how to calculate the evolution of a protein

[scruffy]

That's amazing!

It's all pretty amazing.

 

[scruffy]

Was the first DNA strand fully formed and just waiting for its perfect protein Tinder match?

We don't know.

Here is a great database of interactions between amino acids and nucleotides.

AANT: the Amino Acid-Nucleotide Interaction Database - PubMed

We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these...

pubmed.ncbi.nlm.nih.gov

There are mixed polymers, some of which are currently under investigation.

Here is more information:

https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.202200048

 

[scruffy]

For Sherlock Holmes

Sources:

Peptide bonds in water

Google Scholar

scholar.google.com

Biopolymers 45:351 (1998)

"Tends to zero", highly favoring monomers

And out of water:

From interstellar amino acids to prebiotic catalytic peptides: a review - PubMed

Amino acids were most likely available on the primitive Earth, produced in the primitive atmosphere or in hydrothermal vents. Import of extraterrestrial amino acids may have represented the major supply, as suggested by micrometeorite collections and simulation experiments in space and in the...

pubmed.ncbi.nlm.nih.gov

Air-water interface:

https://www.pnas.org/doi/full/10.1073/pnas.1210029109

The preparation and condensation polymerization of higher alkyl esters of alpha-amino acids - PubMed

The preparation and condensation polymerization of higher alkyl esters of alpha-amino acids

pubmed.ncbi.nlm.nih.gov

Spontaneous formation of polypeptides in the interfacial thin films of amphiphilic amino acid esters: acceleration of the polycondensation and control of the structure of resultant polymers - PubMed

For the purpose of elucidating the effects of molecular arrangements on the reaction rates and the structure of products, polycondensation of long-chain esters of alpha-amino acids in the monolayer on the water surface and the LB multilayers deposited on CaF2 plates were investigated by...

pubmed.ncbi.nlm.nih.gov

Proximity effects in monolayer films: kinetic analysis of amide bond formation at the air-water interface using (1)H NMR spectroscopy - PubMed

The kinetics of amide bond formation in a monolayer film has been studied by proton NMR spectroscopy. Compression of a hexadecyl thioester of N-acetyl glycine (1) and a hexadecyl amide of glycine (2) at the air-water interface produces a single dipeptide product (4) that remains at the surface...

pubmed.ncbi.nlm.nih.gov

Google Scholar

scholar.google.com

Kinetics and effect of copper ions:

In situ observation of peptide bond formation at the water–air interface

We report unambiguous spectroscopic evidence of peptide bond formation at the air–water interface, yielding a possible mechanism providing insight into the formation of modern ribosomal peptide bonds, and a means for the emergence of peptides ...

www.ncbi.nlm.nih.gov

Google Scholar

scholar.google.com

Google Scholar

scholar.google.com

Cobalt works too

The formation of peptide bonds in the coordination sphere of cobalt(3) - PubMed

The formation of peptide bonds in the coordination sphere of cobalt(3)

pubmed.ncbi.nlm.nih.gov

Google Scholar

scholar.google.com

Spectroscopic evidence

Google Scholar

scholar.google.com

Google Scholar

scholar.google.com

Peptide bond formation methods and probability

https://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/peptide-synthesis.html

Chemical Methods for Peptide and Protein Production

Since the invention of solid phase synthetic methods by Merrifield in 1963, the number of research groups focusing on peptide synthesis has grown exponentially. However, the original step-by-step synthesis had limitations: the purity of the final product ...

www.ncbi.nlm.nih.gov

https://core.ac.uk/download/pdf/162922599.pdf

https://dspace.spbu.ru/bitstream/11701/14763/1/__Chemistry_of_Peptide_Synthesis.pdf

Alpha helix formation:

The axis on the left is probability:

https://www.researchgate.net/figure/The-probability-of-the-polypeptide-to-form-an-intact-alpha-helix-as-a-function-of-its_fig4_236939977

The Google scholar ones are pdf's, you'll have to be patient while they download.

 

[zaangalewa]

There is no clear problem statement here, only vague ideas like "trying to build" and "proper spelling sequence" and "right meaning".

The "word problem" is a problem of determining whether two data structures are "equivalent" - that's what the problem is, "are these equivalent" - a question.

You've posted a verbose and meandering "lecture" here, with no clear explanation of what this has to do with protein synthesis, an activity that has nothing to do with the word problem.

