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L&FP39: How the folded structure (and then the “loading”) of tRNA corrects attempts to reduce protein synthesis to “mere” chemistry

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One of the more astonishing rhetorical gambits of objectors to the design inference is to try to suggest that the alphanumeric, code-using, algorithmic information system we see in the D/RNA of the living cell and linked protein synthesis is not really an information system, it all reduces to chemical reaction trains. A common associated gambit is to assert that terms like “code” etc are all readily dismissible analogies.

As a first reminder, protein synthesis as graphically summarised:

Protein Synthesis (HT: Wiki Media)

Of course, it never hurts to remind such objectors of p. 5 of Sir Francis Crick’s $6 million, March 19, 1953 letter to his son, Michael:

Crick’s letter

Notice, his belief right from the outset of discovering the double-helix stricture: “. . . D.N.A. is a code.” This was then drawn out by the early 1970’s, yielding several Nobel Prizes along the way, and it is now a commonplace from primary school on. Here is the “standard” code as tabulated in RNA form, one of about two dozen dialects:

The Genetic code uses three-letter codons to specify the sequence of AA’s in proteins and specifying start/stop, and using six bits per AA

Here, too, is how Yockey fits the Protein synthesis framework into a standard communication system model:

Yockey’s analysis of protein synthesis as a code-based communication process

That brings us to the role of tRNA, as we can see in the lower right, dotted blue box. Notice, the remark that tRNA is loaded with the AA required in protein synthesis, at a universal CCA tool-tip, which is at the 3′ end of the primary tRNA chain. That is, in effect, Chemically, any AA can be loaded at the tip of any tRNA. Indeed, there are cases — such as H pylori (the ulcer germ) — where an AA is loaded then chemically altered to the true target and experimenters have used the universality to add other AAs than the usual twenty found in nature.

Let us therefore look at the plan view, “clover-leaf” secondary structure of tRNA, noting how H-bonding sets up the emerging tool-arm structure:

Also, we can see how the CCA tip [at the A end] attaches to the COOH end of the AA, how the anti-codon is at the opposite end in one of the “loops,” and how it folds into its tertiary, 3-D position-arm structure:

Let me add, it is helpful to look at the structure of an amino acid, which allows modular chaining:

I find a series of videos helpful. First, charging/ loading the tRNA:

Next, translation — yes, a linguistic information-processing process carried out operationally using molecular nanotech (instead of the Si we use in microprocessors in the fetch, decode, execute loop):

Next, for completeness, the ribosome, first as a simplified diagram:

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

Video, with background details:

Fourthly, initiation of actual protein synthesis:

With all of this on the table, I can now headline a comment I made in the Ortho keyboard thread [a thread that is well worth working through], which — predictably — was side stepped rhetorically by objectors:

[KF, 29:] >>I’m late to the party. tRNA folds into a secondary cloverleaf structure then into the arm shape with the anticodon loop at one end and the standard CCA tool-tip that bonds to the loaded AA [COOH end] at the other. [break, let’s remind ourselves of the cloverleaf:]

As the tip is a standard [CCA–> COOH] joint, it is non-specific. That’s not the magic step.

That oh so humble source, Wikipedia, by principle of embarrassment, now tells an astonishing point or two of truth on how:

Aminoacylation is the process of adding an aminoacyl group to a compound. It covalently links an amino acid to the CCA 3′ end of a tRNA molecule. Each tRNA is aminoacylated (or charged) with a specific amino acid by an aminoacyl tRNA synthetase. There is normally a single aminoacyl tRNA synthetase for each amino acid, despite the fact that there can be more than one tRNA, and more than one anticodon for an amino acid. Recognition of the appropriate tRNA by the synthetases is not mediated solely by the anticodon, and the acceptor stem often plays a prominent role.[17] Reaction:

amino acid + ATP –> aminoacyl-AMP + PPi
aminoacyl-AMP + tRNA –> aminoacyl-tRNA + AMP

In some ways, even more tellingly, we find evidence of adaptation to apparent loss of function and/or alternative pathways:

Certain organisms can have one or more aminoacyl tRNA synthetases missing. This leads to charging of the tRNA by a chemically related amino acid, and by use of an enzyme or enzymes, the tRNA is modified to be correctly charged. For example, Helicobacter pylori has glutaminyl tRNA synthetase missing. Thus, glutamate tRNA synthetase charges tRNA-glutamine(tRNA-Gln) with glutamate. An amidotransferase then converts the acid side chain of the glutamate to the amide, forming the correctly charged gln-tRNA-Gln.

This stage is when the correlation between anticodon and targetted AA is assigned. Notice, it is not solely based on the anticodon, reflects conformation of the folded tRNA and in some cases has a workaround compensating for somehow missing information that leads to absence of a particular loading enzyme. H pylori loads a chemically related AA to the true target then brings up enzymes to modify to the correct AA. I have already noted that artificial AAs have been inserted and are capable of loading then being added to peptide chains.

It bears noting that in the tertiary structure, the anticodon and AA are at opposite ends of the tRNA. Which AA is there is set in a way that is modular and there can even be workarounds.

This is of course the point where a mobile, molecular scale position-arm device is loaded with the properly coded AA for protein synthesis. (I assume we can look that up for ourselves.)

Wiki’s disclosures against known ideological bent are not finished, we now go to the ribosome, the molecular machine that assembles a peptide chain based on the mRNA tape, using the coding.

