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
F/N: Here is Orgel, 1973:
. . . In brief, living organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures that are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity . . . . [HT, Mung, fr. p. 190 & 196:] These vague idea can be made more precise by introducing the idea of information. Roughly speaking, the information content of a structure is the minimum number of instructions needed to specify the structure. [--> this is of course equivalent to the string of yes/no questions required to specify the relevant "wiring diagram" for the set of functional states, T, in the much larger space of possible clumped or scattered configurations, W, as Dembski would go on to define in NFL in 2002.] One can see intuitively that many instructions are needed to specify a complex structure. [--> so if the q's to be answered are Y/N, the chain length is an information measure that indicates complexity in bits . . . ] On the other hand a simple repeating structure can be specified in rather few instructions. [--> do once and repeat over and over in a loop . . . ] Complex but random structures, by definition, need hardly be specified at all . . . . Paley was right to emphasize the need for special explanations of the existence of objects with high information content, for they cannot be formed in nonevolutionary, inorganic processes. [The Origins of Life (John Wiley, 1973), p. 189, p. 190, p. 196. Of course, that immediately highlights OOL, where the required self-replicating entity is part of what has to be explained (cf. Paley), a notorious conundrum for advocates of evolutionary materialism; one, that has led to mutual ruin documented by Shapiro and Orgel between metabolism first and genes first schools of thought. Behe would go on to point out that irreducibly complex structures are not credibly formed by incremental evolutionary processes and Menuge et al would bring up serious issues for the suggested exaptation alternative. Finally, Dembski highlights that CSI comes in deeply isolated islands T in much larger configuration spaces W, for biological systems functional islands. That puts up serious questions for origin of dozens of body plans reasonably requiring some 10 - 100+ mn bases of fresh genetic information to account for cell types, tissues, organs and multiple coherently integrated systems. Wicken's remarks a few years later on wiring diagram organisation etc now take on fuller force in light of the further points from Orgel at pp. 190 and 196 . . . ]
kairosfocus
November 6, 2015
November
11
Nov
6
06
2015
01:30 PM
1
01
30
PM
PDT
You asked for the papers that I based my hypothetical system on, I provided them. And all you can respond with is to point out that the conversation is a hypothetical thought experiment? You don't say. If you come up with something intelligent, then I'll respond to you. Until then, have a nice day.Alicia Cartelli
November 6, 2015
November
11
Nov
6
06
2015
01:27 PM
1
01
27
PM
PDT
Carpathian, the red herring-strawman chase continues. FSCO/I -- a summary term for something identified by Orgel and Wicken in the 70's . . . I notice the implied who are you dismissal hint -- is a strong sign of design as cause. So, if such a designer is empirically indicated per inference to best explanation and we are able to see that a designer of life needs very good computation simulation or the equivalent powers indeed and one for the cosmos needs in addition sheer raw power in scads to implement a cosmos, then it seems that we have in hand a pivotal observational base indeed. Just the FSCO/I in those contexts allows us to reasonably infer to design and requisites of design point to significant powers. BTW, on life, I'd suggest that several generations of Moore's law scaling point to pretty awesome computing power so I remain at the point, molecular nanotech lab is all that is required. KF PS: All of us are using computers that 40 - 50 years ago would have been supercomputer territory, or at least big iron mainframe territory. Well do I recall in the 80's hearing of a VAX based national computer centre with several gigs in RAM and how awesome and even vaguely menacing that sounded. Now, that's in our tablets and notebooks.kairosfocus
November 6, 2015
November
11
Nov
6
06
2015
01:23 PM
1
01
23
PM
PDT
Alicia Let me be clear nobody is asking for possible or plausible scenarios we want actual proof. Can you do that?Andre
November 6, 2015
November
11
Nov
6
06
2015
01:23 PM
1
01
23
PM
PDT
Alicia Please stop your bluffing. It's OK to try and deceive me but to deceive yourself is whacky. You've used words like plausible, likely, assumed, coulda, woulda bit absolutely nothing concrete.Andre
November 6, 2015
November
11
Nov
6
06
2015
01:17 PM
1
01
17
PM
PDT
UB: In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world. In comment #50 above you can see a portion of what’s at stake. I am asking what object in the RNA world held the information so that we can talk about how it held that information. Zach: DNA polymers, which are closely related to RNA chemically, could coopt the RNA replication mechanism, coding for its own purposes, perhaps virally.
