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Writing Biosemiosis.org

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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
Alicia Cartelli:
And for the last time, the ribosome is technically not an “enzyme” it is a ribozyme.
What is wrong with you? Mung said:
Alicia, “the ribosome” is not an enzyme.
Glad to see you're finally on board. Your credibility is still shot though.Mung
November 8, 2015
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Kairos, you can use all the Latin phrases you want, but it still just amounts to you denying what the majority of the world has already accepted as scientific fact. I've defended a few things as fact here, but my hypothetical system is not one of them, Andre. You are just lost as usualAlicia Cartelli
November 8, 2015
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A talking point you've tried to defend as a fact. When you find this theory of evolution please make sure to share it with everyone. And you are right for 150 or so years everyone has been trying to prove Darwin right. But how do we trust the convictions of a monkey's mind if there are any convictions in such a mind at all? Darwin was wrong about natural selection acting on variation to build from molecules to man and so are you.Andre
November 8, 2015
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AC:
Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today
Of course the ideologised a priori materialism imposition partyline sez so, but then comes the vera causa observable adequate cause test and bye bye party line. So much the worse for the evidence, we go with the ideology, in effect. Fail. KFkairosfocus
November 8, 2015
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Andre, you're not even making sense anymore. I said it's not a matter of "it has to be. " And I'm not too worried about the theory of evolution being wrong; there's decades of work from thousands of scientists all over the globe independently piecing the process and history of evolution together. My hypothetical system is nothing but a talking point; something you are not equipped to talk about unfortunately.Alicia Cartelli
November 8, 2015
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Alicia Wow.... "it has to be " and if you are wrong? I mean afterll you've only produced hypotheticas... Nothing testable at all.Andre
November 8, 2015
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It's not a matter of "it has to be right," Andre, it's a matter of looking at the claims made and the evidence supporting them an seeing that's it's the best explanation we have for the diversity of life seen today. And you don't know how deep my understanding of engineering is, but it is quite obvious how little people here understand biology. Don't worry about me and my "viruses," I'd be more concerned with your need to argue about things you have no understanding of. Now that seems like borderline lunacy to me.Alicia Cartelli
November 8, 2015
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Alicia I am certain that in your mind Darwinian evolution just has to be true. You may make accusations that we don't understand biology all OK by me by what I do know is that you just have no clue about engineering. Perhaps you might be able to heal your brain from the Darwin virus if you actually spent some time learning about engineering and design principles and how they apply in biology? I can only hope for your cure from the lunacy that has infected you.Andre
November 8, 2015
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Mungy, are you kidding me? They're talking about the ribosome. As I said from the start, your job is to find an enzyme that functions as a peptidyltransferase and "detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that ISN'T the ribosome. And for the last time, the ribosome is technically not an "enzyme" it is a ribozyme. Which is what the authors of the paper you quoted call it in the next line that you conveniently left out. The authors were putting a bit of historical perspective in, and they also mentioned in subsequent lines about the importance of this ribozyme in the "pre-biotic RNA world and contemporary biology."Alicia Cartelli
November 8, 2015
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Alicia Cartelli:
Why not informally hypothesize about what the earliest systems could have been.
Because it's been done already. Heard of John von Neumann?Mung
November 8, 2015
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Everything in biology points to chemical/biological evolution producing life and eventually the diversity of species we see today. Why not informally hypothesize about what the earliest systems could have been. I'm just here for some friendly banter, but it's tough to do when nobody else understands molecular biology. Guess I should've known better.Alicia Cartelli
November 8, 2015
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Alicia Cartelli:
Mung and gpucc, papers on ribosomal proteins and how drugs inhibit the ribosome are really of little help, but I wouldn’t expect you guys to know that.
Actually we understand perfectly. It's the no amount of evidence can convince me syndrome and you are a classic case. Wrapping up, because you've had your chance: Alicia Cartelli:
...there are really no “peptidyl transferase” enzymes...
Alicia Cartelli:
Why do you think I’m asking for the name of the enzyme? I know you won’t come up with one because I know it doesn’t exist.
