Then, you must observe an intelligently designed, complex system which generates codes. Where is this system in nature? And it would always be the intelligence of the designer which generates the code, indirectly, through the designed system. What is your point? "Just like Mapou could design a system that generated or decoded codes, the ID designer could have done the same." OK, and where is that system? In your imagination? "To sum up, the ID designer designed a system that generated codes without his help." Is that a sum up? You just said that a designer could have designed such a system. Please, clarify of what system you are speaking, where we can observe it, how it works. 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. "Just like we see in “Darwinism”." ???? Again, what do you mean? What do you see in darwinism? A designer? A complex designed system? Please, share with us your sightings. (A final clue to you: this post is not a personal attack).gpuccio
November 2, 2015
November
11
Nov
2
02
2015
09:40 AM
9
09
40
AM
PDT
In your view, a representation must have been generated by intelligent intent. In my view, it doesn’t.
An Easy Understanding of Semiosis --and-- The Information Tetrahedron
Waveforms from an AM radio transmitter have a certain period and amplitude and an intelligence intended that. Waves in an ocean have a certain period and amplitude, but no intelligence intended that. That is the argument.
Waves are not translated into physical effects that I am aware of. If you know differently, then explain.Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
09:39 AM
9
09
39
AM
PDT
Upright BiPed:
Now that the “jackasses” comment has followed the deliberate misrepresentation, we have that out of our systems.
There was no misrepresentation by me, deliberate or otherwise. Designed systems can generate code without further input from the designer. God could have created such a system. Does anyone want to dispute that?Carpathian
November 2, 2015
November
11
Nov
2
02
2015
09:31 AM
9
09
31
AM
PDT
Upright BiPed:
What is required for a representation to be a representation?
In your view, a representation must have been generated by intelligent intent. In my view, it doesn't. Waveforms from an AM radio transmitter have a certain period and amplitude and an intelligence intended that. Waves in an ocean have a certain period and amplitude, but no intelligence intended that. That is the argument. Were the "codes" we see intended or not? That is the question to address, not a definition of what a "code" is. Tie your genetic "code" to the intent of a designer. Without that connection, the genetic "code" is simply a pattern we observe. How it came about is the issue.Carpathian
November 2, 2015
November
11
Nov
2
02
2015
09:28 AM
9
09
28
AM
PDT
Now that the "jackasses" comment has followed the deliberate misrepresentation, we have that out of our systems. Stay on topic.Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
09:22 AM
9
09
22
AM
PDT
Mapou:
Jackasses should be attacked personally and forcefully each and every time they act like jackasses. It’s called classical conditioning. LOL.
This is exactly what I see happening if ID ever gets into schools. Teachers like you call students jackasses in front of class. This will show the other students that science is all about being more powerful than the other guy. "If you don't have a good argument just shout louder", will be the lesson. You'll generate some great scientists that way. Keep up the good work.Carpathian
November 2, 2015
November
11
Nov
2
02
2015
09:19 AM
9
09
19
AM
PDT
Carp, please deal with the actual observations. What is required for a representation to be a representation?Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
09:19 AM
9
09
19
AM
PDT
Upright BiPed:
Mapou gave a simple example were he, as an intelligent agent, arranged a system that can create representations to be interpreted as patterns within the system.
The intelligent designer could have designed a means by which coding and decoding systems could have arisen without the need of any intelligence guiding it. Just like Mapou could design a system that generated or decoded codes, the ID designer could have done the same. This system that the ID designer designed, might have not been possible without the designer's hands on guidance. So I have "agreed" with Mapou and I have "agreed" with you. To sum up, the ID designer designed a system that generated codes without his help. Just like we see in "Darwinism".Carpathian
November 2, 2015
November
11
Nov
2
02
2015
09:14 AM
9
09
14
AM
PDT
Jackasses should be attacked personally and forcefully each and every time they act like jackasses. It's called classical conditioning. LOL.Mapou
November 2, 2015
November
11
Nov
2
02
2015
09:14 AM
9
09
14
AM
PDT
Carpathian, A comment in passing... In terms of personal attack, the laurels of the winner belong to Prof Moran. He calls all of us idiots. What can be more generic?! Even in the case of macros generating malicious code, the code causally depends on there being conscious intelligence behind the design and implementation of the code processing system. The same is true in the case of natural languages, cultural codes, mathematics and art. Evidence is undeniable. As soon as you produce a single trustworthy and repeatable demonstration of a naturalistic mechanism giving rise to symbolic control in material systems, you win.EugeneS
November 2, 2015
November
11
Nov
2
02
2015
09:13 AM
9
09
13
AM
PDT
Oh well, scratch my post at #53. The critics don't even get that far. I just did a quick glance at the IDosphere, and the daily critics refuse to even address the details of semiosis itself. Apparently when you are confronted with the necessary physical conditions of the genetic code (von Neumann, Pattee, Crick, Zamecnik, Nirenberg, etc), the proper response is to ignore the material observations and argue over what a "code" is. How much easier it is to stand your ground when your remarks are not constrained by any observations.Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
09:12 AM
9
09
12
AM
PDT
Mapou:
Carpathian knows very well that he/she is lying. It’s what he does. He’s a weaver of lies and deception, just like Zachriel, Moran, Dawkins, Matzke and all the others. And not very bright either.
