Upright BiPed has been proposing what he has called a “semiotic” theory of Intelligent Design, for a while, which I have found confusing, to say the least. However, he is honing his case, and asks Nick Matzke…
…these three pertinent questions regarding the existence of information within a material universe:
- In this material universe, is it even conceivably possible to record transferable information without utilizing an arrangement of matter in order to represent that information? (by what other means could it be done?)
- If 1 is true, then is it even conceivably possible to transfer that information without a second arrangement of matter (a protocol) to establish the relationship between representation and what it represents? (how could such a relationship be established in any other way?)
- If 1 and 2 are true, then is it even conceivably possible to functionally transfer information without the irreducibly complex system of these two arrangements of matter (representations and protocols) in operation?
… which I think clarify things a little.
I think I can answer them, but would anyone else like to have a go? (I’m out all day today).
yet you are now on record as saying the exact opposite:
So which is it Joe? You have to choose. Or explain the apparent contradiction, this holding of two mutually exclusive positions.
What contradiction? Are you saying that you are too stupid to understand that evolution can proceed by design? As in via some preprogrammed genetic algorithm.
Ya see OM your problem is that you equivocate so much you think that all evolution is blind watchmaker evolution. Typical but still sadly pathetic.
What science of the genetic code?
RB:
OMTWO:
It appears that UB has chosen door number three. Shame.
UB has realized that staying here is a waste of time…
Of course it can. Now all you have to do is show *any* evidence for that claim at all.
So your claim is that everything that life might have later needed was front loaded at the origin of life?
Is that your claim?
Whereas you of course are convincing all and sundry with your oh-so-clever arguments.
There any many fully sequenced organisms out there. Please show where in those sequences these preprogrammed genetic algorithms are that control future development.
Upright has mentioned in the past he’s going to publish something or other at “Complexity Cafe”, if that’s a website or journal I’m not sure.
So perhaps he’s had enough “peer review” of his ideas for a re-write…
Yup and the sequence doesn’t have anything to do with the programming and your position still has nothing to offer.
Joe G
Not sure how you expect that to be answered. Are you saying there is no science in the genetic code? Was it elucidated by computer programmers, comms engineers, lawyers and fridge repair men? Amino acids, their side-chain properties in terms of different charge and polarity and backbone bend restriction, the patterns of codon usage groupings, the correlations between codon groupings and the places in which the translated amino acids end up in ‘finished’ proteins, the clustering of departures from the ‘universal’ code’ … this is all relevant to such questions as:
– whether the code can legitimately be referred to as ‘semiotic’.
– whether it is reasonable to infer a precursor system with fewer acids, and if so, how few, and with what core properties?
– whether Common Design or Convergence are legitimate alternative hypotheses to Common Descent for DNA sequence similarity.
– whether function is isolated on narrow ‘peaks’/’islands’, or occupies much broader regions of sequence space than those that the ID-er would prefer.
These people, and others, have done some very painstaking work, to try and get some real answers, rather than spamming blogs with tedious irrelevancies. That science of the genetic code.
LoL! No one knows if Common Descent is legitimate. It can’t be tested, so it isn’t science.
And you have no idea what ID-ers prefer. All you have are strawmen that you keep erecting and refuting.
I am convincing the people who matter- high school students. OTOH your position can’t seem to convinve anyone but the willfully ignorant.
OMTWO,
It appears to be a rather defunct blog. The only other reference I could find was to a 2004 symposium on the evolution of complexity.
Toronto,
Look at what you’ve claimed is not arbitrary – the relationships between the representations, protocols, and effects – the very things that cause the song to play. If they are not arbitrary, then they are physically determined. What you’ve said is that the music box must exist, and it must play Hey Jude.
Suddenly, it’s no longer reducible to the music box after all… and it’s arbitrary.
Since when did hard-coded information stop being information? If I slip my Visa into a card reader, are you suggesting that it doesn’t transfer information if the reader contains the hard-coded protocols for reading the hard-coded information on the card? And “indirection”? Are you suggesting that the reader only transfers information if it decides for itself how the card should be read?
So the protocols for reading my card are an inherent property of the material the card reader is made of?
If you’re going to go, ya might as well go big, right? This is the granddaddy of misplaced objections. Every material thing in the cosmos operates under the material laws of nature. The transfer of Morse code across a wired network occurs by a material process; the CPU in your computer operates by a material process, your name spelled across a piece of paper is a material process. What these examples have in common is that the relationship between the representation and the effect cannot be reduced to the material properties of the representation or the effect. They each require a materially isolated arrangement of matter to physically establish that relationship. This is exactly what takes place in genetic information transfer.
