Darwin Unhinged: The Bugs in Evolution

Well, a pheromone is a code in that it transmits one bit of information - copulate, or don't copulate.

It's way more complicated than that.

https://en.wikipedia.org/wiki/Pheromone

As you will see from my comment above, I don't think the real point is something special about codes except that they require a vast amount of machinery to be in place before they can function at all. You need some form of ribosomes to read the code, some enzymes to duplicate the code (even avoiding the issue of the DNA being copied to RNA prior to use), plus something like t-RNA to scavenge the amino acids.

May I suggest that you read up on the evolution of the ribosome and the genetic code. In particular, consider a proto-ribosome that joins amino acids in random order.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/

Now if you think back to the dawn of time, you can probably imagine some simplifications to that scheme, but you still need a fair pile of machinery to be working before this process can role. Note that until this works, it is meaningless to talk about survival of the fittest, because you don't have any functioning genes, or any generations to pass them on to!

Do you think that DNA is the only heritable molecule?

~~ Paul

It's way more complicated than that.

https://en.wikipedia.org/wiki/Pheromone

May I suggest that you read up on the evolution of the ribosome and the genetic code. In particular, consider a proto-ribosome that joins amino acids in random order.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926754/

Do you think that DNA is the only heritable molecule?

~~ Paul

Paul,

Linda introduced the analogy between a pheromone and the genetic code - perhaps you would agree it wasn't really helpful to our discussion!

I think the reference to random polymers in that paper related to random RNA molecules, but those could, I suppose, give rise to random strings of amino acids if the rest of the mechanism was in place - but so what? The difference between a random heap of letters and a specific code, is exactly what we are talking about!

I believe that the hypothesis that life started as RNA molecules (storing the code and acting as 'enzymes') has been more or less abandoned because these molecules are too unstable.

The problem is that if you propose that the code replication and reading machinery was present in life from the beginning, then it had to be created without the benefit of natural selection -  a feat described well by Fred Hoyle:

A junkyard contains all the bits and pieces of a Boeing-747, dismembered and in disarray. A whirlwind happens to blow through the yard. What is the chance that after its passage a fully assembled 747, ready to fly, will be found standing there? 

Alternatively, life began in an earlier form with no code, but then it isn't clear how anything could evolve - it would simply be a bit of novel chemistry.

Paul, how do you envisage life starting out on earth?

David

But we represent lots of things with tables. The periodic table comes to mind. My objection is to use the fact that we can represent things as tables to imply that those things are designed like humans design.

Hang on. There is nothing in the DNA that we could snip out to interact with the anticodons. What's in the DNA are genes that code for RNAs and proteins that make up the ribosome, tRNA, tRNA synthetases, and so forth. There is nothing like a codon table in the DNA.

Of course there are exceptions.

http://medicine.jrank.org/pages/2292/Gen...-Code.html

There you go.

My assertion is there is nothing stopping a code-like mechanism from being produced naturally, given enough time. To refute my assertion, you can specify the principle that prevents such a thing. But before you do that, you need to carefully define "code." Is the periodic table a code? Are other kinds of selective binding a code?

I'm not asking anyone to roll over. I'm asking for the principle that you must have in mind. Because if you don't have a principle in mind, then surely you are not going to accuse me of making unwarranted assertions without doing a double-take.

Really, you're not doing a double-take here?

You apparently have no principle that prevents nature from inventing a code via evolution. You just assume it can't because humans can. And in the process, you ignore all the research on the evolution of the genetic code.

~~ Paul

I'd say that the periodic table is simultaneously a code and not a code depending on context.

In the human context, tables of all sorts are a kind of extension of written language enabling concepts to be more easily grasped, or data interrelationships to be conveniently presented. All language is a code: it enables ideas originating in human minds to be presented in symbolic terms (spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on). The intention is for ideas to be coded by one mind and transmitted to another mind, where they are decoded back into ideas. Sometimes, as in what I'm doing now, they may be decoded by not only other minds, but also the same mind as a means of checking faithfulness to the original ideas.