You talk of nested stack automatons, but these abstractions (stacks) do not exist in the natural world, they are human inventions (created by intelligent minds) that have no natural analog just as there's no analog for tree organized information (DNA is a chain) or any number of abstractions from finite state machine to push down automatons.

So what on earth is your post about other an attempt to feign erudition and "solve" a "problem" that isn't even clearly stated?

So start again, we have an alphabet of 26 symbols, well what of it? how many total symbols do we have 10? 1,000,000? what are we meant to do with a set of symbols randomly taken from some large set of symbols? lets imagine a huge set of Scrabble tiles, each of which can be any of the 26 letters, what exactly is the problem we are striving to solve here?

I've designed and built programming languages, so I'm no novice to the overall problem domain and symbols, patterns, rewriting rules and so on.

Most recently I designed a grammar using Antlr that can parse stuff like this without problems:

if then = if then
if = else
else goto = then

That is the language has NO reserved words, any word - even a keyword - can be used as a variable name, and one can write code in any number of human dictionaries like English, German and so on, so please don't try to fool me with your mumbo jumbo.

View attachment 1002262

Each of those (and a language-agonistic tool can transform these from one language to another automatically) produces a structurally identical parse tree, there is no other programming language that supports that ability. There is nothing in nature that is equivalent to a digital computer - AKA - symbol manipulator.

It exists no program language which is using "German". We use in such cases the English language. The "German" text sounds totally stupid in German. So where from do you have such an idiocy? From an AS (=artificial stupidity program)?

Program languages are not really a language. It are mathematical constructs how to use whole number artithmetics, how to interpret such numbers in different contextes and what to do with the results. They follow a linear or parallel time structure step by step. I do not think this "program" is transferable into a code which a machine is able to use. A compiler wouldn't know where is the entry code for "place" or "retour". And what could be "X"? And what for heavens sake could be any result or output of this "procedure". This text is just simple nonsense.

 

[CrusaderFrank]

We don't know.

Here is a great database of interactions between amino acids and nucleotides.

AANT: the Amino Acid-Nucleotide Interaction Database - PubMed

We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these...

pubmed.ncbi.nlm.nih.gov

There are mixed polymers, some of which are currently under investigation.

Here is more information:

https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cbic.202200048

We don’t know?

But all we “know” is that these amazingly precise systems “evolved” independently from atoms and molecules with no interest or predilection toward any particular outcome, right?

See how bizarre that sounds?

 

[scruffy]

We don’t know?

But all we “know” is that these amazingly precise systems “evolved” independently from atoms and molecules with no interest or predilection toward any particular outcome, right?

See how bizarre that sounds?

Yes, it's bizarre because it's untrue.

Of COURSE attractors exist. Chickens, foxes, corn. All dynamic systems have attractors.

 

[CrusaderFrank]

Yes, it's bizarre because it's untrue.

Of COURSE attractors exist. Chickens, foxes, corn. All dynamic systems have attractors.

But we're talking about the imaginary force of "evolution", right?

 

[Sherlock Holmes]

It exists no program language which is using "German". We use in such cases the English language. The "German" text sounds totally stupid in German. So where from do you have such an idiocy? From an AS (=artificial stupidity program)?

The German dictionary is simply a beta version, to show the proof of concept. The language has no reserved words by design and because of that we realized that it automatically could use different keyword dictionaries so we experiment and found that it was true. This was not a required capability, it just "fell out" as low hanging fruit from the grammar.

There are other programming languages that use multiple keyword vocabularies, here's another.

Program languages are not really a language. It are mathematical constructs how to use whole number artithmetics, how to interpret such numbers in different contextes and what to do with the results. They follow a linear or parallel time structure step by step. I do not think this "program" is transferable into a code which a machine is able to use. A compiler wouldn't know where is the entry code for "place" or "retour". And what could be "X"? And what for heavens sake could be any result or output of this "procedure". This text is just simple nonsense.

It looks that way to you, but that is not the case. The grammar supports this feature and the code samples parse without problems. You should gather facts before jumping to conclusions. Those samples are tests for the grammar, the grammar is the rules of the language's syntax. The grammar is written in Antlr 4. That is a very powerful parsing technology, the grammar (once stable) can be consumed by an Antlr tool and that generates the parser for you, in a choice of language, Java, C++ or C#.