So, the digital code physically instantiated in an MP3 player is not a part of the physical process that causes the player to play, and that’s why it’s information? But if it’s not part of the physical process, then how is the information transferred?
May simply suggest you study the argument a little more closely.
Recip Bill,
Foregoing rhetorical ploys, the only reason an objector would grant that the entailments are a proper and valid description of the material process, is if they could not demonstrate them to be false. If they cannot be demonstrated to be false, then it is up to the objector to logically demonstrate that a system exemplifying the same material characteristics is the sole result of the material constituents involved. This goes to the very heart of your objection; it does follow that “that representational or symbolic content is a necessary condition for the emergence of systems displaying [these] material entailments”. The observed relationship between the input of the system and the output of that system is either determined by the material make-up being input, or it is not. There is no third option. In genetic translation, the pattern of the input sequence alters the output, but it does not establish what that output will be. Nucleotides only order anticodons; they do not establish which amino acids will be associated with them. That is accomplished in complete material isolation from both the input sequence and the output effect.
Alternatively, you can claim that the system is the non-falsifiable product of chance. At which point the objector is obligated to provide some rationale to demonstrate that sheer chance is preferable to the causally-adequate interpretation of the system.
I am still waiting for you to demonstrate the material observations are false, or that the observations are reducible to the material involved. You may also at any time claim that the system is the product of non-falsifiable chance.
NOTE: Regarding the false claim in your objection… You suggest that all known instances of semiotic information transfer are human. For this to be true, it would require that a bee flying off in a particular direction from the hive (in response to seeing a pattern in the flight of a returning bee) is an inherent material property of that particular pattern in flight, not requiring a physical protocol to establish the relationship between the two.
Madbat,
Yes, one of the things your post requires is a mechanism capable of creating and establishing the immaterial relationships fundamentally required for the recorded information contained in your post to exist. To explain this, you point to an incredibly complex material object, your brain. Whether or not your mental faculties can be reduced to material is not of consequence in this instance; the fact remains that your brain didn’t exist until after billions of years of evolution. So what was the mechanism capable of creating and establishing the immaterial relationships required for the recorded information to exist which organizes inanimate matter into Life in the first place?
“It’s all material” is an objection that has been answered enough times to not need repeating.
Hello Allan,
I appreciate your thoughtfulness in dealing with the evidence itself, but you make a lot of unwarranted assumptions about me personally in the defense of your opinions. Your assumptions are no less warranted than your objections themselves. The argument I presented has nothing whatsoever to do with the size of the code. Cut the code in half, and it’s still the same argument; the material observation are the same. You’ve erected an army of strawmen, and then cut them down one by one, even as you ignore what was actually presented.
Dr Who,
Autocatalytic systems do not transfer recorded information as stated in #1. This objection was answered in the original conversation with Nick Matzke, as follows:
Arbitron,
Is there a material observation I’ve made which you are prepared to challenge? Which one will you claim to be false and then support your objection with material evidence? If there is not one, then your objection can be seen for what it is. Also, to my knowledge David Abel has not published any work that describes the physical entailments of recorded information. If you have information otherwise, I’d like to see it. In any case, my argument makes no reference to Abel’s work, so your comment can once again be seen for its inherent meaninglessness. As for having facts, Nick Matzke and several others (such as Elizabeth Liddle, who’s blog you are on) have agreed that it is inconceivable to record transferable information without utilizing an arrangement of matter to represent that information within a system. Do you agree with them? Do you think the genome contains recorded information in the form of nucleotides sequences which transfer information through a materially isolated protocol? Or, are these material (observable) facts non-existent?
Thorton, Neil Rickert, and Cubist,
– – – – –
– – – – –
You must not be the “Thorton” or the “Neil Rickert” or the “Cubist” I have occasionally seen elsewhere on the web arguing from your position. As I recall it, those persons could at least form a coherent response, even if it was wrong. It is more than apparent from your responses here that neither of you fundamentally understand the argument enough to be making a response to it – much less being condescending.
– – – – –
Hotshoe,
I refer you to my response to Toronto.
Dr Liddle,
I answered your question in my response immediately after you asked it. I just checked, and you can still find my answer there, exactly as it existed prior to you claiming that you could not find it.