The rules for the coding are shared  learnings about the conventions used (the above-mentioned spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on), which constitute the lookup table for communication. These symbols are often codified in dictionaries and explanatory texts of various kinds.

Hence in the human context, all tables are codes: in fact all sharable symbols are codes. So both the periodic table and the codon table are codes in this sense. That said, the items in the two tables point to something in the so-called "real world" (I prefer "the world of perception").

In the case of the periodic table, what's pointed to are the elements and their interrelationships. None of the elements maps 1-to-1 to anything else. Sure, the periodic table is rich in information that can inform understandings about various combinations of elements found in chemical compounds, but it's not a 1-to-1 relationship.

In the case of the codon table, on the other hand, 1-to-1 relationships between codons and anticodons, and of anticodons with amino acids, are represented. The relationships are most often shown as being between codons in mRNA and anticodons in tRNAs. But actually, DNA codons specify mRNA codons, those specify tRNA anticodons, and those in turn are linked with specific amino acids:

[Image: T7.gif]

The mRNA is constructed of nucleotide sequences that match the sense strand of DNA -- you can see this in the correspondence between DNA sense codons and mRNA codons, which are identical except that Uracil (U) is used in mRNA instead of Thymine (T) in DNA.

The sense strand of DNA is accompanied by its anti-sense strand, which latter is used as the template for mRNA. That is why the sequence  on the mRNA matches the sense strand on DNA. Think of a simple code where alphabetic characters are encoded in reverse:

sense:       A B C  D E F
anti-sense: F E D  C B A

Let's suppose the message is "FADE". The anti-sense message would be "AFCB". In DNA, the two complementary messages are on two separate and intertwined strands.

Next, we separate the two messages and transcribe the antisense message (AFCB) into a sense message, which is "FADE" again. This is analogous to the sense message on the mRNA which is identical to the sense message on DNA.

Then the message "FADE" on mRNA is matched by the analogue of an anticodon at one end of a tRNA that contains "AFCB". At the other end is a gizmo that interprets the message and dims a light for us. This is analogous to the translation of codes into proteins, the things that actually do stuff in cells.

Though that's a simple code, it's quite complicated how we would get the message to do its stuff in the "real world". See here for an explanation of sense and anti-sense strands in DNA. Note that in some cases mRNA is a copy of the anti-sense strand of DNA, but we won't go into that here.

Think about this for a moment: usually, the codons are already present on the DNA sense strand; they already specify the complementary anticodons on tRNAs, except for the Thymine-Uracil difference. This difference is actually just the absence of a methyl group in Uracil:

[Image: uracil-thymine.png]

In certain experiments, e.g. here, synthesised single-stranded DNA has been shown to be able to code directly for anticodons, but it doesn't happen in nature. The lack of methylation in uracil, plus the differences in the sugars used by DNA and RNA, make for differences in stability of the two (DNA is the more stable -- for thousands of years, actually -- and is therefore better for storing the code).

Snipping the DNA molecule and directly using the sense strand to specify anticodons won't work because of the thymine/uracil and sugar differences with mRNA. And even if it could, there'd be the problem of re-inserting the DNA strand back in place after translation at the ribosome -- which would apply whether or not the cell possessed a nucleus (as in eukaryotes) or not (as in the archaea and bacterial prokaryotes).

I suggest that it's much easier to have the double-stranded DNA sense/antisense configuration and be able to make a copy using single-stranded mRNA, because that can be done in place by simply unzipping the DNA, which then zips back up after transcription.

You say: Hang on. There is nothing in the DNA that we could snip out to interact with the anticodons. What's in the DNA are genes that code for RNAs and proteins that make up the ribosome, tRNA, tRNA synthetases, and so forth. There is nothing like a codon table in the DNA.

This is nonsense. The code is right there in the sense strand of DNA, which via its anti-sense complement specifies same-sense single-stranded mRNA. IOW, the mRNA is, usually -- apart from the Uracil difference -- a copy of the sense strand of DNA. And even where the mRNA is a copy of the anti-sense strand, the code is still copied from DNA. No DNA, no functioning code. I was simply suggesting why, in evolutionary terms, DNA couldn't have been the direct specifier of anticodons; why there has to be an mRNA intermediary to transport the message.

