Larry Moran Understands the Genetic Code is Real

_{Barry Arrington

May 10, 2020

Intelligent Design}

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Every time we run a series of articles on the genetic code, our combox gets stuffed with comments from materialists claiming the idea that the genetic code is an actual code is fallacious, an error committed only by those ID rubes with an agenda. But, of course, not only is this untrue, it is easily shown to be untrue. There are numerous examples of materialists insisting that the “code” part of “genetic code” refers to a real code; it is not an analogy nor the sloppy use of language. To his credit Larry Moran is one such:

The Real Genetic Code

This is the genetic code. It shows the relationship between a sequence of nucleotides in messenger RNA (mRNA), or DNA, and the amino acids that are inserted into a growing polypeptide chain.

Moran then puts up the Morse Code chart and states:

We do not say that the string of dots and dashes is the Morse Code. We say that it’s a message encrypted using the Morse Code. Similarly, we do not say that a string of nucleotides is the genetic code. It’s the message that’s translated using the Genetic Code.

That the genetic code is an actual semiotic code is not disputed by any serious person. Just Google “genetic code semiotic” and dozens of scholarly articles will pop up discussing how the genetic code is semiotic all the way down and not, as Ortho insists, merely chemical.

It turns out that the real question is not whether the genetic code is a semiotic code. That is glaringly obvious and taken for granted by scientists who have studied the matter. No, the real question is what motivates the materialists who stuff our combox to deny the science.