I take it you didn't have a response that was actually better than a personal attack. If you had, you would have used it.Carpathian
November 2, 2015
November
11
Nov
2
02
2015
09:04 AM
9
09
04
AM
PDT
U.B. @49, Carpathian knows very well that he/she is lying. It's what he does. He's a weaver of lies and deception, just like Zachriel, Moran, Dawkins, Matzke and all the others. And not very bright either.Mapou
November 2, 2015
November
11
Nov
2
02
2015
08:43 AM
8
08
43
AM
PDT
I am wondering if any critics are going to address the content of the article in the OP - that is, that there are three individual yet interdependent instances of arbitrariness that are required to organize the heterogeneous cell?
The combination of these three instances of arbitrariness result in an arrangement of matter that serves as a representation for a thing it otherwise has no systematic relationship with. Furthermore, the arrangement of this representation is independent of the physical properties of the matter it’s made of, and only serves as a representation because it’s organized in a system by a set of contingent regularities that have no basis in thermodynamic law. And all of this is required to encode the amount of information that the system needs to record itself into an open-ended transcribable memory. This memory is actually the fourth and most widely-known example of arbitrariness in the system -- the order of the individual representations in that memory (the information it contains) is indifferent to inexorable law. - - - - - - - - - - - Thus, when we observe the particulars of the genetic translation system, we are not merely looking at features that happen to be coincidental to the system's function – instead, each individual feature we observe imparts a very specific capacity on the system, and each of these capacities are collectively necessary in making the organization of a heterogeneous cell possible. They are necessary because they make the translation of information possible. They make memory and heredity possible. And to whatever extent the origin of life required any additional information to organize the first living cell, we can know by virtue of life’s self-replicating nature that the original informational content of the heterogeneous cell contained at least enough information to replicate and organize the elements of the system described above.
Link Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
08:25 AM
8
08
25
AM
PDT
Hi GP, Thank you for all your input. I want to address the topic between you and Mapou, but it would take me some time to gather up my thoughts, and time is limited just now. So I am jumping past it for now, but I hope to return to it later. The RCSB page you quoted above is in the bibliography on the site.Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
08:17 AM
8
08
17
AM
PDT
Carpathian: Codes can be generated by intelligent agents, both directly and indirectly. But they are always generated by intelligent agents, in all empirical observations. That is a sound basis for inference. If your theory is that codes can be generated by non conscious systems, while that has never been observed, it's up to you to show that your theory has some reason to be entertained. Can you understand this?gpuccio
November 2, 2015
November
11
Nov
2
02
2015
08:13 AM
8
08
13
AM
PDT
To all: Just a few words about how the code is implemented. The true key to the code is recorded in a set of 20 very complex proteins, the aminoacyl t-RNA synthetases. For those interested, I suggest reading this page from the PDB (Protein Data Bank): http://www.rcsb.org/pdb/101/motm.do?momID=16 A few simple quotes:
When a ribosome pairs a "CGC" tRNA with "GCG" codon, it expects to find an alanine carried by the tRNA. It has no way of checking; each tRNA is matched with its amino acid long before it reaches the ribosome. The match is made by a collection of remarkable enzymes, the aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid, thus allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins. ... As you might expect, many of these enzymes recognize their tRNA molecules using the anticodon. But this may not be possible in some cases. Take serine, for instance. Six different codons specify serine, so seryl-tRNA synthetase must recognize six tRNA molecules with six different anticodons, including AGA and GCU, which are entirely different from one another. So, tRNA molecules are also recognized using segments on the acceptor end and bases elsewhere in the molecule. One base in particular, number 73 in the sequence, seems to play a pivotal role in many cases, and has been termed the discriminator base. In other cases, however, it is completely ignored. Note also that each enzyme must recognize its own tRNA molecules, but at the same time, it must not bind to any of the other ones. So, each tRNA has a set of positive interactions that match up the proper tRNA with the proper enzyme, and a set of negative interactions that block binding of improper pairs. ... Aminoacyl-tRNA synthetases must perform their tasks with high accuracy. Every mistake they make will result in a misplaced amino acid when new proteins are constructed. These enzymes make about one mistake in 10,000. For most amino acids, this level of accuracy is not too difficult to achieve. Most of the amino acids are quite different from one another, and, as mentioned before, many parts of the different tRNA are used for accurate recognition. But in a few cases, it is difficult to choose just the right amino acids and these enzymes must resort to special techniques. ... These enzymes are not gentle with tRNA molecules. The structure of glutaminyl-tRNA synthetase with its tRNA (entry 1gtr) is a good example. The enzyme firmly grips the anticodon, spreading the three bases widely apart for better recognition. At the other end, the enzyme unpairs one base at the beginning of the chain, seen curving upward here, and kinks the long acceptor end of the chain into a tight hairpin, seen here curving downward. This places the 2' hydroxyl on the last nucleotide in the active site, where ATP and the amino acid (not present in this structure) are bound.