What I think you may be trying to say in a roundabout way is that although DNA is a code, it doesn't use a lookup table. If so, maybe that's because you can't get past thinking of a lookup table in literal terms. But ordinary language, which is a code (or are you denying that?), apart from our constructions (dictionaries, etc) also doesn't have a literal lookup table, and certainly didn't for thousands of years before spoken language was codified in written terms (it still isn't for some languages). Nonetheless, language has, and always has had, the equivalent of a lookup table in the form of learned rules about its use.

The current theory being pursued by evolutionary biologists focuses on RNA. They think that RNA came first. They conjecture that, prior to the emergence of life, RNA existed and was able to specify simple polypeptides (like proteins, but containing much shorter amino acid sequences). Somehow, this schema complexified and worked backwards towards DNA. This is to avoid the awful implications of the way things are now and have been for at least 3.7 billion years since prokaryotes appeared in the fossil record.

What way is that? Well, DNA specifies mRNA, which specifies tRNAs, which are associated with amino acids, which at the ribosome, become sequenced into proteins. Without DNA, there can be no proteins. At the same time, without proteins, DNA can't be processed: they are present as enzymes and subcellular agglomerates we often think of as machines that do the processing.

Which came first? Proteins, or DNA? They are mutually interdependent and so some way has to be found to decide on this chicken-and-egg situation; because if it can't be resolved, a mechanistic cause-and-effect schema is highly suspect. The fact that the elements of the schema have to be present all at once for it to work, can't be explained in a deterministic way. There'd have to be something akin to intelligence in the explanatory system, and that's the most awful and threatening thing.

Incidentally, you still haven't come up with a naturally-occurring code and explained how it arose without intelligence of some kind. You just keep on asserting that codes could arise naturally, and pushing the burden of proof in my direction. You say:

You apparently have no principle that prevents nature from inventing a code via evolution. You just assume it can't because humans can. And in the process, you ignore all the research on the evolution of the genetic code.

Actually, I do have a principle that prevents nature from inventing a code. That principle is the lack of intelligence of "nature" in the mechanistic way you're thinking of it. I don't know exactly how intelligence plays into the game, it is true, but as I mentioned in an earlier post, it's common and uniform experience that codes have only been observed to have arisen from intelligent consciousness.

Also note that I don't deny evolution has occurred; just that it hasn't happened in a Darwinian fashion. I think evolution is explained by natural selection coupled with non-random mutation, and I think that what has driven the process has been doing so in an "experimental" sort of way, viz. it doesn't "know" exactly how things are going to turn out. My conception of MAL isn't at all like the Abrahamic God.

As for ignoring research, get out of here. You post links, but I have my doubts whether you do much research and really understand them. I suspect you just mine them for supportive tidbits without doing any heavy lifting yourself. Your posts tend to be gnomic -- obscure enough so that you always have enough wiggle room to deny your mistakes.

I'd say that the periodic table is simultaneously a code and not a code depending on context.

In the human context, tables of all sorts are a kind of extension of written language enabling concepts to be more easily grasped, or data interrelationships to be conveniently presented. All language is a code: it enables ideas originating in human minds to be presented in symbolic terms (spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on). The intention is for ideas to be coded by one mind and transmitted to another mind, where they are decoded back into ideas. Sometimes, as in what I'm doing now, they may be decoded by not only other minds, but also the same mind as a means of checking faithfulness to the original ideas.

The rules for the coding are shared  learnings about the conventions used (the above-mentioned spoken and/or written letters, words, sentences, grammar, syntax, tables, mathematical notation, and so on), which constitute the lookup table for communication. These symbols are often codified in dictionaries and explanatory texts of various kinds.

Hence in the human context, all tables are codes: in fact all sharable symbols are codes. So both the periodic table and the codon table are codes in this sense. That said, the items in the two tables point to something in the so-called "real world" (I prefer "the world of perception").