Dr Liddle, it is very clear you dispute that anything semiotic exists within genetic information transfer. The problem for you is that the process has been observed in terms of its physicality alone. Despite your personal preference to see it otherwise, it is those physical observations which you have been unable to challenge. Your situation has now been complicated by your admission that it is inconceivable to record transferable information without the utilization of an arrangement of matter to represent that information within a system, and further, that it is inconceivable to transfer that information without a second arrangement of matter to establish the relationship between the representation and its effect with that system.
It appears that, at this late date, you’d like to summarily wipe the slate clean and pretend as if the preceding 11 months of conversation never took place. Incredibly, you state above that you are prepared to be persuaded, but that I need to answer a specific question; a question that has been answered so many times that I have lost count, a question that would be quite literally insulting to anyone who had engaged it on your behalf the number of times I have. Even so, on this very thread I engaged it yet again, and you simply ignored it.
You created this blog partly in response to the conversation you and I had regarding information transfer going back to May of 2011. That discussion was the topic of your opening thread here, where you eventually recanted your claim to be able to create de novo information transfer within a simulation, claiming that my definition of information was unclear to you (even though you participated fully in the conversation and even complimented me on my definition being “more defensible” than others you were aware of) . You then later followed it up with another thread, which I referred to as an anthropocentric malaise. I backed that claim up with a substantial post going point-by-point in your response. You ignored that response and ceased participating in the thread, even after acknowledging it on more than one occasion – claiming that you would get around to responding at a future date when you had time (even though for months you maintained full participation among many other threads). Now you have made a third thread dedicated to the semiotic argument. Here again, you are claiming that you’ll get around to it someday, which is fair enough if you do. Yet thus far, it appears to be more of the same. You want me to respond to questions that have grown stale in their inability to penetrate the argument. I have absolutely no doubt that you’d love to turn to the physical evidence to challenge the argument before you – but you simply can’t. The material evidence is unavailable to you; and is resoundingly against you instead. It is the same for you as it was for Larry Moran, and Nick Matzke, and Robert Saunders, and Robert Collins, and Mark Frank, and everyone else I have engaged. So in response to your failed position, you seem willing to simply repose the incredible question of ‘what I think are the representations in genetic translation”.
This is the very nature of the argument Dr Liddle; you either do the empirically responsible thing and acknowledge the entirely coherent and observable evidence of the semiotic state in protein synthesis, or you bullshit about it instead. The modest conclusion of the semiotic argument is simply that the transfer of genetic information during protein synthesis materially demonstrates a semiotic state, and therefore requires a mechanism capable of creating it. You are on the wrong side of that evidence.
Upright BiPed,
Exactly.
There are software layers in a computer and hardware levels.
At the software layer, we have your “information”, but at the hardware level, we are working with material processes.
The software layer deals with “meaning”, (protocols and data), but at the hardware level, we are dealing with voltages.
One pin of an input port may be at 0.2V, and another at 0.15V.
We say they represent a “low” or 0 or FALSE.
Another pin may be at 4.9V and we call that “high” or 1 or TRUE.
But, if we have a pin at 1.2V and we are dealing with TTL levels, what does that mean and what information does that represent?
That value is not electrically valid and may even result in damage to a device.
That is what so many here are trying to tell you, that your “information” in a cell is limited in what it can “represent” by chemistry because it is part of the lower level process even though we “describe” it as “information”.
There are configurations of “information” in a cell that cannot exist because of chemistry and therefore the “search space” and “islands of functionality” they represent are much more limited and thus not truly reflected in “unrestricted” probability calculations.
Upright BiPed,
The second error you make is to assume all “information” has “indirection” and must be somehow translated from a “symbolic” form to a “usable” one.
Imagine a switch hooked up to a transistor driving a relay.
If I flip the switch, no CPU or any such process needs to “decode” the voltage level at the switch to determine whether the relay should be energized or not.
The switch is directly hooked up to the transistor and is not “information” to the transistor, it is part of the process.
It is only “information” when we have to show someone what we have found in the working of this device.
In other words, it is “information” only to an observer, not to the devices actually in the circuit.
Most likely represents an open-circuit to an IC input- OR a short-circuit conmnecting two or more points. And last but not least is there is a damaged device on that line.
What device would be damaged by 1.2V? Perhaps a damaged device was causing that low level.
