Darwin Unhinged: The Bugs in Evolution

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.

I'm having trouble understand your use of words here.

If a code is a mapping from an idea to a physical thing, then the genetic code is not a code. The RNA => DNA translation process doesn't have any ideas in mind.

If, on the other hand, you think it's a code just because humans can come up with ideas about the translation mechanism, then I daresay the genetic code is a human fabrication.

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.

I agree that Shannon is relevant. But if we are going to use that as a reason to call the genetic code a code, then the definition inolving idea => physical thing is too limited.

~~ Paul

Me:

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.

I answered that at length. Not remotely surprised that is slid under your radar, or that you outright ignored it. That seems to be your go-to move

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.

Fair enough. I'm happy to agree that the DNA specifies codes that interact with the translation mechanism through an intermediary, the mRNA. There is, however, no table in the DNA.

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.

Note that there is not a 1-to-1 relationship between anticodons and amino acids.

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.

You're right that I can't get past thinking of a "lookup table" in computer science terms. That's where the term comes from. If you insist on misuing the term for any mechanism that humans can represent as a table, then there are hundreds of natural mechanisms that use lookup tables, including the periodic table. The idea becomes useless, although it does apparently open the door for a plethora of codes.

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.

I don't understand what you think the RNA world idea is avoiding.

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.

You just said that simple polypeptides could be formed without DNA.

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.

Yes, this is an issue that biologists are grappling with. Do I need to post the same papers yet again? Does anyone feel like doing any reading?

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.

You still haven't said anything except that humans produce codes and so therefore nature cannot. I guess I will post this paper yet again:

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

Separately, the following argument was presented up above:

"1. Semiotic systems are regularly seen to arise from intelligent agents. As a corollary, semiotic systems have never been known to arise from purely natural causes. Indeed, in every instance in which we see a semiotic system and know the provenance, it started with an intelligent agent.
2. There is a semiotic system in biology.
3. Therefore, the most likely explanation is that it came from an intelligent agent."

Do you care do discuss why that argument begs the question?

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 have read the entirety of the two papers that I keep posting. Perhaps you could find out the degree to which I understand them by actually discussing them.

~~ Paul

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?

Well not necessarily because I accept there isn't a hard demarcation line, but coding for one thing is vastly different from coding for an almost infinite number of possibilities (OK there is probably an upper limit to protein chain size).

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

The title of this paper is "Evolution of the genetic code through progressive symmetry breaking", so my question is, how does evolution operate in the absence of a genetic code? I mean, this point is crucial, if you don't have an organism that has any means to pass its structure on to its offspring, then what does it mean to talk about evolution?

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

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.

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

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

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

~~ Paul

Define  a "heritable chemical ", and then lets see if it doesn't contain an implicit code.

The real problem with this discussion is that it inevitably involves mountains of hypothetical s created in a desperate attempt to avoid the idea that something designed life. There also seems to be a desire to blur the distinction between pre-biotic life and life.

It is amusing that  Louis Pasteur was famed for proving that life does not develop spontaneously, and yet most scientists are utterly convinced that it can develop spontaneously given a little more time!

You're right that I can't get past thinking of a "lookup table" in computer science terms. That's where the term comes from. If you insist on misuing the term for any mechanism that humans can represent as a table, then there are hundreds of natural mechanisms that use lookup tables, including the periodic table. The idea becomes useless, although it does apparently open the door for a plethora of codes.

I can't really believe you mean that! The periodic table is something humans created to help them understand chemistry, the genetic code is actually used by the chemistry of life - we only use it to understand the process of life's chemistry using it!

David

Well not necessarily because I accept there isn't a hard demarcation line, but coding for one thing is vastly different from coding for an almost infinite number of possibilities (OK there is probably an upper limit to protein chain size).

Wait a minute. We are talking about the evolution of the genetic code, not the evolution of proteins. The question is whether the genetic code could evolve by naturalistic means.

The title of this paper is "Evolution of the genetic code through progressive symmetry breaking", so my question is, how does evolution operate in the absence of a genetic code? I mean, this point is crucial, if you don't have an organism that has any means to pass its structure on to its offspring, then what does it mean to talk about evolution?

Here is a proof that evolution happens, by Marvin Minsky:

"There is a population of things that reproduce, at different rates in different environments. Those rates depend, statistically, on a collection of inheritable traits. Those traits are subject to occasional mutations, some of which are then inherited.

Then one can deduce, from logic alone, without any need for evidence, that:

THEOREM: Each population will tend to increase the proportion of traits that have higher reproduction rates in its current environment."