In the case of the periodic table, what's pointed to are the elements and their interrelationships. None of the elements maps 1-to-1 to anything else. Sure, the periodic table is rich in information that can inform understandings about various combinations of elements found in chemical compounds, but it's not a 1-to-1 relationship.

In the case of the codon table, on the other hand, 1-to-1 relationships between codons and anticodons, and of anticodons with amino acids, are represented. The relationships are most often shown as being between codons in mRNA and anticodons in tRNAs. But actually, DNA codons specify mRNA codons, those specify tRNA anticodons, and those in turn are linked with specific amino acids:

[Image: T7.gif]

The mRNA is constructed of nucleotide sequences that match the sense strand of DNA -- you can see this in the correspondence between DNA sense codons and mRNA codons, which are identical except that Uracil (U) is used in mRNA instead of Thymine (T) in DNA.

The sense strand of DNA is accompanied by its anti-sense strand, which latter is used as the template for mRNA. That is why the sequence  on the mRNA matches the sense strand on DNA. Think of a simple code where alphabetic characters are encoded in reverse:

sense:       A B C  D E F
anti-sense: F E D  C B A

Let's suppose the message is "FADE". The anti-sense message would be "AFCB". In DNA, the two complementary messages are on two separate and intertwined strands.

Next, we separate the two messages and transcribe the antisense message (AFCB) into a sense message, which is "FADE" again. This is analogous to the sense message on the mRNA which is identical to the sense message on DNA.

Then the message "FADE" on mRNA is matched by the analogue of an anticodon at one end of a tRNA that contains "AFCB". At the other end is a gizmo that interprets the message and dims a light for us. This is analogous to the translation of codes into proteins, the things that actually do stuff in cells.

Though that's a simple code, it's quite complicated how we would get the message to do its stuff in the "real world".


See here for an explanation of sense and anti-sense strands in DNA. Note that in some cases mRNA is a copy of the anti-sense strand of DNA, but we won't go into that here.

Think about this for a moment: usually, the codons are already present on the DNA sense strand; they already specify the complementary anticodons on tRNAs, except for the Thymine-Uracil difference. This difference is actually just the absence of a methyl group in Uracil:

[Image: uracil-thymine.png]

In certain experiments, e.g. here, synthesised single-stranded DNA has been shown to be able to code directly for anticodons, but it doesn't happen in nature. The lack of methylation in uracil, plus the differences in the sugars used by DNA and RNA, make for differences in stability of the two (DNA is the more stable -- for thousands of years, actually -- and is therefore better for storing the code).

Snipping the DNA molecule and directly using the sense strand to specify anticodons won't work because of the thymine/uracil and sugar differences with mRNA. And even if it could, there'd be the problem of re-inserting the DNA strand back in place after translation at the ribosome -- which would apply whether or not the cell possessed a nucleus (as in eukaryotes) or not (as in the archaea and bacterial prokaryotes).

I suggest that it's much easier to have the double-stranded DNA sense/antisense configuration and be able to make a copy using single-stranded mRNA, because that can be done in place by simply unzipping the DNA, which then zips back up after transcription.

You say: Hang on. There is nothing in the DNA that we could snip out to interact with the anticodons. What's in the DNA are genes that code for RNAs and proteins that make up the ribosome, tRNA, tRNA synthetases, and so forth. There is nothing like a codon table in the DNA.

This is nonsense. The code is right there in the sense strand of DNA, which via its anti-sense complement specifies same-sense single-stranded mRNA. IOW, the mRNA is, usually -- apart from the Uracil difference -- a copy of the sense strand of DNA. And even where the mRNA is a copy of the anti-sense strand, the code is still copied from DNA. No DNA, no functioning code. I was simply suggesting why, in evolutionary terms, DNA couldn't have been the direct specifier of anticodons; why there has to be an mRNA intermediary to transport the message.

What I think you may be trying to say in a roundabout way is that although DNA is a code, it doesn't use a lookup table. If so, maybe that's because you can't get past thinking of a lookup table in literal terms. But ordinary language, which is a code (or are you denying that?), apart from our constructions (dictionaries, etc) also doesn't have a literal lookup table, and certainly didn't for thousands of years before spoken language was codified in written terms (it still isn't for some languages). Nonetheless, language has, and always has had, the equivalent of a lookup table in the form of learned rules about its use.