So, an RNA template replicator exists. Then a DNA molecule - with a purpose - takes over. Perhaps virally. Like I said Zach, no one can take away your faith, nor can anyone falsify anything you wish to propose from that faith.Upright BiPed
November 6, 2015
November
11
Nov
6
06
2015
12:59 PM
12
12
59
PM
PDT
Initial work was done in the late 70s, early 80s: Wolfenden et al. (1979) Science Wolfenden et al. (1981) Biochemistry Recent work has applied this to an early-earth environment and the evolution of early translational systems: Wolfenden et al. (2015) PNAS Carter & Wolfenden (2015) PNAS They point to chemical interactions that were likely important in the evolution of the earliest translational machinery.Alicia Cartelli
November 6, 2015
November
11
Nov
6
06
2015
11:52 AM
11
11
52
AM
PDT
Carpathian- There isn't any evidence for a world without the current transcription and translation system
How these configurations of matter came to be is what the debate is about.
And all you have to explain it is "it just happened" and "a long series of luck accidents".Virgil Cain
November 6, 2015
November
11
Nov
6
06
2015
11:43 AM
11
11
43
AM
PDT
Upright BiPed: In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world. DNA polymers, which are closely related to RNA chemically, could coopt the RNA replication mechanism, coding for its own purposes, perhaps virally.Zachriel
November 6, 2015
November
11
Nov
6
06
2015
11:34 AM
11
11
34
AM
PDT
Alicia Please post some links to your papers..... You know as well as I do you're bluffing.Andre
November 6, 2015
November
11
Nov
6
06
2015
11:23 AM
11
11
23
AM
PDT
kairosfocus:
In short, FSCO/I is evidence.
FSCO/I is a label you use to describe configurations of matter. How these configurations of matter came to be is what the debate is about. Simply adding attributes to your label does not win the day for ID. Your side brings up the improbability of "nature" to produce these configurations and I am bringing up the improbability of a designer other than the Genesis God to build these configurations. Show me how a non-living, non-god entity, that cannot control the physics of the universe, is able to design and then distribute life. Since the ID designer pre-dates life, he cannot be alive and also cannot be God if ID is to be taken as science. Walk me through that process.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
10:10 AM
10
10
10
AM
PDT
kf, over at TSZ I've introduced the term Theopodophobia. What do you think?Mung
November 6, 2015
November
11
Nov
6
06
2015
10:05 AM
10
10
05
AM
PDT
kairosfocus:
The first does not call for anything more than a molecular nanotech lab some generations beyond Venter et al.
