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Writing Biosemiosis.org

 

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.

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A representation doesn’t achieve the status of being a representation by any physical dynamic of its own. This is to say, there is no chemical or physical property of a representational medium that makes it a representation. It only achieves that status by being organized in a system with some other arrangement of matter (one that is capable of producing a specified effect). This relational architecture – with one arrangement of matter evoking an effect, while another arrangement of matter determines what the effect will be – sets up the physical discontinuity that has been long-noted by scientists and philosophers of every stripe. 

But this discontinuity between a representation and its effect is not the only instance where arbitrariness exists in the genetic translation system. Through conversations and research, I found where two other examples of arbitrariness had been identified. In many ways, these additional instances of arbitrariness are even more profound than the first. This includes those (rare) representations that exist as spatially-oriented patterns of objects. I referred to this phenomenon as dimensional semiosis on the Biosemiosis.org site -- where a finite set of spatially-oriented patterns are collectively used to encode information in a one-dimensional linear string. This coding structure imparts a significant advancement in the utility of the genetic translation system. It enables the system to record an open-ended amount of information, and it allows that information to be efficiently copied between mediums. In turn, this type of encoding requires a separate set of systematic parameters (protocols, rules) in order to function, and these additional rules are themselves arbitrary to physical law.

When I began this project, I operated under the premise that in a material universe, the translation of information must have material consequences that are observable and uniquely describable. While information theorists and genetic researchers debated the mathematical content of information, it seemed to me that -- since the translation of information causes tangible material effects -- we should be able to observe and understand the material process of bringing those effects into being.

As I researched the subject, I found that the process was indeed well-understood. In my opinion, it was the semioticians that had the greatest understanding of the process, specifically those who approached the issue from a physics point of view. And though they may present their research with certain materialist's assumptions, the simple fact remains that they’ve provided great insight into the chemo-mechanical consequences of information in the natural world. So, with an understanding gained from the physical semioticians, there is an answer to an obvious question at this point -- what is it that makes these three instances of material arbitrariness essential to the organization of the heterogeneous living cell? The answer is in what they do.

The first instance is the essential material condition that allows physical effects to be produced through the process of translation. It allows a system to produce effects that are not determined -- and therefore not limited -- by the arrangement of the representation being translated. This independence enables a range of potential outcomes that dwarfs the number of effects produced without translation. In short, translation enables prescriptive and temporal control over the entire range of effects required to organize the living cell. That organization would simply not be possible otherwise.

The second instance begins to enable the capacity for open-ended heredity and variation. Whereas all representations have a discontinuity between the arrangement of the medium and the determination of its effect, a spatially-oriented representation goes even further. As a spatially-oriented pattern, the functional properties of the pattern (i.e. those properties that the system recognizes and responds to) are independent of the dynamic properties of the medium itself. This independence enables the system to encode significantly more information (via combinatorial expansion) subject only to having the protocols necessary to produce the specified effects. Spatial-orientation also makes a representation efficiently transferable among different mediums. Both of these capacities (open-endedness and the ability to copy and transfer the information) are fundamental to the organization of a heterogeneous living cell.

The third instance is inseparably linked to the second instance. Whereas the second instance reflects the arbitrary spatial orientation of objects within a representation, it's actually this third instance that establishes that spatial orientation as an individual representation. In other words, the reason that an arrangement such as “011” (as an example) can operate as a spatially-oriented representation is because the system that receives that representation has established 0’s and 1’s as objects to be recognized by the system. The system has further established that three of these objects read in a linear sequence constitutes an individual representation, and that the order of the objects in the sequence determines one representation from another. A linear sequence of spatially-oriented representations must also be read in a particular direction in order to be correctly received, and thus, a function is required to establish the correct orientation of reading. Each of these parameters are context specific, not universal. They are the systematic regularities (rules, protocols) that enable the system to successfully function. They accomplish this by formalizing the conditions of the system's operation. In DNA, these conditions are formalized by being encoded in the very information that the representations themselves make possible. They are part of the informational content being represented, and they are not determined by physical law.

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.

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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.

 

 

Comments   

#1 Coe Davidson 2015-10-31 17:39
Great article, but people should read your Biosemiosis site to understand it best. ;-)
#2 CardioRD 2015-10-31 19:22
First off, congratulations on the site. It's really well done. Secondly, I have been watching the conversation at TSZ about codes. This article (and the Biosemiotics site) just about answers everything they are asking. Your argument is devastating.
#3 Upright BiPed 2015-10-31 20:02
Hello Coe and Cardio. Thank You! Coe you may be right. I am hoping that visitors will take the time to peruse through the information on Biosemiosis.org . Again, thanks.
#4 EugeneS 2015-11-01 15:41
It's a great website. Very nicely done. And I agree, a very detailed and well laid out argument.
#5 Upright BiPed 2015-11-01 16:18
Thank you very much Eugene. I've seen your comments and interactions on the web, and I very much value your consideration. I hope you will help me to promote dialogue about these important observations.
#6 Coe Davidson 2015-11-02 08:50
I've now had time to read through your entire biosemiosis site. Wow. Its a great presentation! I sent in a contribution. I wish for you nothing but success. Do you have social media?

Also, earlier today I looked in to what your critics responded. They have nothing. Many are being clearly dishonest, which says a lot.

Thanks for the information!
#7 Upright BiPed 2015-11-06 20:34
Hello again Coe, Thank you. Yes, I am working on social media efforts and will release that soon. Stay tuned.
#8 BR Spriggins 2015-11-18 15:20
This is not what I expected to find here, but your opponent said that he thought you had done your homework and "there was a lot of knowledge bound up here". He was talking mostly about Biosemiosis.org . Given his background, that is a clear compliment. I agree with him in both instances. Well done. But you need more participants though.
#9 BR Spriggins 2015-11-18 15:23
Oh, and I love the Darwinian Flowchart. I laughed out loud.

Good luck to your adventure.
#10 Upright BiPed 2015-12-05 17:30
Thank you BR. If you can help encourage conversations wherever you see fit, I would surely appreciate it.

Again, thank you.
#11 earthsinternet 2016-05-03 06:00
I love that you created this website on this specific subject. If it's okay, I've provided a link at the end of one of my posts on epigenetics. My background is working woth whole plant systems in both habitat restoration and commercial landscaping. But I am fascinated with mechanisms for replicating on a biomimetic basis. Hence I collect and use specific fungi and bacteria for the specific plant hosts I work with. I chose companion plants which will interconnect underground and share various messaging signals to their neighbours. So much of this fascinating epigenetics within plant communities goes unnoticed by the US Forest service who view many native plants within the forest system as competitive invasives to their plantation mentality of oversight, especially with reforestation practices which hinder instead of promote regeneration.

Anyway, here is the post I've used yoour link in:

primary-water.blogspot.se/2016/04/epigenetic-mechanisms-defined.html

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