HT:ET

Comments

JVL, yup. tech leaps are a classic for creative out of left field design. KFkairosfocus_{May 11, 2020
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Kairosfocus: Bloatware is a relative thing, our genome is 3.1 bn baseprs and molecular nanotech makes a 2 m string coil into a cell of micron scale. Some things just are inherently complex. That is certainly the message of underlying chemistry. Of course. But when we're talking about von Neumann self-replicating machines and we keep saying: oh, it would have to do this and that and that as well . . . It's not just the manhours or time, it's the difficulty trying to get it all to work together and quickly without too many faults. I suspect incremental changes work in islands of function as a controlled random walk. That’s how the immune system acts in key part. To go to other islands is another story. That would require technological leaps. Design with built-in adaptability within limits. But you can't program technological leaps. You have to start outside the existing system don't you? The idea of core and fringe gives resiliency, but loss of information can be fatal. Of course. Anyway, it all just sounds hideously messy and complicated and even hard to define. And if we can't even come up with a decent model of the kind of system we are talking about then . . . what good is it? And does it really mirror biological systems? Can it mirror biological systems if we can't even get it functioning?JVL_{May 11, 2020
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36, Bloatware is a relative thing, our genome is 3.1 bn baseprs and molecular nanotech makes a 2 m string coil into a cell of micron scale. Some things just are inherently complex. That is certainly the message of underlying chemistry. I suspect incremental changes work in islands of function as a controlled random walk. That's how the immune system acts in key part. To go to other islands is another story. That would require technological leaps. Design with built-in adaptability within limits. The idea of core and fringe gives resiliency, but loss of information can be fatal. KFkairosfocus_{May 11, 2020
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Kairosfocus: I added, multiple copies, maybe with safeguards. It's getting rather complicated! Thinking about it from a software point of view. As for information sources, what are the general candidates? Assuming the self-replicators can respond to local unforeseen conditions then it seems like taking a wild guess makes more sense! Otherwise, how could you possibly program all the various options for stuff you don't know is coming? Having a designer around defeats the whole point of being self-replicating if we're adding on some kind of evolutionary possibility. Also we're talking about lots of detectors and wiring and data storage and evaluative algorithms. You'd have to make guesses about lots of possible ranges of environmental conditions and possible approaches. And how do you trigger those decisions? It's getting real messy. As for, complexities, yes that surfaces the complexities so it’s a feature not a bug. I know but we're starting to talk about something that might be approaching bloatware: i.e. we keep adding features and functionality which requires more storage space, more required troubleshooting, more possible conflicts, probably more crashes and bugs, a lot more development time and a much more complicated operating system. Just think about how big the coding for Microsoft Word is and that's only handling encoded text (a limited character set) according to set rules and it's not supposed to replicate or change to suit local conditions. If you want self-replicating machines to 'evolve' that's going to entail millions of lines of code with multiple copies? And that's saying nothing about all the subsidiary resources required.JVL_{May 11, 2020
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JVL, I added, multiple copies, maybe with safeguards. As for information sources, what are the general candidates? As for, complexities, yes that surfaces the complexities so it's a feature not a bug. The obvious grand sandbox is a computer system. KFkairosfocus_{May 11, 2020
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Kairosfocus: Instantly, defining an integral operator leads to the same for integration. H’mm what happens to fundl th calc with that? I don't remember! You'll have to do some more investigating. Nope, go layer-cake. A physical layer has others above, interacting with it. Could you be more specific regarding biological entities and structures; just to make sure I'm following. , i didn’t pick that up directly but yes it is a logical extension. As to how to do that without wrecking functionality, that is the billion dollar question. Yes, that is the question!! IF a von Neumann self-replicating machine just made random copying errors in its operational code on occasion then chances are the program would just stop or hang. Or the device would malfunction in some way. Unless there was some kind of code redundancy built in (like a second copy) that allowed for fatal errors to be ignored or ameliorated in some way. (But how would the operating system decide?) Regardless, most changes would not be beneficial. IF a von Neumann self-replicator made higher-level functional changes so as to intentionally alter its morphology for some purpose then a) where did the information come from, b) how was it evaluated, c) was the new design already pre-loaded as an alternative or choice given certain conditions? It gets kind of messy. Is it really a good analogy to living systems? It seems to bring up too many issues that are difficult to answer.JVL_{May 11, 2020
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UB & JVL, i didn't pick that up directly but yes it is a logical extension. As to how to do that without wrecking functionality, that is the billion dollar question. My first guess would be, multiple copies, some secured, some with sandboxes to experiment. Self destruct to safeguard. KFkairosfocus_{May 11, 2020
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JVL, First, thanks on D^1/n operators, looks like a conceptual cousin to the j*[] right angle AC rot operator that applied twice to x gives -x, so j is sqrt[-1]: >>as an analogue of the functional square root for the differentiation operator, that is, an expression for some linear operator that when applied twice to any function will have the same effect as differentiation.>> Instantly, defining an integral operator leads to the same for integration. H'mm what happens to fundl th calc with that? And lo and behold, our friendly Laplace transforms enter. Okay, this makes very good sense! Oh, back on life vs reduction to mechanisms. Nope, go layer-cake. A physical layer has others above, interacting with it. You may recall I speak of the Smith cybernetic loop with higher order controllers not just the in the loop machine. Bring in quantum influences at relevant scale and "ghost in the machine" takes on really scary meaning! (There's even room for "virus" infestations . . . as in, we can even have "demons" and an "indwelling" welcome Spirit.) I get the feeling we could create a really strange sci fi world this way . . . KFkairosfocus_{May 11, 2020