Bt anyway I worked for a company that used non-zero and non-one levels for something- we called it a “code violation” and two sode violations followed by a specified sequence would alert the receiver that there was an incoming signal to respond to.
The information was in the design of the circuit.
Toronto, your response is incoherent with regard to the topic.
Your original objection was that the example of information transfer I gave didn’t actually transfer information because the information was “hard-coded” and therefore part of the system. But all information must be “hard-coded” in a material medium in order to exist at all, and that medium is necessarily part of the system it operates within.
So I asked you how information was transferred if it wasn’t part of a material system. You’ve responded by ignoring every single thing I posted, and simply returned with:
This does nothing to address the point. With software, you are still dealing with a material process. If you are not dealing with a material process, then please describe the nonmaterial process by which information is transferred within a system.
You also stated :
You’ve become quite lost in your argument. I never introduced the term “indirection” to the conversation – you did that yourself. My immediate response was that it has nothing to do with the issue at hand. The fact that you are now suggesting it is a fault on my part is simply stupefying.
One is left to wonder just what the hell you are talking about.
Quite frankly, it seems that following my last response to you, you are merely saying something in order to have something to say. Your response did not address a single thing I said, it only introduced another layer of unrelated babble. Given that this is the case, there is no longer a reason to respond to you.
UB:
That is factually incorrect. An excellent reason to grant your “material entailments” arguendo it to direct attention to a fatal flaw in the argument you build upon those claimed “entailments.” That flaw is lethal whether or not your “entailments” are true or false.
To wit: it would no more follow from an observation that all known instances of semiotic information transfer exhibit your “material entailments” that all systems exhibiting these “entailments” are necessarily semiotic, than it follows from the fact that all rainstorms make the ground wet that demonstrating that the ground is wet confirms the existence of a rainstorm – to repeat Thorton’s felicitous example (which recapitulates the logic of my comment vis murder.) It only follows that “Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state” if you define a “semiotic state” as “a system that demonstrates these ‘entailments.'” In which case this “confirmation” is tautological.
Nothing in your reply addresses this objection.
UB:
Not “logically.” However, contemporary biology is tasked by its own foundational assumptions to elucidate how these relationships arose across history by natural means. Such questions are settled empirically, not logically. This is the stuff of empirical science, not logical sparing.
Yours is, however, a telling statement, in that it exhibits your apparent belief that you have shown “logically” that biological functions such as the transcription of DNA into proteins are semiotic, and therefore can’t have originated by unguided processes. And it exhibits your apparent belief that these questions can be settled from within an armchair.
In examining this, It is worth looking more closely at your misuse of the term “entailment.” “Material evidence,” independent of theory, doesn’t have entailments. Rather, definitions, propositions, and theories have entailments. As an example, It follows as an entailment of the definition of “bachelor” that each bachelor you encounter will be male. This relationship isn’t established or confirmed by means of “material observations,” – we don’t sex each bachelor we encounter to confirm that all bachelors are indeed male, as though another outcome was possible or the action is even intelligible. Rather, the result follows from the definition of “bachelor” within our culture, because definitions can have entailments.
Your “material observations” concerning the “transfer of recorded information” aren’t “entailments” at all. They are, at best, your proposed description of the minimum characteristics of the transfer of recorded information. By itself, it is an interesting description that may have merit. In a sense, these characteristics become your definition of “transfer of recorded information.” It is therefore no surprise that whenever you observe the transfer of recorded information as you define it it exhibits these characteristics.
However, your follow-on claim that systems that exhibit those minimum characteristics are also necessarily semiotic is no more than that – a claim. The only sense in which “semiotic status” follows as an entailment of your “material entailments of the transfer of recorded information” is in the sense that you have defined “semiotic state” as “a system that exhibit these minimum characteristics.” But nothing in that compels one to accept that definition, or that claim.
As I parse this, I am seeing more clearly where your argument goes off the rails (apart from the first logical train wreck I identified above.) Perhaps you think that a system that exhibits “the presence of these material characteristics” necessarily entails “a semiotic state” in the same sense that “the presence of a bachelor” necessarily entails “the presence of a male.” You certainly state your position with conviction that that is so. But that simply doesn’t follow. It certainly doesn’t follow from your description/definition of information transfer, and most of us would further argue that “semiotic” communication entails many characteristics, most often exemplified in human communication, that are wholly absent from your proposed minimal characteristics of the transfer of recorded information. Hence we argue that “semiotic” and your “material entailments” are not coterminal.