The Antlr-4 parser tools are extremely powerful, it uses an unlimited lookahead in order to resolve ambiguities, this is what makes it possible to have no semicolons, and makes it possible to have literal constants like this:

See 'base_address'? The literal value can be written flexibly, in this case it's a hex constant 0000 1F00 C000 0000:h That example contains semicolons but these are optional.

The language is the result of a lot of work, I've designed and built compilers in the past.

 

[Sherlock Holmes]

zaangalewa Look:

That's the generated parse tree for a test file, I just ran this here.

 

[Fort Fun Indiana]

But we're talking about the imaginary force of "evolution", right?

Francis, this doesn't belong in the science section.

 

[zaangalewa]

The German dictionary is simply a beta version,

Again: A program code is not really a language. A program code simulates a machine with mathematical structures.

to show the proof of concept. The language has no reserved words by design and because of that we realized that it automatically could use different keyword dictionaries so we experiment and found that it was true. This was not a required capability, it just "fell out" as low hanging fruit from the grammar.

There are other programming languages that use multiple keyword vocabularies, here's another.

It looks that way to you, but that is not the case. The grammar supports this feature and the code samples parse without problems. You should gather facts before jumping to conclusions. Those samples are tests for the grammar, the grammar is the rules of the language's syntax. The grammar is written in Antlr 4. That is a very powerful parsing technology, the grammar (once stable) can be consumed by an Antlr tool and that generates the parser for you, in a choice of language, Java, C++ or C#.

The Antlr-4 parser tools are extremely powerful, it uses an unlimited lookahead in order to resolve ambiguities, this is what makes it possible to have no semicolons, and makes it possible to have literal constants like this:

View attachment 1003807

See 'base_address'? The literal value can be written flexibly, in this case it's a hex constant 0000 1F00 C000 0000:h That example contains semicolons but these are optional.

This "program" is just simple no program. It's a kind of text which gives someone the delusion it has something to do with a program.

The language is the result of a lot of work,

This remembers me to Eugen Roth.

Ein Mensch malt, von Begeisterung wild,
Drei Jahre lang an einem Bild.
Dann legt er stolz den Pinsel hin
Und sagt: "Da steckt viel Arbeit drin."
Doch damit wars auch leider aus:
Die Arbeit kam nicht mehr heraus.

Bad Translation:

A man paints, wild with enthusiasm,
For three years on a picture.
Then he proudly puts down the brush
And says: “A lot of work went into it.”
But unfortunately that was the end of it:
The work never came out.

I've designed and built compilers in the past.

The German dictionary is simply a beta version, to show the proof of concept. The language has no reserved words by design and because of that we realized that it automatically could use different keyword dictionaries so we experiment and found that it was true. This was not a required capability, it just "fell out" as low hanging fruit from the grammar.

There are other programming languages that use multiple keyword vocabularies, here's another.

It looks that way to you, but that is not the case. The grammar supports this feature and the code samples parse without problems. You should gather facts before jumping to conclusions. Those samples are tests for the grammar, the grammar is the rules of the language's syntax. The grammar is written in Antlr 4. That is a very powerful parsing technology, the grammar (once stable) can be consumed by an Antlr tool and that generates the parser for you, in a choice of language, Java, C++ or C#.

The Antlr-4 parser tools are extremely powerful, it uses an unlimited lookahead in order to resolve ambiguities, this is what makes it possible to have no semicolons, and makes it possible to have literal constants like this:

View attachment 1003807

See 'base_address'? The literal value can be written flexibly, in this case it's a hex constant 0000 1F00 C000 0000:h That example contains semicolons but these are optional.

The language is the result of a lot of work, I've designed and built compilers in the past.

Please do not try to tell me bullshit. If you made compilers then you know what is machine code.

 

[zaangalewa]

zaangalewa Look:

View attachment 1003809

That's the generated parse tree for a test file, I just ran this here.

Eh? A tree diagram. So what? The program you wrote it not able to work - so it's impossible that this diagram is a test file.

 

[scruffy]

The German dictionary is simply a beta version, to show the proof of concept. The language has no reserved words by design and because of that we realized that it automatically could use different keyword dictionaries so we experiment and found that it was true. This was not a required capability, it just "fell out" as low hanging fruit from the grammar.

There are other programming languages that use multiple keyword vocabularies, here's another.

