Checking back in. Nothing has changed. Not a person here is willing to address the system as it physically is – instead, everyone immediately rushes to go on defense and change the subject. This issue is not about what anyone thinks came before the existing system; it is not about how it came into being — it is only about the physics of the system as it is.
It’s a simple thing. In order to self-replicate, the living cell must specify itself among alternatives. To that end, when DNA is used to control protein synthesis, it relies on a code to convey that specification. A system of physical constraints (aaRS) are required to establish the genetic code, and they themselves are specified and constructed from gene sequences using that same code. Thus, those sequences that specify the constraints must be coordinated with one another in order to achieve function (self-reference, closure). There is nothing about this that is the slightest bit controversial. Dan himself posted a link to a paper that reaffirms what has been widely known for more than half a century: “Storage and directed transfer of information is the key requirement for the development of life. Yet any information stored on our genes is useless without its correct interpretation. The genetic code defines the rule set to decode this information. Aminoacyl-tRNA synthetases are at the heart of this process”. Moreover, this organizational requirement was predicted by John Von Neumann in 1948 using Alan Turing’s logic of a programmable system of symbols, and the correct physical implementation of the system was predicted by Francis Crick in 1955 and confirmed by Hoagland and Zamecnik shortly thereafter. Furthermore, physicists and systems scientists have confirmed protein synthesis is “rate-independent control of a rate-dependent process”, that is, a system using symbolic tokens of memory (codons) and a set of non-holonomic constraints (aaRS) to establish open-ended control over the construction of proteins. And as already noted, a segment of biologists (including significant luminaries in the field) have openly acknowledged the reality of symbolic control; indeed an entire discipline has risen around it.
My opening comment on this thread was that the public is often mis-led by scientists and science popularizers who speak about the origin of life and suggest a self-replicating RNA can not only act as a catalyst but can also convey information like DNA. But a self-replicating RNA does not establish the coordinated set of constraints required to convey information like DNA. A self-replicating RNA does not establish rate-independent control of a rate-dependent process.
And for the offense of knowing these facts and speaking of them here, I have been positioned by the moderators as an uninformed and disrespectful menace, as everyone else jumps to defend their personal assumptions – that is, defend their assumptions from valid experimental results and the recorded history of science. The attempts to change the subject have been non-stop, and the display of pedantry is just over the top.
The territorial lines seem fairly well drawn. The house thinks that the symbolism in the gene system is just a convenient metaphor, while the actual physics and history of science demonstrate otherwise. Indeed, it is the fundamental requirement of the system.
I told Mercer that under his views (which prominently features the complete denial of evidence and history) he would be so handicapped that he could not even know that the computer he is typing on uses a system of symbols – i.e. he could only claim it uses symbols because he knows in advance that a human built it that way, but he has otherwise thrown out any method of measuring the system to empirically demonstrate the symbolism. He would then be left with nothing to press forward but his doctrinaire insistence as his evidence. And lo and behold, he did just exactly that. First he tells me “I know that there are many codes, symbolic and/or abstract, in computing” and then eventually (after a never-ending screed of insults) he ends up telling me how “seriously” he is taken in science; after all, he is a man of 42 publications and has been awarded $6 million dollars in grants! I would certainly never begrudge a man or woman for enjoying some success in their chosen field, but what is amazing to me is that he (as an empiricist) thinks he can (more or less) brow-beat me into relinquishing to his authority – in place of documented empirical results and recorded history to the contrary. For me, that is a non-starter. I can tell Mercer exactly what rate-independent control is and how it is implemented in the gene system, while he shakes his fist and demands an “abstraction” – a term he neither defines nor puts into service to make any point whatsoever. The purpose of the demand is to avoid the evidence, not engage it in earnest. He reminds me of a somewhat obscure singer-songwriter of the 70’s named Ricki lee Jones. She wrote a lyric “Take a deep breath and break the chain.” That ain’t going to happen with Mercer. His approach to the evidence and history won’t change one iota – it’s all wrong. Von Neumann was wrong. Charles Sanders Peirce was wrong. Brenner was wrong. Pattee is wrong. Anyone who says that a symbol system can be identified by physical measurement is wrong. They are all wrong.