The current theory being pursued by evolutionary biologists focuses on RNA. They think that RNA came first. They conjecture that, prior to the emergence of life, RNA existed and was able to specify simple polypeptides (like proteins, but containing much shorter amino acid sequences). Somehow, this schema complexified and worked backwards towards DNA. This is to avoid the awful implications of the way things are now and have been for at least 3.7 billion years since prokaryotes appeared in the fossil record.

What way is that? Well, DNA specifies mRNA, which specifies tRNAs, which are associated with amino acids, and at the ribosome, become sequenced into proteins. Without DNA, there can be no proteins. At the same time, without proteins, DNA can't be processed: they are present as enzymes and subcellular agglomerates we often think of as machines that do the processing.

Which came first? Proteins, or DNA? They are mutually interdependent and so some way has to be found to decide on this chicken-and-egg situation; because if it can't be resolved, a mechanistic cause-and-effect schema is highly suspect. The fact that the elements of the schema have to be present all at once for it to work, can't be explained in a deterministic way. There'd have to be something akin to intelligence in the explanatory system, and that's the most awful and threatening thing.

Incidentally, you still haven't come up with a naturally-occurring code and explained how it arose without intelligence of some kind. You just keep on asserting that codes could arise naturally, and pushing the burden of proof in my direction. You say:

You apparently have no principle that prevents nature from inventing a code via evolution. You just assume it can't because humans can. And in the process, you ignore all the research on the evolution of the genetic code.

Actually, I do have a principle that prevents nature from inventing a code. That principle is the lack of intelligence of "nature" in the mechanistic way you're thinking of it. I don't know exactly how intelligence plays into the game, it is true, but as I mentioned in an earlier post, it's common and uniform experience that codes have only been observed to have arisen from intelligent consciousness.

Also note that I don't deny evolution has occurred; just that it hasn't happened in a Darwinian fashion. I think evolution is explained by natural selection coupled with non-random selection, and I think that what has driven the process has been doing so in an "experimental" sort of way, viz. doesn't "know" exactly how things are going to turn out. My conception of MAL isn't at all like the Abrahamic God.

As for ignoring research, get out of here. You post links, but I have my doubts whether you do much research and really understand them. I suspect you just mine them for supportive tidbits without doing any heavy lifting yourself. Your posts tend to be gnomic -- obscure enough so that you always have enough wiggle room to deny your mistakes.

 
You agree evolution occurs by Natural Selection and you think it's an experiment without a goal. That is Darwin. As for your belief in design of some sort it's up to you to present evidence. We'll be awaiting.

 
You agree evolution occurs by Natural Selection and you think it's an experiment without a goal. That is Darwin. As for your belief in design of some sort it's up to you to present evidence. We'll be awaiting.

Nice nuanced response, steve. Did you actually read his post or just see that it was Michael posting and go to your usual box of stock responses?

Nice nuanced response, steve. Did you actually read his post or just see that it was Michael posting and go to your usual box of stock responses?

Just another gnome who wouldn't understand a nuance if it came up and punched him on the nose.

Just another gnome who wouldn't understand a nuance if it came up and punched him on the nose.

Please elucidate the difference from what you wrote to what you meant.

Nice nuanced response, steve. Did you actually read his post or just see that it was Michael posting and go to your usual box of stock responses?

I think it's important to always remember that a lack of an alternative does not magically make issues with the primarily accepted model disappear. They are real issues. Those issues are not rendered irrelevant because people don't have a fully supported alternative, especially when little research has been conducted into any such alternative path. Additionally it seems clear that it might be difficult to scientifically uncover intelligent intent or something of the like, if such a thing exists. Regardless, evolutionary theory as it is rests on incredibly shaky reasoning that is rarely challenged at all, which probably has led to a lot of the discord surrounding the issue.