Yet:
The crystallographic structures compellingly confirmed that peptidyl transferase is an RNA enzyme.
oops. big oops. credibility gone.Mung
November 8, 2015
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Alicia The first transitional machinery.... Do you have any actual first transitional machinery to make your case? I bet you the only place we'll find the first transitional machinery is in you imagination. Why are we entertaining trolls?Andre
November 8, 2015
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I could probably pull up 50 articles about the details of ribosomal function, all published in the last few months. I don't know what you guys think you're accomplishing by linking these articles, the first translational machinery was almost nothing like what we see today. I would assume the only thing they share is some type of peptidyltransferase activity. (How's that search for an enzyme name going mungy?)Alicia Cartelli
November 8, 2015
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Ribosomes are composed of two subunits, one small and one large; this study focused on the assembly of the small subunit, which happens first. “Following ribosome assembly, all ribosomes must have the same composition with four ribosomal RNAs and all ribosomal proteins in their appropriate positions... We wanted to understand how four ribosomal RNAs and 79 different proteins are assembled to make a functional ribosome that later is able to produce all cellular proteins.” As has been pointed out upthread, it's an absolute miracle that two different translation systems were discovered, the ACToy one, and then the one we actually see.Mung
November 8, 2015
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gpuccio:
Mung and all: This is very recent, and could be of some help: Ribosomal Proteins: Role in Ribosomal Functions
Thank you. Also just showing up over at ENV was a link to this article. Researchers explore how a cell’s protein-making factories are assembled Ribosomes, the molecular factories that produce all the proteins a cell needs to grow and function, are themselves made up of many different proteins and four RNAs. And just as an assembly line must be built before it can manufacture cars, these tiny factories must be constructed before they can put proteins together.Mung
November 8, 2015
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Sure there is, yes, yes, and yes, Virgy. I'm not avoiding any questions, I'm trying to avoiding stupidity. I guess I should stop visiting UD.Alicia Cartelli
November 8, 2015
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Alicia Cartelli, how clueless are you? There isn't any evidence for a more primitive cell, so you lose, again. Do you think physicochemical processes can A) produce your ribozyme B) provide the raw materials to carry on and C) be capable of evolving new functions? I know why you would want to avoid those questions.Virgil Cain
November 8, 2015
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Are you kidding me Andre, how clueless are you? Just because we have a huge amount of regulation in our cells, that doesn’t mean the first living cells three billion years ago couldn’t get away with inefficient and unregulated processes. I’m done speaking with you, it’s pointless. Sorry Mung, it’s tough to keep track of all the scientifically illiterate I encounter on here. Anyways, from the start when you said “There’s also an enzyme that detaches the amino acid from the tRNA so that it can be added to the peptide chain. And, of course, there is the ribosome,” I have been ~99% sure that you were wrong. The first sentence is the ribosome. The ribosome has the only peptidyl transferase activity that “detaches the amino acid from the tRNA so that it can be added to the peptide chain.” I gave you a chance to prove me wrong, so one more time, all you have to do is come up with the name of an enzyme that “detaches the amino acid from the tRNA so that it can be added to the peptide chain,” that isn’t “the ribosome.” Goodluck! Kairos, I just wanted to talk about a hypothetical first translational system and how it could possibly evolve, but that’s asking too much of the biologically illiterate here. Mung and gpucc, papers on ribosomal proteins and how drugs inhibit the ribosome are really of little help, but I wouldn’t expect you guys to know that.Alicia Cartelli
November 8, 2015
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While we’re speaking hypothetically, what about
And this is where the newest meatbag on UD (to my knowledge) took off. If wishes were horses . . .Vy
November 8, 2015
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It is not impossible for an entity that can see or control the future like the God of Genesis.
Glad you know.
For any other designer trying to engage in biological ID, it is impossible.
I agree it is impossible but for different reasons.
That leaves the only designer capable of biological design, the Christian God.
Yup.
This makes the ID movement religious.
Nope. That's the point ID separates from biblical creation (YEC) and aliensdidit. I could very well say evolution is religious because it elevates time, chance and probablymaybecouldness to godhood much like the ancient Greeks did with night, chaos, love, earth etc. but I doubt you'll agree with me. Do remember that Michael Ruse is on record for calling evolution a religion:
Evolution is promoted by its practitioners as more than mere science. Evolution is promulgated as an ideology, a secular religion—a full-fledged alternative to Christianity, with meaning and morality.I am an ardent evolutionist and an ex-Christian, but I must admit that in this one complaint—and Mr [sic] Gish is but one of many to make it—the literalists are absolutely right. Evolution is a religion. This was true of evolution in the beginning, and it is true of evolution still today. ‘… Evolution therefore came into being as a kind of secular ideology, an explicit substitute for Christianity.