Notice, the position-arm action at molecular level:

The ribosome has three binding sites for tRNA molecules that span the space between the two ribosomal subunits: the A (aminoacyl),[19] P (peptidyl), and E (exit) sites. In addition, the ribosome has two other sites for tRNA binding that are used during mRNA decoding or during the initiation of protein synthesis. These are the T site (named elongation factor Tu) and I site (initiation).[20][21] . . . .

Once translation initiation is complete, the first aminoacyl tRNA is located in the P/P site, ready for the elongation cycle described below. During translation elongation, tRNA first binds to the ribosome as part of a complex with elongation factor Tu (EF-Tu) or its eukaryotic (eEF-1) or archaeal counterpart. This initial tRNA binding site is called the A/T site. In the A/T site, the A-site half resides in the small ribosomal subunit where the mRNA decoding site is located. The mRNA decoding site is where the mRNA codon is read out during translation. The T-site half resides mainly on the large ribosomal subunit where EF-Tu or eEF-1 interacts with the ribosome. Once mRNA decoding is complete, the aminoacyl-tRNA is bound in the A/A site and is ready for the next peptide bond to be formed to its attached amino acid. The peptidyl-tRNA, which transfers the growing polypeptide to the aminoacyl-tRNA bound in the A/A site, is bound in the P/P site. Once the peptide bond is formed, the tRNA in the P/P site is deacylated, or has a free 3’ end, and the tRNA in the A/A site carries the growing polypeptide chain. To allow for the next elongation cycle, the tRNAs then move through hybrid A/P and P/E binding sites, before completing the cycle and residing in the P/P and E/E sites. Once the A/A and P/P tRNAs have moved to the P/P and E/E sites, the mRNA has also moved over by one codon and the A/T site is vacant, ready for the next round of mRNA decoding. The tRNA bound in the E/E site then leaves the ribosome.

The P/I site is actually the first to bind to aminoacyl tRNA, which is delivered by an initiation factor called IF2 in bacteria.[21] However, the existence of the P/I site in eukaryotic or archaeal ribosomes has not yet been confirmed. The P-site protein L27 has been determined by affinity labeling by E. Collatz and A.P. Czernilofsky (FEBS Lett., Vol. 63, pp. 283–86, 1976).

This is a tape-controlled assembly process dependent on the correctly loaded tRNAs to operate correctly. Where, proteins are the workhorse molecules of the cell.

Indeed, we effectively have a transfer machine with a miniature assembly line, with preloaded parts attached to position-arm carriers brought up and applied then exiting even as the target of the manufacturing process is being produced and held in place until complete.

Illustrating:

The mRNA tape, of course, carries initiation, stepwise elongation, finite succession and halting. Thus we see an algorithm at work, with an information bearing tape as controller and an assembly line using mobile position-arm units.

This is seriously advanced automation and manufacturing, using algorithms and code on string data structures [let’s only mention editing to form mRNAs], thus language. Where the coding is present twice in two separate subsystems, processed effectively independent of one another. DNA is unzipped and used to assemble mRNA precursors, which are edited to form the control tape. Separately, tRNA is created with the implicit anticodon, again stored in the master tape, DNA. Properly folded tRNAs are loaded with the appropriate AA or a precursor that is modified to be correct.

These are then brought into the ribosome under proper manufacturing control and peptide chains are built for further formation into proteins used in cellular processes including this one.

Chicken-egg loops abound, pointing to FSCO/I and islands of function requiring initial manufacture to a design, on pain of fruitlessly, aimlessly wandering in seas of non function and exhausting the blind search capability of the observed cosmos.

At this stage, it is manifest why a design inference on protein synthesis is robust and empirically grounded. As for means:

clever designer[s] + molecular nanotech lab –> clever FSCO/I rich design

Of course, one is free to reject such, but in all responsible fairness needs to provide a cogent, empirically warranted explanation.>>

Such an empirically warranted, blind watchmaker blind chance and/or mechanical necessity explanation remains conspicuously absent, even as agent explanations are ideologically locked out, never mind the significance of LANGUAGE and ALGORITHMS here.

Oh. yes, let me give a simplified overview of the context of protein synthesis:

So, now, we can see the molecular nanotech in action and how it uses a base of Chemical-Physical processes, but we actually have a layer-cake architecture, once code enters as codes are based on arbitrary symbols that have to be decoded on the receiver side of a system. Echoing Yockey as seen above, the general architecture:

A communication system

Thus, we see how we can stack codes and protocols:

In terms of information-processing machines, this layer-cake stack becomes a stack of virtual machines, through which the design of the obvious, physical layer is developed to enable the virtual interactions:

This brings out one of the key underlying fallacies of the dominant evolutionary materialistic scientism ideology: its mind-blindness that leads it to over-emphasise the physical layer, failing to see that that layer is shaped by needs, purposes and considerations relating to design. So, if such is imposed, it invites selectively hyperskeptical lockout of the implications of evidence that shows higher, information, meaning and purpose layers plausibly arising due to language-using agency in action. Where, language reduced to machine code is a manifestation of language at the physical level.

A further error is to then play the ideological, “gold standard” dismissible or even “no evidence” gambit. Having blinkered oneself ideologically, one then is selectively hyperskeptical and dismisses or denigrates inconvenient evidence. Then, the metaphysical question-begging is announced as “there’s no evidence that X . . .” — where, X takes on any inconvenient value.