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Upright BiPed: Actually, that was one of his stated goals — to understand the necessary conditions whereby the process of replication would “proceed in such a manner that each automaton will produce other automata which are more complex and of higher potentialities than itself”. Fascinating . . . how would they decide what changes to make? Was it just random variations or explicit, defined modifications? He allowed for the introduction of new information into an existing functional description. So, where did the new information come from? Depends on the answer to what changes were allowed and how decided. Interesting stuff.JVL_{May 11, 2020
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.
I wasn’t clear if he allowed for the self-replicators to change their programming.
Actually, that was one of his stated goals -- to understand the necessary conditions whereby the process of replication would “proceed in such a manner that each automaton will produce other automata which are more complex and of higher potentialities than itself”. He allowed for the introduction of new information into an existing functional description. - - - - - - - - - UB out.Upright BiPed_{May 11, 2020
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Kairosfocus: No reason why not. Indeed there are about two dozen genetic code “dialects.” Yes, it's not true the code is the same for all of life, just most of it!! What is “living”? It turns out that the vNSR model extends to key aspects of that strange automaton, the living cell. I can see there could be some comparisons . . . I'll have to read the source material a bit more I think. Whether or not he did, incorporate a universal constructor — give it something to do — and voila, self-mod is on the table. Yes, but . . . by comparing life to mechanisms aren't you supporting the materialist view that we're all just machines? That's what confused me about comparing to von Neumann self-replicators. I’m not clear. Do you mean multiple integrals and partial differentials? If not, where can I see that stuff? https://en.wikipedia.org/wiki/Fractional_calculus I think you'd have to have someone step through it though, it's messy.JVL_{May 11, 2020
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JVL: on points, I gotta get moving for the day: >>Yes . . . if the code is arbitrary could it have been something else?>> No reason why not. Indeed there are about two dozen genetic code "dialects." >> I was under the impression that von Neumann’s self-replicators were strictly mechanical, i.e. non-living.>> What is "living"? It turns out that the vNSR model extends to key aspects of that strange automaton, the living cell. >>I wasn’t clear if he allowed for the self-replicators to change their programming. >> Whether or not he did, incorporate a universal constructor -- give it something to do -- and voila, self-mod is on the table. Getting effective self-mod is another story, of course. You will see that my summary sketch has a UC in it. >>we even have fractional integration and differentiation. That’s really weird stuff.>> I'm not clear. Do you mean multiple integrals and partial differentials? If not, where can I see that stuff? More operators, please. KFkairosfocus_{May 11, 2020
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Kairosfocus: Codes are symbolic and necessarily have high contingency in elements (are arbitrary) but conform to protocols, in effect syntax and semantics. Yes . . . if the code is arbitrary could it have been something else? Then, all of this gets fitted into a von Neumann Kinematic Self-replicator, which may be difficult to summarise algebraically but fits with block diagram/flow chart frameworks. I spent some time checking on this this morning. But I was under the impression that von Neumann's self-replicators were strictly mechanical, i.e. non-living. And I wasn't clear if he allowed for the self-replicators to change their programming. In a former generation, Mathematicians were exceedingly uncomfortable with explorations of the visual. Mandelbrot and Fractals etc have made a sea-change. There is such a thing as process logic that can be visualised and at least in part expressed algebraically [especially if one goes over to the complex frequency domains]. Yes, we even have fractional integration and differentiation. That's really weird stuff. We’eze be rite-brain operators. de ole dowg can learn some new tricks!JVL_{May 11, 2020
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Upright BiPed: Larry Moran thinks the gene code is an actual code, and he also thinks it is the product of an unguided process. Yes, that seems to be his position. And that confused me because I thought a true code was strictly an arbitrary symbolic association with no underlying physical causations. I would think Dr Moran would believe that the code arose through chemical affinities. It seems like he is using code in a very limited sense. Well, differently than I would have expected. The group of materialists on this website (the ones you support and argue alongside of day after day) argue that the gene code is not a code, and also believe it’s the product of an unguided process. Yes, that is/was my stance which is why I was shortchanging our discussions because I thought our disagreement was on whether the code was purely arbitrary or arose via chemical reactions. But reading through some material I'm not sure so I wanted to clarify things a bit. Do you see the distinction there? One says it’s a) a code, and b is a natural product, while the other argues it’s a) not a code, and b) a natural product. . . . . Design proponents, on the other hand, argue that is it a) a genuine code, and b) a product of intelligence. Yup, that seems to sum things up cleanly. Now, do you happen to recall that I was pushing you to grasp this distinction in our last conversation? Your comrades here at UD do not want to have to deal with the evidence that the code is a product of intelligence (that would be the design inference “b” above) so they stubbornly deny the overwhelming scientific evidence of “a” as a means to avoid it I was avoiding accepting that it was actually a code because I thought a code had to be an arbitrary association and I had read about some work which implied that it might not be completely arbitrary. But