And that's not a quotemine despite the baseless claims of the Darwine choir.Vy
November 8, 2015
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Oops, mangled a sentence -- here I repost: In short I pointed out that the actual empirical evidence in hand does not allow us to translate an inference to design of cell based life on earth [into inferring] as to whether a designer of such life would be within or beyond the observed cosmos. KFkairosfocus
November 8, 2015
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Mung and all: This is very recent, and could be of some help: Ribosomal Proteins: Role in Ribosomal Functions http://www.els.net/WileyCDA/ElsArticle/refId-a0000687.html Published online: June 2015
Abstract The assignment of specific ribosomal functions to individual ribosomal proteins is difficult due to the enormous cooperativity of the ribosome; however, important roles for distinct ribosomal proteins are becoming evident. Although ribosomal ribonucleic acid (rRNA) has the major claim to certain aspects of ribosome function, such as decoding and peptidyltransferase activity, there are also protein-dominated functional hot-spots on the ribosome such as the messenger RNA (mRNA) entry pore, the translation factor-binding site and the exit of the ribosomal tunnel. The latter is binding site for both chaperones and complexes associated with protein transport through membranes. Furthermore, the contribution of ribosomal proteins is essential for the assembly and optimal functioning of the ribosome. Key Concepts A universal nomenclature for the ribosomal proteins was introduced in 2014, which terminates the babylonic chaos of the various nomenclature systems. About two thirds of the bacterial ribosomal proteins have counterparts in archaeal and eukaryotic ribosomes. Both rRNA and ribosomal proteins are essential for assembly, structure and function of the ribosomes. A few ribosomal proteins are essential for the assembly, but lack a function in the mature ribosome. In addition to rRNA-dominated functional hot-spots such as the decoding centre and the peptidyl-transferase centre, there are also protein-dominated functional hot-spots such as the entry pore for the mRNA on the 30S subunit, the docking site for G-protein factors and the exit of the tunnel harbouring the nascent peptide chain.
gpuccio
November 8, 2015
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Q: How does one restrict the activity of an enzyme that does not even exist? Inhibition of ribosomal peptidyltransferase by chloramphenicol. Kinetic studies. A: By introducing an inhibitor that does not exist!Mung
November 8, 2015
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SB: Thanks for intervention at 381: https://uncommondescent.com/intelligent-design/writing-biosemiosis-org/#comment-586804 and again at 393 https://uncommondescent.com/intelligent-design/writing-biosemiosis-org/#comment-586864 I add, that having substituted a strawman caricature that the design inference is about in effect directly inferring designer per god of gaps and appeal to ignorance (instead of on tested, observed empirically reliable sign, inferring design process as best explanation causal process), C is pounding away at the strawman of his own making. So, he does not understand the actual design inference process, which is inference to best current causal process explanation on tested, reliable sign.He is too caught up in the caricature of his own manufacture. Worse, he likely then imagines we are lying as "intelligent design creationists," by way of the design inference that has been presented ever so many times. I have even taken time to elaborate the Dembski flowchart, to a more comprehensive aspect by aspect framework. I doubt that he realises that such is ideologically distorted, agenda serving caricature in disregard to duties of care to truth and fairness on his part. Let us hope that he and others of like ilk will at length wake up from their self-bewitchment of believing their own agit-prop. KFkairosfocus
November 7, 2015
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GP, oops, 388. KFkairosfocus
November 7, 2015
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Mung, muy interesante. KF PS: The authors seem to strain to push in RNA world, not realising the IoF, needle in haystack search, chicken-egg loop significance of: "The PTC is characterized by the most pronounced accumulation of universally conserved rRNA nucleotides in the entire ribosome."kairosfocus
November 7, 2015
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GP, 397 and 381 https://uncommondescent.com/intelligent-design/writing-biosemiosis-org/#comment-586823 : Need I say, constraints on functional sequences point to precisely the reality of molecular level deeply isolated islands of function . . . where IoF is of course a descriptive phrase I picked up from you many years past. That of course points onward to the beyond astronomical resources, needle in haystack blind watchmaker search challenge just to get to the component parts of the cell, much less to organise and operate the cell as a whole. Beyond lie the dozens of multicellular body plans. So, we are looking here at digitally coded, functionally specific information [dFSCI] backed up by the functional requisites of operating DNA as a physical string based storage medium . . . do I need to talk about birds nests in fishing line triggered by line twisting as just a first regulatory issue? -- and the molecular nanotech info processing, communication, control/regulatory and linked numerically controlled machinery such as the ribosome. Scads of FSCO/I to be addressed where on inductive and analytical grounds it is a strong sign of intelligently directed configuration as cause. AKA, design. KFkairosfocus
November 7, 2015
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AC: Pardon but empirically uncontrolled, speculative hypotheses do not count, especially in a context that is foundational to the matter and where an alternative that otherwise meets inference to best explanation is being ideologically locked out. In short, your onward response boils down to admission that you cannot pass the observed adequate cause, vera causa test. The design inference, as of right earned by inductive and analytical basis, sits at the table of discussion for the tree of life, from the roots on up to body plans including ours. KFkairosfocus
November 7, 2015
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Carpathian (et al): This thread has been picked up elsewhere at UD, I clip a response from there: ________________ >>Per clearing up the smoke of burning strawmen, I note that the matter to be explained per observation is biological life on earth. Encapsulated, smart-gated, metabolising automaton using code-based vNkSR cell based life. In the exchange you did not link, 342 in context, I wrote (but having a RW life had not got back to follow up yet, this is a wee hours pause to comment):
FSCO/I — a summary term for something identified by Orgel and Wicken in the 70’s . . . — 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.