Likewise, Rumraket has spent the entire thread trying his absolute best to misunderstand the issue. As I have said over and over again, DNA conveys information by virtue of codons (symbolic tokens of memory) which are established by a system of non-holonomic constraints operating in the system. It is this system that enables the living cell with open-ended evolutionary potential (where the system can freely specify any protein, or any variation of any protein). This is rate-independent control over the rate-dependent process of protein construction. In stark contrast, a self-replicating ribozyme is a purely dynamic object, and does not establish this rate-independent control over anything. Rumraket then goes on to make explicit the very point I have been making all along. He says: (when OoL people talk about a self-replicating ribozyme being able to convey information like DNA) “they speak about its capacity to function as a template for its own replication”. Yes exactly!! But “functioning as a template for its own replication” occurs in a completely dynamic (rate-dependent) process – which has nothing in common with the (open-ended) rate-independent conveyance of information from a sequence of codons in DNA.
Then there is Roy. Please allow me to give you a couple of statements. The first of these statements will be yours:
#1 Roy: “Which codons lead to the attachment of which amino-acids is established by the set of tRNA molecules that are present.”
#2 “The aminoacyl-tRNA synthetases are an essential and universally distributed family of enzymes that plays a critical role in protein synthesis, pairing tRNAs with their cognate amino acids for decoding mRNAs according to the genetic code.” – published in the journal of The RNA Society
Here’s another:
#3 “Aminoacyl-tRNA synthetases (ARSs) are essential and ubiquitous ‘house-keeping’ enzymes responsible for charging amino acids to their cognate tRNAs and providing the substrates for global protein synthesis.” – published in the Nature
…and another:
#4 “The accurate synthesis of proteins, dictated by the corresponding nucleotide sequence encoded in mRNA, is essential for cell growth and survival. Central to this process are the aminoacyl-tRNA synthetases (aaRSs) … The aaRSs are essential for coupling the correct amino acid and tRNA molecules” – published in FEMS Microbiology Review
Notice the difference?
tRNA do not establish the genetic code, the aaRS do that. Those aaRS are proteins, and as such, they are specified among alternatives by a corresponding set of genes. For any of those genes to function, they all have to exist in a coordinated state.
By the way, endless pedantry is usually an ugly defense.
Oddly enough he is not. In fact, Pattee generally eschews some of the language and concepts used by many biosemioticians. Pattee was basically drafted into the biosemiotician’s project because of his physical analysis of the gene system, but he finds much of their language and concepts to be hopelessly ambiguous and ultimately useless to his work. His goal was to understand the appearance of symbolic control at its most primitive level, and therefore he considers a good portion of their work to be tied to the wrong end of a 4 billion-year evolutionary timespan. I remember once reading the correspondence among a group of highly-placed semioticians, with Pattee among them. There was a point where one of the lead organizers of the group, Italian embryologist Marcello Barbieri, called out Pattee. Apparently Pattee, (I can’t recall the details off the top of my head) had used a particular term in one of his papers that (more or less) offended the sensibilities of some the biosemioticians on board. Pattee reminded Barbieri and the group that he defined his terms in the language of physics, and so … (that’s that). But it was an interesting juxtaposition, with the physicist who avoids the ambiguous language of the semioticians, being confronted for using terms that he supports with appropriate physics.
… and on that note, there is still no one on this thread that will acknowledge that my observation is correct. Speaking about the OoL and suggesting that a self-replicating RNA can both serve as a catalyst and also carry genetic information like DNA is not only factually incorrect, but it is wildly misleading to not mention that all the RNA self-replicator needs to do to convey information like DNA is to first solve the biggest mystery in biology – the origin of symbolic control over dynamics. But no one here is going to acknowledge that is the truth of the matter, even though it is sharply established by prediction, confirmation via experiment, and unambiguous physical analysis. Therefore I would suggest that it is not my “arrogance” that has been on supreme display in this thread, it is that of the forum participants and moderators. In the end, none of that matters because the physics of the system is not going to change.
Yes Dan, I bet you have.