I'm not sure that is the right use of the word code now. As already stated, all claims are subject to evidence. This materialist, in a purely rhetorical offer, is willing to cease denying the overwhelming evidence that the code is a code, if design proponents will just promise to not make the logical inference that follows. Hmm . . . I can see what you're saying. I suppose some of it comes down to how the word code is used by people like Dr Moran 'cause I would have said his use was wrong. ”You are not merely disagreeing with the interpretation, you are avoiding acknowledgement of the science and history behind the interpretation. You are saying the science (clearly documented in the literature and is not even in question) is not what it is, and then telling yourself that you are merely disagreeing with the interpretation.” Okay. So . . . Your emphasis on semiotics means you believe the code is an arbitrary assignment, it could have been something else, maybe lots of something elses. If it's arbitrary then some biologists would say it was just a happy accident or a random freeze, it could have been something else but that doesn't mean it was specified by an intelligence. But based on semiotic analysis that says design to you. Yes? Please direct me to anyplace which gets at the nub of this matter. I have been trying to read up on Semiotics and von Neumann self-replicating machines to see if I can grasp yours and kairosfocus' arguments better. I might be a bit slow 'cause I'd rather really sort this out in my head than just rush to reply.JVL_{May 11, 2020
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Larry Moran is more than welcome to try to capture the 10 million dollar prize for demonstrating nature can produce coded information. That no one has won that prize says it all, really.ET_{May 11, 2020
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JVL, complexity is as a yardstick beyond 500 - 1,000 bits and the specification is based on requisites of an interlocking functional system. The code uses prong height in the DNA form, is transcribed and edited into mRNA form, which is then a control tape for a transfer machine, the ribosome. That machine is in effect a molecular nanotech assembly line for proteins to order . . . including by hijacking viruses. It works with tRNA's with anticodons at one end and CCA- tool tips that couple to the -COOH end of AA's at the other, enforcing an amine -block-COOH . . . amine -block-COOH . . . pattern in peptide chains. Those then fold (or are chaperoned to fold) into functional shapes that may require multiple parts and added ions etc. The ribosome blends rRNA and proteins. All of this is tied into chirality. Codes are symbolic and necessarily have high contingency in elements (are arbitrary) but conform to protocols, in effect syntax and semantics. The overall cluster is not plausibly explicable on blind chance and/or mechanical necessity due to cosmos scale search challenge in implied configuration space. This last being a cut-down multidimensional phase space as momentum is not relevant. Then, all of this gets fitted into a von Neumann Kinematic Self-replicator, which may be difficult to summarise algebraically but fits with block diagram/flow chart frameworks. In a former generation, Mathematicians were exceedingly uncomfortable with explorations of the visual. Mandelbrot and Fractals etc have made a sea-change. There is such a thing as process logic that can be visualised and at least in part expressed algebraically [especially if one goes over to the complex frequency domains]. Engineers, Chemists -- esp organic ones -- architects, managers, computer scientists and applied scientists have a much higher respect for visual, process-flow and structural logic. We'eze be rite-brain operators. KFkairosfocus_{May 11, 2020
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. JVL at #15 What in the world is it about this that you find so hard to grasp? Larry Moran thinks the gene code is an actual code, and he also thinks it is the product of an unguided process. The group of materialists on this website (the ones you support and argue alongside of day after day) argue that the gene code is not a code, and also believe it’s the product of an unguided process. Do you see the distinction there? One says it's a) a code, and b is a natural product, while the other argues it's a) not a code, and b) a natural product. Both of these claims (a and b) are subject to evidence. Design proponents, on the other hand, argue that is it a) a genuine code, and b) a product of intelligence. It remains a fact that both claims are subject to evidence. There is nothing difficult in that to understand. Now, do you happen to recall that I was pushing you to grasp this distinction in our last conversation? Your comrades here at UD do not want to have to deal with the evidence that the code is a product of intelligence (that would be the design inference “b” above) so they stubbornly deny the overwhelming scientific evidence of “a” as a means to avoid it. Here is what that looks like: ”I tell you what, I will meet you half way and concede that DNA is a language and a code if you concede that when you are claiming this, you are not claiming that this means they are designed.” As already stated, all claims are subject to evidence. This materialist, in a purely rhetorical offer, is willing to cease denying the overwhelming evidence that the code is a code, if design proponents will just promise to not make the logical inference that follows. This is why I said to you: ”You are not merely disagreeing with the interpretation, you are avoiding acknowledgement of the science and history behind the interpretation. You are saying the science (clearly documented in the literature and is not even in question) is not what it is, and then telling yourself that you are merely disagreeing with the interpretation.”Upright BiPed_{May 11, 2020
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Is this a fair description:
A detailed conceptual proposal for a physical non-biological self-replicating system was first put forward by mathematician John von Neumann in lectures delivered in 1948 and 1949, when he proposed a kinematic self-reproducing automaton model as a thought experiment. Von Neumann's concept of a physical self-replicating machine was dealt with only abstractly, with the hypothetical machine using a "sea" or stockroom of spare parts as its source of raw materials. The machine had a program stored on a memory tape that directed it to retrieve parts from this "sea" using a manipulator, assemble them into a duplicate of itself, and then copy the contents of its memory tape into the empty duplicate's. The machine was envisioned as consisting of as few as eight different types of components; four logic elements that send and receive stimuli and four mechanical elements used to provide a structural skeleton and mobility. While qualitatively sound, von Neumann was evidently dissatisfied with this model of a self-replicating machine due to the difficulty of analyzing it with mathematical rigor. He went on to instead develop an even more abstract model self-replicator based on cellular automata.[16] His original kinematic concept remained obscure until it was popularized in a 1955 issue of Scientific American.