In short I pointed out that the actual empirical evidence in hand does not allow us to translate an inference to design of cell based life on earth does not in itself suffice to infer as to whether a designer of such life would be within or beyond the observed cosmos. Something that . . . had you been familiar with say the first actual technical work by Thaxton et al (TMLO) . . . you should know has been acknowledged by leading design thinkers for over 30 years. Your talking points have majored on distorting this into an argument to in effect be that inferring design on FSCO/I in cell based life is an inference to God as designer. Not so, kindly stop the caricaturing. Next, you make a typical materialist error, conflating life with biological life; and often, biological life on earth. This generates a perceived contradiction that is sometimes triumphalistically put up by the ill-informed. I suggest that you need to step up to the level of worldview thinking, and recognise that there are serious views out there that have a much broader understanding of life than biological life and biological life on earth. Views, that cannot be cavalierly dismissed by dressing up inherently self-refuting evolutionary materialist scientism in a lab coat. Going up to cosmological level, the evidence in hand points to multi-dimensional fine tuning of the observed cosmos in ways that fit it for C-chemistry, aqueous medium, cell based life. Where, we evidently sit on a locally deeply isolated operating point on physics and cosmological arrangements, making an inference to design a best explanation even in the face of multiverse speculations. Not least, as it is implausible to find ourselves in this sort of world on such, a Boltzmann Brain type world or similar would be far more reasonable to expect on such speculations. This level brings to the table the sort of point championed by leading astrophysicist (and lifelong agnostic), Sir Fred Hoyle, a generation ago:
From 1953 onward, Willy Fowler and I have always been intrigued by the remarkable relation of the 7.65 MeV energy level in the nucleus of 12 C to the 7.12 MeV level in 16 O. If you wanted to produce carbon and oxygen in roughly equal quantities by stellar nucleosynthesis, these are the two levels you would have to fix, and your fixing would have to be just where these levels are actually found to be. Another put-up job? . . . I am inclined to think so. A common sense interpretation of the facts suggests that a super intellect has "monkeyed" with the physics as well as the chemistry and biology, and there are no blind forces worth speaking about in nature. [F. Hoyle, Annual Review of Astronomy and Astrophysics, 20 (1982): 16]
That, would be a far more useful context for your reflection, especially when the two halves are tied together with wider worldview issues such as the requisites of that responsible, rational intellectual freedom that are necessary to turn discussion into anything more than blind programming issuing glyphs representing -- oops, that is already loaded with issues necessitating responsible, rational freedom -- ultimately meaningless mouth noises. Especially when linked, underlying ontological, cosmological and moral issues are brought to the table in that light. Because, on pain of self-referential absurdity, we must be responsibly and rationally free to seriously discuss. (No this is not strictly self-evident to most of us today, we typically lack the understanding and background for that insight that absent such freedom, rationality itself collapses.) Finally, I suggest this as an in a nutshell summary (with onward info) on what ID actually is: https://uncommondescent.com/intelligent-design/btb-3-what-is-intelligent-design-id-is-it-scientific/ -- which was put up for reference only a few days past.>> _________________ More can be added, but I trust the above is sufficient to outline the matter. KFkairosfocus
November 7, 2015
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