Later in the thread, we see a case:

[EG, 57:] >>KF

It is noteworthy that algorithmic, alphanumeric code — a linguistic phenomenon — remains stubbornly as only the product of intelligence.

In fact, to the best of our knowledge, it remains stubbornly as only the product of human intelligence.>>

Obviously, the molecular nanotech in the living cell is antecedent to not only human life but cell based life. To this, I therefore responded:

[KF, 59:] >> you know full well that no one takes seriously the notion that we exhaust possibilities for intelligent beings. Looking to linked logic of being, we exemplify intelligence but in no way that implies exhausting it. Therefore the rhetorical gambit to try to suggest that cases of human intelligence forbid us from inferring characteristics of intelligence that could go beyond humans, is nonsense. That this has been used as a common atheistical talking point despite cogent correction only underscores the weakness of the atheistical case. Especially, when the issue on the table is linguistic, algorithmic, alphanumerical code not only antecedent to human life but constitutive of cell based life . . . >>

Attempted piling on:

[JVL, 60 :] >>KF: EG, you know full well that no one takes seriously the notion that we exhaust possibilities for intelligent beings.

But the only intelligent beings we know of that are even close to accomplishing highly sophisticated feats of engineering are human beings. We’ve got no living quarters, no spacecraft, no midden piles, no processing plants, pretty much nothing.

I’m perfectly happy to guess that there are other intelligent beings in the universe but, so far, we have zero evidence they exist. And we certainly have no evidence they have visited Earth.>>

My onward response:

[KF, 61:] >> we are contingent, intelligent, responsible and rational. We exemplify what is possible, we do not exhaust it. So, as you know or should know, it is an abuse of inductive reasoning to infer from our case or to suggest from our case that we exhaust possibilities for such beings. This becomes all the more blatantly fallacious and even desperate when it is used as a rhetorical gambit to try to blunt the evidence that in the heart of the living cell is alphanumeric, algorithmic, linguistic code. And that evidence alone — the evidence of the whole world of cell based life — is striking and has been striking since March 19, 1953. This is not an “isolated”readily dismissed case, we are talking about a central, keystone aspect of cell based life. The rhetorical resort is utterly telling on the force of the evidence and on the ruinous nature of selective hyperskepticism and resulting refusal to entertain the force of evidence. Precisely, what we have now seen live with the “gold standard” fallacy in the face of a pandemic and mounting evidence. So, this is not merely an academic oddity, it is a ruinous error we are dealing with. >>

EARLY U/D: While this OP was being developed, there was another comment:

[JVL, 62:] >>Kairosfocus: So, as you know or should know, it is an abuse of inductive reasoning to infer from our case or to suggest from our case that we exhaust possibilities for such beings.

I’m not, I’m just saying that we have no evidence of such beings except for humans.

The rhetorical resort is utterly telling on the force of the evidence and on the ruinous nature of selective hyperskepticism and resulting refusal to entertain the force of evidence.

Yes but you haven’t been completely successful getting most scientists to agree with your evidence. In the world common forum we’d have to call that disputed at best.>>

The evidence in question is the Genetic Code, as in, a standard term, there for a cause. Where, appeal to one sided “consensus” on a matter of controversy only underscores the need to actually face rather than evade evidence. My response:

[KF, 65:] >> JVL, the “no evidence” gambit is a signature selectively hyperskeptical fallacy. The evidence has been on the table, taught in every school, for coming on two full generations. As Crick noted from the outset, in the form of a belief: ” . . . the D.N.A. IS a code” and that belief was then drawn out in multiple Nobel Prize winning work over the next 20 years. The evidence you are trying to dismiss is the molecular nanotech, prong height [ . . . similar to von Neumann’s kinematic self replicator . . . ] 4-state per symbol code used algorithmically to build proteins, and requiring chicken and egg causal loop molecular nanomachines constituting a von Neuman kinematic self replicator. That is, despite denials and dismissals, LANGUAGE is at the heart of the design for cell based life. That has to be faced as we contemplate the protein synthesis machine code and its dozens of dialects. The repeated attempt to dismiss simply inadvertently underscores the force of the point and how telling it is. >>

Let’s add, an illustration of what a vNSR is like . . . and note, this was proposed in 1948, so for example the tape element and the assembly machinery [where tRNA is a position-arm assembly element that works in the ribosome as an assembly line transfer machine]:

Transfer machines? Oh, lesee again:

Refresher, Ribosome in action:

Step by step protein synthesis in action, in the ribosome, based on the sequence of codes in the mRNA control tape (Courtesy, Wikipedia and LadyofHats)

Oh, but I saved the best for the last. UB replies to EG on the same set of rhetorical stunts:

[UB, 64:] >>#51
Ed, sometimes you just try too hard. It’s a bad look.

Allow me to remind you of something that you seem to forget with incredible regularity. We are all human beings here, Ed. On average we were all pushed and prodded in our youth to develop a lifelong sense of judgement and to make proper distinctions between things like right and wrong, truth and fiction, vice and virtue, and so on, and so forth. It is one of the things that is most common between us, regardless of our cultures, and with any luck, by the time we reach maturity, we end up with a healthy guiding experience of being part of, and watching, human relationships. Among those many common experiences is the experience of someone who simply will not answer a valid question. This is an inevitable experience where not answering the question actually becomes their answer. We understand this predicament and we recognize what it looks like in our human brothers and sisters – with all the denials and the (often flagrant) excuses and the deflections of this and that and the other. What I am getting at here Ed, is that we all know what cookie crumbs in a little boy’s bed actually means, as a very simple example which any parent would understand.