Note there is no mention of a genetic code. You only need inheritable chemicals that affect the organisms' fitness and also mutate. It could be bits of RNA or bits of protein or even something else.

Define  a "heritable chemical ", and then lets see if it doesn't contain an implicit code.

The code exists to map DNA sequences to amino acid sequences. If there is no mapping, then there doesn't need to be a code.

The real problem with this discussion is that it inevitably involves mountains of hypothetical s created in a desperate attempt to avoid the idea that something designed life. There also seems to be a desire to blur the distinction between pre-biotic life and life.

Why go off the rails now? Of course there are hypotheticals. That's the way science works. What would you expect to see if science was somehow not the rig job that you appear to believe it is? No hypotheses, just some magic instant-answer?

And how can you say this with a straight face when the alternate proposal is that some sort of intelligence did it, with no hypotheses about how it works and with no evidence of it? It is, right now, nothing but an inference from human design.

I can't really believe you mean that! The periodic table is something humans created to help them understand chemistry, the genetic code is actually used by the chemistry of life - we only use it to understand the process of life's chemistry using it!

There is no genetic code table in the cell. The table was invented by humans to help explain what is going in with the chemistry. The periodic table is also a nice table to explain what is going on with valence electrons in atoms. What exactly is the difference? I'm willing to listen to a difference, but so far everyone is just accusing me of being an uncooperative curmudgeon.

~~ Paul

I can't really believe you mean that! The periodic table is something humans created to help them understand chemistry, the genetic code is actually used by the chemistry of life - we only use it to understand the process of life's chemistry using it!

Well put, David. But he really does mean it -- such a literalist!

On the one hand, he seems to acknowledge the existence of the genetic code -- but on the other, believes somehow it isn't really a code because (to his way of thinking) it has no lookup table.

He agrees that in computer science, codes can be created that have lookup tables that can be written down. But so too can the lookup table for the genetic code -- I posted it earlier.

The fact that the literal table can't be found anywhere in the cell stumps him, and he simply can't get past that, even though thousands of biologists routinely accept that there is a genetic code, and its lookup table  has been written down and referenced for decades.

He's so adamant about mind of any kind not being involved in the invention of the DNA code -- he prefers to think that mindless evolution somehow invented it. I don't think he can see the inconsistencies in his arguments. I'm afraid he's a hopeless case.

Note there is no mention of a genetic code. You only need inheritable chemicals that affect the organisms' fitness and also mutate. It could be bits of RNA or bits of protein or even something else.

The code exists to map DNA sequences to amino acid sequences. If there is no mapping, then there doesn't need to be a code.

There is no genetic code table in the cell. The table was invented by humans to help explain what is going in with the chemistry. The periodic table is also a nice table to explain what is going on with valence electrons in atoms. What exactly is the difference? I'm willing to listen to a difference, but so far everyone is just accusing me of being an uncooperative curmudgeon.

~~ Paul

No different than a bee's honey-gathering dance, decoded by bees back at the hive.  Symbols convey information about the environment.

The code or codes that unfold ontogentic* development most likely are self-created as artifacts of the struggle for life and experience. The communication systems that enable the bio-information needed by life are a natural language that evolved organically.  

At the organic level, the bioinformatic mapping is from a set of instructions signalling to developing organ function of a targeted healthy state. 

Its not about the magic chemical DNA.  DNA dialects are just one nexus in a diverse matrix of functional communication channels in biology.  The endocrine system alone has its own language and multiple bio-functions with which it interacts.

The difference between a periodic chart and the natural language of DNA/RNA/Ribosome communication is that natural language is describing an in situ process in real environments.  A periodic table on a powerpoint slide; in front of a group of chemists focused on its information in a real discussion might be a fairer analogy.  

In my estimation the period table is a natural event done by naturally behaving animals.  The intelligence is from the nature of thinking animals, whose minds obey the rules and laws of information's, storage, structured retrieval and transfer.  The difference in my viewpoint from both; you Paul, and from David, is that the information is not shadowing DNA chemistry and magically creates new chemicals with the property of inheritance.  

In my version; information is actualizing and riding the chemicals like little pony trains.  The structured information that says go and stop, rest or high-alert, approach/avoid, are jumping on the bio-information channels and takes them forward.  Forward into the willing of their enactment, as efferent signals.  The meaning that is our emotions and intentions are these structured information objects.

The living cells exhibit integration and regulation that are the hallmarks of a healthy animal is one of vast amounts of intra- and inter-cellular communication.