So, not only the genetic code is in itself an impossibility for non conscious causes (a symbolic correspondence between 64 combinations of three letter words in a four symbol alphabet to an output space of twenty aminoacids, including start and stop symbols); but also, the implementation of the code is extremely complex, and requires long and big proteins which can only be synthetized by the code itself. Just for reference, here is tha AA length of the 20 AA tRNA synthetases in humans: Class I: Arginine: 660 AAs Cysteine: 726 AAs Glutamate: 523 AAs Glutamine: 775 AAs Isoleucine: 764 AAs Leucine: 1176 AAs Methionine: 593 AAs Tyrosine: 528 AAs Tryptophan. 471 AAs Valine: 1264 AAs Class II: Alanine: 968 AAs Aspartic acid. 500 AAs Asparagine: 548 AAs Glycine: 739 AAs Histidine: 509 AAs Lysine: 597 AAs Phenylalanine: 508 + 589 Proline: 475 AAs Serine: 514 AAs Threonine: 433 AAs This is just to give you the flavor of what is at stake here. The point is, these complex proteins do recognize with high fidelity both the aminoacid and the anticodon (or, more in general, the tRNA) separately, each protein recognizes the appropriate couple of molecules, and there is no other biochemical connection between the correct aminoacid and the correct tRNA (or tRNAs): the only connection is established by the existence of the right protein in the system. In UB's terms: that's discontinuity at its best!gpuccio
November 2, 2015
November
11
Nov
2
02
2015
08:09 AM
8
08
09
AM
PDT
Carp, Mapou gave a simple example were he, as an intelligent agent, arranged a system that can create representations to be interpreted as patterns within the system. In order to function, the system requires both the arrangement of the representations as well as the means to interpret them. You lifted his example out of its context, and are now daring him to prove to you that his statement was wrong -- as if he is to demonstrate that the system that he arranged could have appeared on his test bench without his input. You didn't think things through. And you most assuredly have not conceptualized the issues yet. Just once, take your blinders off and deal with the observations as they are presented, without carelessly jumping at the chance to deny them. Can you do that Carp? Actually do it? Can you?Upright BiPed
November 2, 2015
November
11
Nov
2
02
2015
08:05 AM
8
08
05
AM
PDT
Virgil Cain:
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.
You are assuming that the genetic "code", was the result of an intelligent designer, but that is the very thing you and ID are trying to prove. See Mapou's comment above.
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
So as I read it, you can infer but we have to demonstrate . That's not science 101. You and ID should have to prove the point you are trying to make. Show that an intelligent designer is a probable cause of life.Carpathian
November 2, 2015
November
11
Nov
2
02
2015
07:56 AM
7
07
56
AM
PDT
Mapou:
The discovered patterns can still be called representations (or codes) even though they were not directly made by an intelligent coder.
Exactly! We call DNA "code", but it was not directly made by an intelligent coder. Will you now try to prove to me that your statement was wrong?Carpathian
November 2, 2015
November
11
Nov
2
02
2015
07:46 AM
7
07
46
AM
PDT
Why is the following so difficult to follow? 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.Virgil Cain
November 2, 2015
November
11
Nov
2
02
2015
07:13 AM
7
07
13
AM
PDT
gpuccio @37 & @43 Excellent points! Very insightful comments! Thank you. PS. RE: @44 yes, noticed the same update problem.Dionisio
November 2, 2015
November
11
Nov
2
02
2015
06:00 AM
6
06
00
AM
PDT
1 12 13 14 15 16

Leave a Reply