Just who would run this lab if life doesn't exist yet?Carpathian
November 6, 2015
November
11
Nov
6
06
2015
09:59 AM
9
09
59
AM
PDT
Andre, the Hong paper visually shows you how the majority of proteins in ATP synthase are made up of peptide sequences that are not highly conserved. There are some select regions in these proteins that are, but the vast majority of the amino acids vary among different species. This was the opposite of what gpuccio was trying to claim. I was just showing him the error in his ways. No magic wand needed Mungy, simply chemical interactions. The series of papers I am referring to are Wolfenden et al. 2015. Do you guys really think it’s just coincidence that 19 of the 20 amino acids follow this dichotomy? The paper shows it exists, I am applying the information to this hypothetical first living molecule. Mapou, I love when you use the term “dirt worshippers.” It just goes to show everyone the typical level of intelligence they can find here at UD.Alicia Cartelli
November 6, 2015
November
11
Nov
6
06
2015
09:58 AM
9
09
58
AM
PDT
kairosfocus, A computer simulation of the pre-Cambrian world would be logistically impossible. An ID type of designer, who is not God, would not have the resources to run trillions of simulations of the entire global ecosystem of Earth. We could not if we harnessed all the world's computing power be able to even simulate the global weather for a year and come up with an accurate forecast for Portland any particular day of 2016. We would not be able to even input the data from every point on Earth at a pre-determined date and time. This would be crucial before being able to run an accurate simulation. Now include the genomes of every single organism and their interactions with the climate and each other and try to predict what the predator to prey relationship would be everywhere on Earth. It's logistically impossible to predict what the future will be like. You have to know beforehand just like the God of Genesis. As far as tuning parameters, just how would a non-god do this? A non-god has no control over the laws of physics. Today's weather depends on yesterday's and we can't do anything about that. Only a god could. If I'm wrong, show me how to accomplish that.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
09:56 AM
9
09
56
AM
PDT
Carpathian, I think you need to actually take a good look at protein synthesis, from unzipping, creating mRNA, transfer to ribosome, start, extension, halting, folding, and the use of codes that manifest themselves in loading the universal CCA joint of the tRNA with specific AAs. This points to mRNA as machine level code, with a NC nanotech assembler that uses it to create the workhorse molecule of the cell. Again, you are off on a red herring, strawman chase. KFkairosfocus
November 6, 2015
November
11
Nov
6
06
2015
09:54 AM
9
09
54
AM
PDT
Carpathian, all of this is in reality a red herring. We do know inductively on trillions of cases in point backed by relevant analysis of needle in haystack searches, that functionally specific complex organisation and associated information, FSCO/I, is a strong, empirically robust, index of design as cause. The world of life is chock full of such, from OOL up. The cosmos that is fine tuned for life is, too. The first does not call for anything more than a molecular nanotech lab some generations beyond Venter et al. (Where the integration of intelligently gated encapsulation, metabolic automata and code based self replication to get the cell going, points to how reproduction itself is a further instance of the FSCO/I to be explained, not an easy rhetorical out to dodge the need to properly explain FSCO/I. As in, reproduction based on codes has to be accounted for first, before "evolution" can be appealed to, which then runs into the issue of islands of function and needing to account for highly complex new body plans, all the way from goo to Godel.) The second does point to a very powerful designing entity beyond the physical cosmos and able to instantiate it. In short, FSCO/I is evidence. Evidence that on inference to best current, empirically grounded explanation (on trillions of cases) points to design. And we also have the point that purposeful intelligently directed configuration is the credible cause of design pointing to designers. So FSCO/I is by implication evidence pointing to designer. The proper way to address it is not to in effect find excuses to foot-drag and resist. If you have good evidence that FSCO/I can and reliably does come about by blind watchmaker chance and necessity, we are open to it. But, we are also very aware that a major reason for this sort of rhetoric as you are indulging, is that the party of magical dirt cannot come up with credible counter examples. So, the very style of objections you are making is back-handed, grudging testimony to the strength of the design inference. Thank you for your inadvertent support. KFkairosfocus
November 6, 2015
November
11
Nov
6
06
2015
09:46 AM
9
09
46
AM
PDT
Virgil Cain:
Carpathian: This research indicates it is not a coded translation but rather a chemical reaction No, it doesn’t. It says there is a correlation.
Here's something for you to mull over. This is a variable char DNA_1; This is a pointer to a variable. char *pDNA; To put it extremely simply , DNA_1 can be used as is, but pDNA is not the final data as the code it contains has to be translated by the processor in order for the actual data to be accessed. That is a level of indirection that does not exist in DNA, according to the research cited by Alicia Cartelli.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
09:41 AM
9
09
41
AM
PDT
Carpathian, start with, run a computer/mathematical simulation based on knowledge of the capabilities of chemistry and the self replicating system; say in a terraforming environment. Then inject plants, animals etc in ecosystem webs, and tune relevant parameters, making sure to design robust not brittle things. Indeed, as was already pointed out, you seem to be fixated on brittle systems not robust, adaptable ones. We already do a lot of things like that, including Monte Carlo type simulations in decision support systems. KFkairosfocus
November 6, 2015
November
11
Nov
6
06
2015
09:36 AM
9
09
36
AM
PDT
Virgil Cain:
Carpathian: For any other designer trying to engage in biological ID, it is impossible. Virgil Cain: Just repeating your tripe doesn’t make it so.