Now Ed, you have been told that a physicist can practice their craft and measure the physical system that enables the use of language. A physicist can measure that system by its necessary physical entailments (and their relationships to one another). A physicist can therefore exclusively identify the use of language among other physical systems, and the gene system has been thus identified. This has been done. Furthermore, you’ve told that the physicists measurement and identification is a confirmation of a previous prediction – a prediction that the gene system would necessarily function by way of encoded language, which is itself an additional confirmation on the very nature of such systems. In other words, Ed, the conclusion that the gene system uses a code (for crying out loud) is a conclusion that comes through science without even a hair out of place.

Having to stoop to “Francis Crick was sloppy” as your next maneuver (to avoid the physics) is therefore quite a sight to see. It makes you look weak, poorly motivated, and as common as you can humanly be, just as non-answers often do. You should probably stop using that excuse.>>

Houston, we’ve got a problem. END

PS: I cannot but give a promotion to a comment by UD newbie (as a commenter . . . by his admission, he’s been lurking for years), Chris Messier, noting also the too often “misunderestimated” BA77’s contribution . . . as in, go read the thread. Chris:

[CM, 12:] >>First of all, thank you to BA77 for all the amazing info I’ve gleaned from your comments over the years. So much of the material you cite is _way_ over my head, but I take what I can manage

DaveS wrote:
“I’m severely underqualified for this discussion, but I wouldn’t mind seeing more detail on this”
I’m also very unqualified, so maybe I can give it a try, since I really like the whole DNA coding-mRNA-tRNA-protein pathway.

If I’m understanding what the author meant,
//There is a point in time and space where an association is made between a codon and an anticodon.//
That is, inside the ribosome the mRNA codon is ‘read’ by a tRNA molecule with the matching anticodon. That’s the first ‘association’.

The next one
//There is also a point in time and space when there is an association made between an anticodon and an amino acid.//
Simply put, that is accomplished by the tRNA molecule. But to get tRNA you need the aminoacyl tRNA synthetases, one for each of the 20 tRNA molecules

An animation of protein synthesis
https://youtu.be/kmrUzDYAmEI

A short one on aminoacyl tRNA synthetases
https://youtu.be/180_sM9iYVk

Two related montages I made. The first one Joe DeWeese covers tRNA
https://youtu.be/sOI5u01LwyQ

The second one Stephen Meyer describes Francis Crick’s elucidating the need for translation of DNA in order to get to proteins, through what he called the ‘adaptor hypothesis’
https://youtu.be/rDLPjxzt1YE>>

PPS: LM, too, is well worth pondering at 11:

[LM, 11:] >>I sometimes want to throw up my hands in exasperation watching you all talk past each other. Let me approach it another way though I don’t expect success.

Let’s return to Sev’s original comment to the OP. (Edited for brevity.)
Seversky@1

Seriously?? You are both denying the material/physical structure and functions of the genome and a computer, that there is no physical chain of events between me pressing the ‘A’ key on my keyboard and the letter ‘A’ appearing on my screen? ….

Yes Sev, there is a nice neat physical chain of events from the ‘A’ key to the pattern of pixels that are displayed on my screen. Odd the pattern I see on the keyboard looks nothing like what shows up on the screen. It’s gone from an upside down ‘V’ with a bar across the middle to a small circle with a bar on the right. Encoded one way, output completely different. We’ll set that aside for just a bit.

Now let’s compare that to the cell. Again what’s happening is physical. There’s a series of DNA bases that when physically read by the right enzyme in the presence of enough of the right kind of amino acids will output a protein. There’s a vague similarity in your example to the transfer of the ‘A’ key (plastic with inlaid white marks) to its unlike ‘a’ (with light and dark pixels).

But wait! We’ve left something out. Who selected the ‘A’ key before pressing it? Why it was Sev. He’s an integral part of the whole process. And who recognized the output as having meaning? Of the thousands and thousands of possible shapes (fonts) that could represent the concept of ‘A’ who recognized ‘a’ as a representative of the concept of ‘A’? I believe that was Sev again!

Who selected those base pairs to represent that particular protein? Don’t you wonder about the Who that is just as much a part of the processes in the cell as the who was that picked that key?

Col. 1:17 He is before all things, and in him all things hold together.>>

36 Replies to “L&FP39: How the folded structure (and then the “loading”) of tRNA corrects attempts to reduce protein synthesis to “mere” chemistry

  1. 1
    kairosfocus says:

    How the folded structure (and then the “loading”) of tRNA corrects attempts to reduce protein synthesis to “mere” chemistry

  2. 2
    daveS says:

    KF,

    Just so I’m clear, you’re saying that the origin of this system is not due simply to chemistry, correct?

    Not that there’s anything ‘supernatural’ going on in the day-to-day functioning of this system.

  3. 3
    kairosfocus says:

    DS,

    what is going on minute to minute in our bodies is a highly automated, self replicating, information using process based on molecular nanotechnology. These processes are of a level of sophistication that dwarfs our own primitive information and communication technology. The process is not magic, it is a highly integrated systems technology founded on physical structures, forces and processes.