* Ontogeny is the origination and development of an organism, usually from the time of fertilization of the egg to the organism's mature form—although the term can be used to refer to the study of the entirety of an organism's lifespan. Wikipedia 

Well put, David. But he really does mean it -- such a literalist!

On the one hand, he seems to acknowledge the existence of the genetic code -- but on the other, believes somehow it isn't really a code because (to his way of thinking) it has no lookup table.

Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.

He agrees that in computer science, codes can be created that have lookup tables that can be written down. But so too can the lookup table for the genetic code -- I posted it earlier.

The fact that the literal table can't be found anywhere in the cell stumps him, and he simply can't get past that, even though thousands of biologists routinely accept that there is a genetic code, and its lookup table  has been written down and referenced for decades.

It stumps me? I was simply objecting to the claim that there is a table somewhere in biology. And if simply being able to write down a table is all that is required for a code, then the periodic table is a code.

Why don't people give a damn about what a code is while they are going on and on about its magical nature?

~~ Paul

I answered that at length. Not remotely surprised that is slid under your radar, or that you outright ignored it. That seems to be your go-to move

I read all your posts the first time and I read them again just now. You didn't answer this question regardless of what you think. "What really chaps your arse about ToE?" You see the question I'm actually asking is, What philosophy or ideology creates this normative state of mind in you that apparently ToE cannot occur by entirely natural means?

Looking over what you've written I see you've not answered this question either.

Paul beat me to it in post 487. I'll rephrase his question a bit though. What is an example problem with "Darwinian theory" ? And describe a non-Darwinian theory that will explain said problem thoroughly?  This includes Modern Synthesis.
http://psiencequest.net/forums/thread-da...8#pid11748

You didn't answer this question either http://psiencequest.net/forums/thread-da...7#pid11507

Do we have to play this game? I'm happy to acknowledge that it's a code. But if the central argument is that a code cannot evolve, doesn't it make sense first to define exactly what a code is? Apparently handwaving is sufficient.


It stumps me? I was simply objecting to the claim that there is a table somewhere in biology. And if simply being able to write down a table is all that is required for a code, then the periodic table is a code.

Why don't people give a damn about what a code is while they are going on and on about its magical nature?

~~ Paul

Firstly, how do you define a code? Does it involve encoding and decoding? Are there rules? Can it be represented symbolically? Does it convey meaning or determine function? Is it structured (not haphazard)? 

Here is something I found online:

Biosemiotics: a new understanding of life
Marcello Barbieri

The link between sign and meaning, in turn, calls attention to a third entity, i.e., to their relationship. A sign is a sign only when it stands for something that is other than itself, and this otherness implies at least some degree of independence. It means that there is no deterministic relationship between sign and meaning. Different languages, for example, give different names to the same object precisely because there is no necessary connection between names and objects. A semiotic system, therefore, is not any combination of two distinct worlds. It is a combination of two worlds between which there is no necessary link, and this has an extraordinary consequence. It implies that a bridge between the two worlds can be established only by conventional rules, i.e., by the rules of a code. This is what qualifies the semiotic systems, what makes them different from everything else: a semiotic system is a system made of two independent worlds that are connected by the conventional rules of a code. A semiotic system, in conclusion, is necessarily made of at least three distinct entities: signs, meanings, and code. 

Here, at last, we have a definition where it is stated explicitly that a code is an essential component of a semiotic system. It is the rules of a code that create a correspondence between signs and meanings, and we can say, therefore, that an act of semiosis is always an act of coding, i.e., it is always a convention. More precisely, we can say that an elementary act of semiosis is a triad of ‘sign, meaning, and convention’, whereas a semiotic system is a whole set of signs and meanings that are linked together by all the various conventions that make up a code. 

Signs, meanings, and conventions, however, do not come into existence of their own. There is always an ‘agent’ that produces them, and that agent can be referred to as a codemaker because it is always an act of coding that gives origin to semiosis. In the case of culture, for example, the codemaker is the human mind since it is the mind that produces the mental objects that we call signs and meanings and the conventions that link them together. We come in this way to a general conclusion that can be referred to as ‘the code model of semiosis’: a semiotic system is a triad of signs, meanings and code that are all produced by the same agent, i.e., by the same codemaker. 

This conclusion is highly relevant to biology because it tells us precisely what we need to prove in order to show that the cell is a semiotic system. We need to prove that in every living cell there are four distinct entities: signs, meanings, code and codemaker.