Then show everyone how it is possible for a biological designer to even gather the information required to know what to evolve. How far ahead would he have to look? Does he control the weather? Can he fine-tune the universe? All of these require a Genesis type of god.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
09:20 AM
9
09
20
AM
PDT
Cartelli:
Yup, I’m squirming away! If the peanut gallery has anything intelligent to say though, I’m all ears. I won’t hold my breath.
Funny, but we have not been holding our breath waiting for the dirt worshippers to say anything intelligent either. Worshipping the power of dead dirt to create life is not very intelligent, to say the least.Mapou
November 6, 2015
November
11
Nov
6
06
2015
09:07 AM
9
09
07
AM
PDT
Zachriel, In order to propose that life began in an RNA world that transitioned into a DNA-Protein system, you have to build a DNA-Protein system in an RNA world. In comment #50 above you can see a portion of what’s at stake. I am asking what object in the RNA world held the information so that we can talk about how it held that information.Upright BiPed
November 6, 2015
November
11
Nov
6
06
2015
08:53 AM
8
08
53
AM
PDT
Carpathian:
For any other designer trying to engage in biological ID, it is impossible.
Just repeating your tripe doesn't make it so.Virgil Cain
November 6, 2015
November
11
Nov
6
06
2015
08:50 AM
8
08
50
AM
PDT
I love how Alicia comes here, spews a few bluffs, ignores the refutations and then acts as if she refuted what IDists have said. And of course she always spews the condescending diatribe when she can't bluff her way through.Virgil Cain
November 6, 2015
November
11
Nov
6
06
2015
08:49 AM
8
08
49
AM
PDT
Carpathian:
This research indicates it is not a coded translation but rather a chemical reaction
No, it doesn't. It says there is a correlation.Virgil Cain
November 6, 2015
November
11
Nov
6
06
2015
08:47 AM
8
08
47
AM
PDT
Mung:
Alicia Cartelli: But yes, recent research has demonstrated that there is a chemical link between the amino acids added and the nucleotide sequences that code for them. Mung: And now you have just gone from a system without translation to a system of translation, with a wave of your magic wand. You’ve just completely ignored the problem that needs to be explained.
This research indicates it is not a coded translation but rather a chemical reaction . This is not then a system that translates codes. It is instead one of chemical reactions.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
08:45 AM
8
08
45
AM
PDT
John Maynard Smith and Eors Szathmary know what needs to be explained: "We discuss how the translating machinery may have originated in Chapter 4."Mung
November 6, 2015
November
11
Nov
6
06
2015
08:40 AM
8
08
40
AM
PDT
Zachriel: Yes, RNA can code for proteins, and can also act as a peptide ligate. RNA carries the message, which has already been encoded.Mung
November 6, 2015
November
11
Nov
6
06
2015
08:36 AM
8
08
36
AM
PDT
Vy:
Carpathian: . . . has to build multiple organisms for a future that is a century away and unknown Vy: And this is impossible because . . . ?
It is not impossible for an entity that can see or control the future like the God of Genesis. For any other designer trying to engage in biological ID, it is impossible. That leaves the only designer capable of biological design, the Christian God. This makes the ID movement religious.Carpathian
November 6, 2015
November
11
Nov
6
06
2015
08:36 AM
8
08
36
AM
PDT
Upright BiPed:
AC, I didn’t “brush off” your comments, its just that your proposition isn’t new and doesn’t clarify any of the important issues.
That is correct. As I say, I read that paper, carefully. And it doesn't say what Alicia needs it to say and it's not even attempting to explain translation.Mung
November 6, 2015
November
11
Nov
6
06
2015
08:30 AM
8
08
30
AM
PDT
1 3 4 5 6 7 16

Leave a Reply