    As this involves a vNSR, it is inherently full of chicken-egg loops and FSCO/I implying deeply isolated islands of function in vast configuration spaces utterly beyond the plausible blind search capability of the observed cosmos. That FSCO/I in this case involves coded information, a linguistic phenomenon. The only actually observed source for FSCO/I is intelligently directed configuration . . . which here includes cases such as beaver dams and some animal nests etc.

    Codes and languages have only language-using intelligence as an empirically warranted plausible source.

    In that context, as I have pointed out [echoing all the way back to the pioneers of modern design theory and bringing out Plato’s contrast: nature vs ART-ificial, as opposed to supernatural] such plausibly can be explained on molecular nanotech some generations beyond Venter et al. This is also found in the UD Weak Argument Correctives, a standard backdrop for any discussion at UD.

    I have also frequently suggested that within a century we will likely be able to create de novo cell based life, we are already at threshold for vNSRs.

    So, the suggestion of a natural/supernatural dichotomy as primary reference is fallacious: from c 360 BC phusis vs techne has been on the table.

    Where the issue of a designer beyond the cosmos is on the table is the point where we find that the observed cosmos sits at a deeply isolated operating point that supports C-chem, aqueous medium cell based life, starting with element abundances and linked particle/nuclear processes.

    KF

  4. 4
    daveS says:

    KF,

    Thanks, that answers my question.

  5. 5
    awstar says:

    Per Crick’s letter:
    “You can now see how Nature makes copies of the genes. Because if the two chain unwind into two separate chains, and if each chain then makes another chain and come together on it, then because A always goes with T, and G with C, we should get two copies…”

    You might be able to rationalize that Nature is just using chemistry if it’s just matching A with T and G with C, but when you look at the process of making it happen, it screams DESIGN!!! Just watch any youtube video on Okazaki fragments and you cannot believe it’s just chemistry any longer.

    From Khan Academy: Molecular mechanism of DNA replication

    DNA polymerases can only make DNA in the 5′ to 3′ direction, and this poses a problem during replication. A DNA double helix is always anti-parallel; in other words, one strand runs in the 5′ to 3′ direction, while the other runs in the 3′ to 5′ direction. This makes it necessary for the two new strands, which are also antiparallel to their templates, to be made in slightly different ways.

    One new strand, which runs 5′ to 3′ towards the replication fork, is the easy one. This strand is made continuously, because the DNA polymerase is moving in the same direction as the replication fork. This continuously synthesized strand is called the leading strand.

    The other new strand, which runs 5′ to 3′ away from the fork, is trickier. This strand is made in fragments because, as the fork moves forward, the DNA polymerase (which is moving away from the fork) must come off and reattach on the newly exposed DNA. This tricky strand, which is made in fragments, is called the lagging strand.

    The small fragments are called Okazaki fragments, named for the Japanese scientist who discovered them. The leading strand can be extended from one primer alone, whereas the lagging strand needs a new primer for each of the short Okazaki fragments.

  6. 6
    kairosfocus says:

    AW, an interesting point, though of course Crick was there talking about replicating the DNA. Some of that is antecedent to making mRNA, the control tape for the Rhyzome transfer machine used to make proteins. The OP is mainly about the position-arm device, tRNA and how it is loaded. Notice, especially the H Pylori workaround of misloading with a related AA then chemically modifying to the true target. Think about what that suggests could be done! KF

  7. 7
    Barry Arrington says:

    KF
    You quote Crick: “D.N.A. is a code.” (emphasis in the original). The emphasis on “is” must be fatal to the “it’s just a sloppy analogy” crowd (are you listening JVL and Ed?). He did not say “D.N.A. is like a code.” He did not say “D.N.A. is analogous to a code.” By emphasizing “is,” he clearly meant to say that D.N.A. is the same thing as encoded language. Nor was he the last to recognize the obvious. Even arch-atheist Richard Dawkins is more honest than Ed George and JVL and Ortho: “Each nucleus … contains a digitally coded database larger, in information content, than all thirty volumes of the Encyclopedia Britannica.”

  8. 8
    Barry Arrington says:

    Orthomyxo says he cannot understand the straightforward demonstrations KF provides. His inability to understand this demonstration is certainly incongruous (to say the least) with his cocksure certainty that it is nothing but chemical reactions all the way down. It is as if he said, “No, I can’t understand a high school level demonstration of how DNA works. But I am utterly certain I know how DNA works.”

  9. 9
    Pater Kimbridge says:

    So, folding is not chemistry?

  10. 10
  11. 11
    kairosfocus says:

    PK, strawman. Go to the just linked or scroll up and notice the gen comms model. Notice the bridge CODE-DECODE, and the expansions into the now commonplace layer-cake comms models such as TCP/IP. Observe, too, how above a similar layered model obtains for modern computers. In that light, look at Yockey’s application of the telecomms architecture model from Shannon et al. A common point is that there’s a lot more to an information and communication system than physical hardware and its specifically physical interactions. It is organised per an architecture designed to foster communication through codes and protocols, where info processing has the further aspect of data structures and algorithms; along with, fetch, decode, execute. Surely, you are familiar with hardware/software partitioning and the idea of levels of languages and programs. Notice, hardware, software, [coherent, structured, functional, systematic]organisation, architecture. In that context, D/RNA provides string data structures, some of which are used for protein synthesis, through the tape controller mRNA. tRNA acts as a position-arm unit and the OP discusses how its CCA tool tip for loading AAs is the point where the code is brought down to the machine level for building peptide chains for proteins in the molecular nanotech transfer machine we call the ribosome. Where, the overall entity is a von Neumann Kinematic Self Replicator. In this context, coded algorithms stored in the string data structures manifest language and goal-directed — purposeful — procedure. Those are strong signs of intelligently directed configuration. KF

  12. 12
    Pater Kimbridge says:

    KF, I’ll see your strawman, and raise you a word-salad snowstorm smokescreen Gish-gallop.