Me:

Some things I've noticed. People love science as long as it does not threaten their existential beliefs. TOE does just that. If the study of psi had the same depth of knowledge as does evolutionary theory does you'd and a few others would say psi is a bonifide science backed up by a big marching band. Tell me what really chaps your arse about TOE?

Still waiting for the answer. 
 
The only time you have anything to say is when you say it to me. Are you me personal fanboy? It seems you are. I've never had one and don't know whether to be pleased or alarmed.

"The formal definition of a code according to Perlwitz and Waterman (see below) is a set of symbols that uniquely map a point in space “A” to a point in space “B.” In other words there is special symbolic correspondence between a letter or word (idea) and a real physical entity. The word “coffee” represents a beverage made from cocoa beans, for example. Symbolic relationships of this kind are only created in the mental world; they by definition do not exist in the purely material world."

The first sentence says that a code maps a point in space A to a point in space B. The second sentence suddenly asserts that space A is a space of ideas. How do we resolve the apparent inconsistency between those two sentences?

If the second sentence is to be assumed, then the process of translation from RNA to DNA does not involve a code.

~~ Paul

Symbolic relationships being created in a "mental world" (whar's that), which is not part and parcel of phenomenal reality --- is precisely what I am arguing against with a worldview that information and meaning are real and measurable. Informational "space" is a scientific concept.  There is no inconsistency in the definition; as symbols refer to symbols and not physical targets most of the time in conversation and in data gathered from experiements.  Your claim of inconsistency is a linguistic mistake.  The "pointing" goes to mapping theory, about which there is a lot written.  The ideas of Bayesian probability and those of Hilbert space are found to work well together.

Translation - -whether in the specific sense of RNA/DNA communication or in the sense of changing one coding format to another -- IS BY DEFINITION subject to Shannon Coding Theorem.  In bio-semiotics; measurable error correction takes place, as would be expected when using a noisy channel.  Living things learned and used the practical aspects of information theory as much as they subconsciously learned chemistry and physics.

Living things evolved to exploit physical mechanisms, such as sight, locomotion, hearing, smell, echo-location, etc .... for survival purposes.

In a congruent context - living things evolved informational mechanisms, such as sense of sense, understanding past events, planning future events, social awareness, logical rules, etc.....  for survival purposes.  The capability for intelligence was always a real probability.  Living things as a whole actualized intelligence and used it to evolve adaptability.

Linda introduced the analogy between a pheromone and the genetic code - perhaps you would agree it wasn't really helpful to our discussion!

No, I wouldn't agree. We also mentioned polymorphic crystals and the periodic table. The goal is to try to pin down a definition of code that includes natural mechanisms that people think are coded and excludes ones that are not. One definition was given in post #510 that appears to exclude the genetic code.

Don't you think it's important to pin down the definition?

I think the reference to random polymers in that paper related to random RNA molecules, but those could, I suppose, give rise to random strings of amino acids if the rest of the mechanism was in place - but so what? The difference between a random heap of letters and a specific code, is exactly what we are talking about!

People keep asking me to describe how the genetic code evolved, as if I somehow know. One possibility is that it started with random assembly of amino acids and then evolved a simple mechanism that could distinguish between broad categories of amino acids, eventually evolving more specificity. This idea is explored in detail in this paper:

http://www.sciencedirect.com/science/art...9314000113

So the question is: At what point in this long story of the genetic code does the evolution become impossible?

I believe that the hypothesis that life started as RNA molecules (storing the code and acting as 'enzymes') has been more or less abandoned because these molecules are too unstable.

No, it hasn't been abandoned. The research focuses on how it might have evolved in the face of the instability. There are, of course, other proposals that don't start with an RNA world.

The problem is that if you propose that the code replication and reading machinery was present in life from the beginning, then it had to be created without the benefit of natural selection -  a feat described well by Fred Hoyle:

No one proposes that the genetic code existed "from the beginning." Check out this paper:

https://www.researchgate.net/publication...e_Ribosome

Alternatively, life began in an earlier form with no code, but then it isn't clear how anything could evolve - it would simply be a bit of novel chemistry.

Why is a code necessary for evolution? Evolution requires heritable chemicals with variation.

~~ Paul