It looks that way to you, but that is not the case. The grammar supports this feature and the code samples parse without problems. You should gather facts before jumping to conclusions. Those samples are tests for the grammar, the grammar is the rules of the language's syntax. The grammar is written in Antlr 4. That is a very powerful parsing technology, the grammar (once stable) can be consumed by an Antlr tool and that generates the parser for you, in a choice of language, Java, C++ or C#.

The Antlr-4 parser tools are extremely powerful, it uses an unlimited lookahead in order to resolve ambiguities, this is what makes it possible to have no semicolons, and makes it possible to have literal constants like this:

View attachment 1003807

See 'base_address'? The literal value can be written flexibly, in this case it's a hex constant 0000 1F00 C000 0000:h That example contains semicolons but these are optional.

The language is the result of a lot of work, I've designed and built compilers in the past.

WAY off topic.

 

[Sherlock Holmes]

Again: A program code is not really a language. A program code simulates a machine with mathematical structures.

Nobody here has said that a "program code is a language" I would never say that nor would I write so poorly. If I said something that you disagree with then just quote my words and I'll happily explain things.

This "program" is just simple no program. It's a kind of text which gives someone the delusion it has something to do with a program.

It's a test source file, written purely for testing the grammar and parser, it's not mean to represent a real problem, it is just test text that we use to test the grammar/parser, the text is syntactically correct, obeys the rules of the grammar.

Please do not try to tell me bullshit. If you made compilers then you know what is machine code.

I would never dream of doing so, and of course I understand what "machine code" means, why do you think I don't?

 

[Sherlock Holmes]

Eh? A tree diagram. So what? The program you wrote it not able to work - so it's impossible that this diagram is a test file.

Yes, programming language grammars are hierarchical, they transform a linear text stream into a tree a and then that tree is eventually converted into target object code by the code generator. I've been speaking to you about the grammar specifically the grammar and not the language's semantics which is completely distinct from the grammar.

The test source files are nothing more than legal syntactic test files used to unit test the grammar/parser code. If we adjust the grammar slightly (say to support a new operator like say +> then we need to ensure that we've not messed up the rules of the grammar, it needs to be tested to ensure it still recognizes the test files.

You seem to be struggling with something but I don't know what, you seem to think the test files are meant to be real world meaningful runnable code, but they're not, they are just made up text (that strictly obeys the grammar rules) to stress test the grammar and parser.

Do you know what a grammar is in programming language theory? have you ever used Antlr?

ANTLR

www.antlr.org

Those guys have an online grammar "lab" too for people to play around as they learn Antlr, you can write a grammar and test it in that lab, look:

That window on the upper right is a test input, that's what my test file is too, a test input. The test is used to ensure that the grammar (seen in the left window) works as expected, the left hand window defines the rules that define the syntax for the language, you can see too their lab tool generates a tree.

Here, there are lots of grammar files supplied with Antlr (which is free) you can look at the grammar rules for your favorite language in here.

Antlr is VERY powerful and is one of the reasons my language can do what it can, Antlr uses a strategy called ALL(*) here's the author's PhD paper on this new parsing strategy.

 

[ding]

Eh? A tree diagram. So what? The program you wrote it not able to work - so it's impossible that this diagram is a test file.

He didn't say it was. He said it was a "generated parse tree" FOR A TEST FILE.

 

[Sherlock Holmes]

He didn't say it was. He said it was a "generated parse tree" FOR A TEST FILE.

I really don't know what to make of his remarks. It could be he's just never heard of languages with no reserved words, some people (even experienced programmers) are very surprised when they encounter them because it clashes with how they think a computer processes a programming language.

But there's a hostility too in his replies, quite nasty actually.

 

[Sherlock Holmes]

I think my best advice to zaangalewa is to show this thread to someone he knows is an experienced software engineer, they might be better placed to explain all this to him after reading everything I've said.

 

[ding]

I really don't know what to make of his remarks. It could be he's just never heard of languages with no reserved words, some people (even experienced programmers) are very surprised when they encounter them because it clashes with how they think a computer processes a programming language.

But there's a hostility too in his replies, quite nasty actually.

Yeah, I can't quite figure him out. I think it's a political division thing.

 

[scruffy]

Yeah, I can't quite figure him out. I think it's a political division thing.

It's a cultural thing. Arrogant Germans who believe they're superior. I've had him on ignore for years.