  13. 13
    kairosfocus says:

    PK, doubling down, compounded with projection and dismissive obscurantism. If you are unaware of and/or unwilling to engage relevant systems architecture issues then all you can do is posture with empty rhetorical gambits. KF

  14. 14
    doubter says:

    It seems to me that the import of all of this fascinating microbiological process can boil down to a very much simpler electromechanical analogy. Say one of the old IBM ball-type electric typewriters. Each keystroke on the keyboard is processed electromechanically to convert the keystroke into electrical impulses that are processed by electronic digital logic into rotational positioning commands for the type ball to go to the position for the commanded letter, followed by electromechanical positioning of the ball for the commanded letter position on the page, then electromechanical actuation of the ball to impress the letter on the paper, followed by advance of the ball to the next letter position, and so on through the document.

    Overall, this is an information-rich logically designed process which (starting with the input of the meaningful character string) can’t be reduced to the physics of the individual electronic and mechanical steps of the process. The logical design information has some other source, namely conscious intelligence. But each step in this overall process past the key actuation itself is indeed reducible to an electronic and/or mechanical principle or law. So, reducibility to law-like behavior of matter and energy is no indication whatsoever of the origin of the design of the overall mechanism that employs these principles. This origin lies in an entirely different and higher realm of existence, namely conscious intelligence.

  15. 15
    Belfast says:

    PK,
    Kairosfocus has found you an argument.
    He is not responsible for your understanding of it.

  16. 16
    kairosfocus says:

    D, and that functional organisation is expressed in a system architecture that guides the specific details and interaction of a selectric type “golfball” typewriter. It is architecture that we are looking at. KF

  17. 17
    daveS says:

    One reason I asked about whether the “day-to-day functioning” of this system is just chemistry/physics is that in the other thread, there is a lot of discussion about how there is an abstract “language” behind all this purely physical machinery.

    If we’re talking about things such as formal languages (e.g., the set of all bit strings of finite length), then that makes sense to me. Some formal languages can be recognized by a purely mechanical device.

    But this language lurking in the background must be very different from natural human languages, correct? I wouldn’t expect many ID proponents to believe that an arrangement of molecules would be able to interpret the English language, for example.

  18. 18
    Barry Arrington says:

    Pater Kimbridge

    So, folding is not chemistry?

    Utterly devastating. How could KF ever even hope to counter your scintillating application of logic and the piles of evidence you’ve amassed?

    Well, KF gave it a go at comment 11.

    You counter at comment 12:

    word-salad snowstorm smokescreen Gish-gallop

    Good heavens man! Do you stay up nights crafting these responses? This is the stuff of doctoral dissertations. What am I talking about? I don’t know who you are of course. But with the ability to craft arguments like that, I’m assuming you already have a doctorate in molecular biology. I frankly don’t see how KF will ever be able to hold his head up again. With 11 simple words you have utterly destroyed him. Bravo sir. Bravo.

  19. 19
    jawa says:

    KF and BA,

    Perhaps your always-objecting interlocutors don’t understand KF’s clear explanation in this OP, simply because they don’t want to understand it.

    Any argument you present could help the anonymous readers to understand the discussed topic, but it may not make even a tiny scratch in the “denying” attitude of your stubborn interlocutors. That’s why they seem to behave like trolls.

    It has nothing to do with poor reading comprehension or insufficient education. It’s lack of wisdom, required to become a genuine truth seeker.

  20. 20
    jawa says:

    The DNA it’s a library of different codes:
    1. GCAT-based 3-character code that is transcribed to pre-mRNA, spliced time mRNA and translated to aminoacids by the ribosomes in combination with the tRNAs and aaRS to form proteins.
    2. GCAT-based code that is transcribed to ncRNA that is used as components of cellular machinery or as regulatory signals.
    3. GCAT-based code for promoter regions, enhancers, TF-binding sites, etc.

    Outside the DNA there are epigenetic markers and histone code that are used to regulate the cells.

  21. 21
    kairosfocus says:

    DS, kindly, note the way that both hardware and software are involved, along with an architecture that drove the organisation and facilitates the programmed action. Software implies language, which is as real — constraining how being works, here — as numbers are. So the reductionism that ideologically blinds itself to the codes, data structures, explicit and implicit information, functional organisation and architecture in this case is an example of selective hyperskepticism; reflecting a common anti-mind mentality that haunts our age. We know how information processing, communicating machines and systems work and that is at work in this case also. It is time to take off ideological blinkers. KF

    PS: Programming languages, especially at machine level, are different in many ways from natural, fully street functional languages. That is a commonplace, part of why they are difficult to learn and work with. That does not change their core, linguistic character and import. Namely, they are an exceedingly strong sign of language using, purposeful, highly logical, systematic, designing, high IQ, deeply knowledgeable intelligence at work.