JVL_{May 11, 2020
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Kairosfocus: PS: Kindly note my discussion here: https://uncommondescent.com/design-inference/how-the-folded-structure-and-then-the-loading-of-trna-corrects-attempts-to-reduce-protein-synthesis-to-mere-chemistry/ Yes, I had already looked at that which was one of the reasons I decided to work a little harder at the subject. Just trying to get my head around the parts of the system that indicate design. I used to think it was just that the code was arbitrary, i.e. not dictated by any chemical affinities. But there's more than just that it seems. I know you frequently focus on the presence of a certain level of complex and specified information. It's clear that Dr Moran thinks it's a code so which part of the science is he denying. I'd just like to focus my learning down a bit. If that makes sense. Kind of like starting with the genetic codes greatest hits from an ID point of view.JVL_{May 11, 2020
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KF @18: Exactly right.jawa_{May 11, 2020
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JVL, the creation of a COMPLEX, functionally specific code system involving linguistic elements and associated organisation of machine language execution machinery per an architecture points to design as best explanation . . . notice my specific context of modern sense inductive warrant in an empirically grounded scientific context. In this case it is compounded by chicken-egg causal loops in a von Neumann Kinematic Self-Replicator. The protein synthesis framework is a key case study here, with the role of the Ribosome as a transfer machine (i.e. we have a molecular nanotech assembly line, actually hundreds in a typical cell), mRNA -- as edited!!!! -- as control tape and tRNA as position-arm effectors with universal joint tool tips. Where, DNA is a library of executables and regulatory files. KF PS: Kindly note my discussion here: https://uncommondescent.com/design-inference/how-the-folded-structure-and-then-the-loading-of-trna-corrects-attempts-to-reduce-protein-synthesis-to-mere-chemistry/kairosfocus_{May 11, 2020
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Kairosfocus: So, that's a yes then. Does the identification of a code preclude derivation by natural processes? (I understand that Upright BiPed and maybe Barry Arrington will attack me for running away from this issue earlier. I have had a think about it, read some of the other comments made in the mean time and will try and engage more this time. I have to say though, as if it weren't obvious, that the topic of semiotic systems is not something I am really conversant on. So partly I'd just like to get more acquainted with that.)JVL_{May 11, 2020
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JVL, we know the Monod premise is deeply entrenched in biology etc, so it is unsurprising that many imagine that somehow the systems of biological life "must" have come about by blind chance and/or mechanical necessity. For, one locked into such a view, that's all that is ultimately available. At the same time, from Crick on, it has been utterly clear that DNA is an alphanumeric code. The deduction is obvious. However, the problem is, that, manifestly, for FSCO/I beyond 500 - 1,000 bits, the blind search capacity of the Sol system or the observable cosmos is nowhere near enough to make this anything but an appeal to repeated statistical miracles all the way across the tree of life. The thinking is an ideologically driven deduction that is analytically implausible and observationally unfounded. By contrast, with trillions of cases, FSCO/I is readily formed by intelligently directed configuration. KF PS: There is an incoherence in evolutionary materialistic scientism. The same blind forces that "must" be at work cannot credibly account for a rational, responsible, significantly free intelligent mind. For that matter, on the FSCO/I challenge, it cannot account for effective brains and central nervous systems that are complex computational substrates. It cannot even adequately account for origin of neurons or even a first living cell.kairosfocus_{May 11, 2020
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So, because Dr Moran says the genetic code is a real code and because he also thinks it was developed by unguided processes you would say his thinking is inconsistent. Correct?JVL_{May 10, 2020
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Can biological cells be really programmable? Are they kidding? https://uncommondescent.com/design-inference/how-the-folded-structure-and-then-the-loading-of-trna-corrects-attempts-to-reduce-protein-synthesis-to-mere-chemistry/#comment-701326jawa_{May 10, 2020
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Any news on the Evo2.0 OOL $10M prize? Are Dr Cronin and Dr Szostak there yet? :)jawa_{May 10, 2020
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The beauty of the DNA is that it contains genetic code that is translated to aminoacids to form proteins, but in addition to that, the DNA also contains gene regulatory code in the TF-binding sites, promoter regions, enhancers, etc. DNA also contains the instructions to transcribe non-protein-coding RNA that serve as machine components or regulatory signals. Around the DNA there is also epigenetic code and the histone code associated with the chromatin remodeling feature. Lots of bells and whistles in that DNA thingy. :)jawa_{May 10, 2020
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Barry Arrington @3: Yes, you're correct. My mistake. I did not recognize that text.jawa_{May 10, 2020
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Calling the genetic code a code is not the evidence for Intelligent Design. The system and components required to carry it out is the evidence for Intelligent Design. Meaning we don't care what you want to call it. It's just more convenient using the word code because it fits the definition. And it makes it less obvious that you are want to deny reality.ET_{May 10, 2020
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It fits the definition of a code, Bob O'H. Codons REPRESENT amino acids in the same way that dots and dashes represent letters. There isn't any hidden secret messageET_{May 10, 2020
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