  22. 22
    kairosfocus says:

    Jawa, sadly yes and of course yes, respectively. KF

  23. 23
    kairosfocus says:

    BA, I guess your sarcasm overloaded your satire, you need to study Babylon Bee some more; tut, tut. And, oh, yes, PK’s resort to “Gish Gallop” as a dismissive term bakes in willful slander into his mindset Internet atheist-trolls who imagine themselves to be oh so bright and tells us that he is coming from the soap boxes of today’s equivalent to the village atheist of old. So, meet the ever-resentful Internet Atheist-troll from the fever swamps, shedding destructive mind-virus particles with every wag of his — overwhelmingly, his — tongue. There is a principle that holds doubly for those not here to defend themselves: your right to freely wag your tongue ends where my reputation begins. With that resort, PK consigned his credibility allowance to the dustbin. KF

  24. 24
    kairosfocus says:

    PK, in case you did not see my comment to DS, tRNA etc composition, synthesis and folding involve chemistry and physics but is not nothing-buttery reducible to such. If your ideology not only leads you to bake in slander and hyperskepticism but blinds you to the significance of systems architecture, functional organisation and requisites of cybernetics, then it is undermining your ability to think straight. As it is, your stunts above have shredded any remnants of credibility granted under duty of charity. Baking in slander as you did, does that. KF

    PS: I take a leaf from BA77’s book, and give scripture. Here, context that draws out a lot of the force of the neighbour-love principle:

    Lev 19:11 ‘You shall not steal, nor deal deceptively, nor lie to one another. 12 You shall not swear [an oath] falsely by My name, so as to profane the name of your God; I am the Lord.

    13 ‘You shall not oppress or exploit your neighbor, nor rob him. You shall not withhold the wages of a hired man overnight until morning. 14 You shall not curse a deaf man nor put a stumbling block before the blind [–> a fortiori, including the metaphorically blind or deaf], but you shall fear your God [with profound reverence]; I am the Lord.

    15 ‘You shall not do injustice in judgment; you shall not be partial to the poor nor show a preference for the great, but judge your neighbor fairly. 16 You shall not go around as a gossip among your people, and you are not to act against the life of your neighbor [with slander or false testimony]; I am the Lord.

    17 ‘You shall not hate your brother in your heart; you may most certainly rebuke [–> others: reason frankly with] your neighbor, but shall not incur sin because of him. 18 You shall not take revenge nor bear any grudge against the sons of your people, but you shall love your neighbor (acquaintance, associate, companion) as yourself; I am the Lord. [AMP]

  25. 25
    awstar says:

    KF @ 6

    AW, an interesting point, though of course Crick was there talking about replicating the DNA. Some of that is antecedent to making mRNA, the control tape for the Rhyzome transfer machine used to make proteins. The OP is mainly about the position-arm device, tRNA and how it is loaded.

    Understood. What I tried to do was relate to those like me, who seem to have an attention deficiency due to lack of brain capacity and lack of patience, resulting in skimming over long presentations to get to the quick of it.

    It seems to me that the quick of it is that Chemistry is not Biology. Biology is more like an engineering discipline that is more concerned with purpose, design and information than it is with the physical processes of grouping molecules together.

    In studying the replication process of DNA, even a Chemistry 101 student can see that Chemistry is not Biology when shown how Nature makes something that ought to be relatively easy to do and turns it into something very elaborate, complex and sophisticated in order to insure it’s purpose is accomplished. And its purpose in replicating the DNA is to insure high degrees of accuracy as well as speed, because the continuation of life depends on it. Something we all could do better at emulating — especially me.

  26. 26
    daveS says:

    KF,

    kindly, note the way that both hardware and software are involved, along with an architecture that drove the organisation and facilitates the programmed action.

    Those are the terms I was searching for. Clearly there is hardware, but how do we know there is software? How do we know that this physical system was deliberately designed to “execute” abstract instructions? That’s an inference.

    Of course you have a rationale for making this inference, but that’s the question I have been trying to ask.

  27. 27
    kairosfocus says:

    DS,

    I could flippantly suggest, ask Bill Gates.

    However, hardware/software (and firmware between) partitioning is an old Micro-kids vs Hardy Boys debate. Hardware is tangible, software is informational and intangible. The DVD is hardware, the software is stored in its configuration, in part. Where, hardware configuration insofar as it reflects selection across alternative configurations, implies information content. ALL hardware thus embeds some software aspects, tied to their functionally constrained coherent configuration. However, certain hardware is chosen for its information storing, transfer or retrieval capability.

    This is closely tied to . . . surprise [not?] . . . the logic of structure and quantity.

    Mathematical aspects.

    Where, you probably know my recent short paper [thanks, JB!] in which I pointed out a candidate solution to the Wigner paradox: structure and quantity matters are not directly causal but reflect constraints on logic of being.

    Where, information is a manifestation of structure and quantity that is used to remove uncertainty, specify state, expres or store or transfer messages or signals or data, indicate or prescribe action, provide feedback, actuate action, provide warrant etc. Unsurprisingly, it can be measured on various scales, depending on what is of interest. WLOG, organisation and information — to in principle arbitrary precision — can be described or specified across a span of alternatives, by an efficient structured chain of Y/N questions, naturally leading to number of bits-in-context as a family of metrics. (For simple example, ponder AutoCAD and DWG files.)

    In the case of D/RNA, we have string structures in a family of molecules yielding a contingent prong-height mechanism to store information, at up to 2 bits per base on a GCAT/U chain. That is similar to a Yale-type lock, and to von Neumann’s proposal for the vNSR. Of course, the carrying capacity and actual information vary due to redundancy effects.

    In that context, we can and routinely do measure information content, similar to how we may measure energy [another intangible] based on actual or potential effects.

    In an information age, that is not in serious doubt, and apart from rhetorical convenience, it is not in doubt that D/RNA carries coded digital information.

    But how do we conclude that such plausibly comes from design?

    First answer, beyond 500 – 1,000 bits, do we routinely or even just reliably see it coming about by blind chance and mechanical necessity? Blatantly, not. Meanwhile there are trillions of cases of intelligent cause. Where, this is backed by search challenge for large config spaces. All of which is familiar — and factual.

    Where we see FSCO/I we are inductively entitled to infer design., for cause as just outlined.

    The problem is not the strength of the argument — trillions to zero with a ready analysi8s of why — but that this cuts across entrenched interests and deeply stamped paradigms.

    KF

  28. 28
    jawa says:

    Note that this Nobel Prize scientist predicted back in 1967 that cells could be programmed.

    Will Society Be Prepared?

    By Marshall W. Nirenberg

    Science  11 Aug 1967:
    Vol. 157, Issue 3789, pp. 633
    DOI: 10.1126/science.157.3789.633

  29. 29
    jawa says:

    Cracking the regulatory code
     

    How does the same DNA sequence, present in almost every cell in the body, give rise to diverse tissues that have distinct functions?

    genetic variants that drive inter-individual differences in complex traits, including disease, are often found in non-protein-coding regions of the genome that might determine how and when genes are expressed.

     move beyond descriptive work to an understanding of the actual mechanisms that underlie gene-regulatory programs

    factors affecting gene expression (for example, chromosome accessibility, transcription-factor binding and the modification of DNA by methyl groups)

    Genetic variants can affect aspects of the gene-regulatory cascade other than levels of RNA

    The rate of gene transcription, the mechanism of RNA processing and the rate of translation are three such examples.

  30. 30
  31. 31
    daveS says:

    KF,

    I could flippantly suggest, ask Bill Gates.

    What do you think he would say? I’d ask him, but he never replies to my emails.

  32. 32
    kairosfocus says:

    DS, Microsoft is the summary of his answer. KF

  33. 33
    daveS says:

    Coincidentally, that’s the punchline of a joke explaining Melinda Gates’ disappointment after their honeymoon. :rimshot:

  34. 34
    jawa says:

    Dynamic control of endogenous metabolism with combinatorial logic circuits

    Controlling gene expression during a bioprocess enables real-time metabolic control, coordinated cellular responses, and staging order-of-operations. Achieving this with small molecule inducers is impractical at scale and dynamic circuits are difficult to design. Here, we show that the same set of sensors can be integrated by different combinatorial logic circuits to vary when genes are turned on and off during growth. Three Escherichia coli sensors that respond to the consumption of feedstock (glucose), dissolved oxygen, and by-product accumulation (acetate) are constructed and optimized. By integrating these sensors, logic circuits implement temporal control over an 18-h period. The circuit outputs are used to regulate endogenous enzymes at the transcriptional and post?translational level using CRISPRi and targeted proteolysis, respectively. As a demonstration, two circuits are designed to control acetate production by matching their dynamics to when endogenous genes are expressed (pta or poxB) and respond by turning off the corresponding gene. This work demonstrates how simple circuits can be implemented to enable customizable dynamic gene regulation.

    “combinatorial logic circuits” in biology?
    Nah, that can’t be right, because biology is all chemistry. 🙂

  35. 35
    jawa says:

    Design of fast proteolysis-based signaling and logic circuits in mammalian cells

    Cellular signal transduction is predominantly based on protein interactions and their post-translational modifications, which enable a fast response to input signals.

    Owing to difficulties in designing new unique protein–protein interactions, designed cellular logic has focused on transcriptional regulation; however, that process has a substantially slower response, because it requires transcription and translation.

    Here, we present de novo design of modular, scalable signaling pathways based on proteolysis and designed coiled coils (CC) and implemented in mammalian cells.

    A set of split proteases with highly specific orthogonal cleavage motifs was constructed and combined with strategically positioned cleavage sites and designed orthogonal CC dimerizing domains with tunable affinity for competitive displacement after proteolytic cleavage.

    This framework enabled the implementation of Boolean logic functions and signaling cascades in mammalian cells.

    The designed split-protease-cleavable orthogonal-CC-based (SPOC) logic circuits enable response to chemical or biological signals within minutes rather than hours and should be useful for diverse medical and nonmedical applications.

    Designed cellular Boolean logic circuits in biology?

    Nah, that can’t be right.  Biology is all chemistry.

  36. 36
    daveS says:

    KF,

    One point concerning your paper, the part about constructing the real numbers from power series: I believe you would want to consider power series whose sequence of partial sums is Cauchy rather than convergent. For example, a power series which has a sum of sqrt(2) (for a particular x in Q) doesn’t converge in Q. However, such a power series is one representative of a class of series which you can define to be sqrt(2).

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