The reason for your inclination to prefer a definition of “semiotic” that is implicitly equivalent to “the presence of your ‘material entailments'” seems clear enough to me. You’ve been coy about it, but you obviously wish to claim that it is inherently, even logically impossible that semiotic information transfer can have originated without intelligent agency, and therefore it is impossible that information transfer from DNA to sequences of amino acids can have originated absent intelligent agency. But as an argument intended to compel that conclusion, your semiotic theory fails.
This paragraph nicely exemplifies a problem inherent in your argument, identified above. Specifically, it assumes – perhaps unwittingly – the necessary equivalence of “requires a physical protocol establishing a relationship (etc.)” and “semiotic” information transfer. You can propose that equivalence, but nothing in your argument entails or compels it – other than your definitions, which themselves are no more than claims. As does your entire argument, this statement assumes its conclusions.
Upright BiPed,
My purpose here is to show “onlookers” how bad your arguments are.
If a reasonable discussion can come out of it that’s fine, but not necessary.
Of course I introduced the term because you don’t seem to understand that “indirection” is a characteristic of transferring or storing “information”.
You can’t use the term “transferring information” without using “indirect references” to the “data”.
You claim to understand biology by making analogies to computers but you don’t even understand them well enough to even use the terms properly.
Joe G,
What I meant by this is that the “information” represented by 1.2V is ambiguous to a TTL level device that is reading it.
In 5V TTL, a low is 0.8V or below and a high is 2.2V or above.
So what does that represent to a healthy device reading it when the level is not in either window?
That’s what I was trying to say, that there are restrictions, at the hardware level, to what we can claim is valid information and the same applies to living cells.
Not all “information” is allowed and thus the “search space” and “improbability”, shrinks.
Upright BiPed to English Translation: “I couldn’t address the valid points raised against my pet hypothesis, so I decided to post a snarky non-answer and hope no one notices the difference.”
UB
It is true that the argument remains intact when you cut the code in half … and when you cut it in half again … and again … but ultimately, you are left one amino acid (for the sake of argument).
You have a ribosome, an RNA-based enzyme that takes two substrates (tRNA/mRNA) and condenses the amino acids into a peptide chain. It sits at the end of a biochemical pathway that includes an aaRS which charges the tRNA with the amino acid. That system is no different from many another biochemical pathway – a series of chemical inputs and outputs. Now, you may argue that all biochemical pathways are IC, but that is a different argument.
But what is added by calling that system ‘semiotic’? In the simplified version, there is no code; there is simply a chemical mechanism, somewhat convoluted, whose output is a molecule formed from condensation of repetitive units of one amino acid. It is no more (or less) informational than any other chemical system.
Now, I accept that this reduction may be a complete fantasy. There may never have been such a system. But the point was not to knock down straw men, but to unpack the argument to its chemical heart and then rebuild. A simple one-acid system would become a two-acid system by duplication of an aaRS. By increments, codon groups can become subdivided, until usage becomes critical. IF a simple one-acid system is not semiotic, how does a two-acid system become so? Or, are all interactive enzymatic systems semiotic?
I see the responses that were posted overnight, and will be happy to respond in the next 24 hours or so.
Thanks…
Thank you, Upright BiPed.
No, you did not. I asked:
Your response was:
It is utterly relevant. If you are going to appeal to semiotics in your argument then you need to explain how they map on to the process you are arguing about. And saying that a question is “not relevant” is not answering it.
I profoundly disagree that it is “not relevant”.
There are many kinds of information transfer in biology: from environment to population genome; from parental genome to offpring genome; from organism genome to organism phenotype; from cell to cell within a multicellular organism; from the environment to the sensory apparatus of an organism.
All these information transfer processes involve DNA, in lots of different ways. I see nothing “semiotic” about any of them, nor do I see any mystery about how the “information” is produced. For example, the information that is passed from the environment to my retina is simply generated by light reflected off, or given off by, objects. Nothing “semiotic” about that, until I start to recognise the pattern of light as one of your posts. Then it becomes vehicle of information transfer between an intelligent sender (you) and an intelligent receiver (me), and I recognise the information not merely as information about an object that I must avoid spitting at, but as information from an intelligent member of a community of symbol-users of which I am also one.
I dispute that the word “semiotic” is relevant to genetic information transfer. And you dispute that my dispute is relevant!
My situation is complicated by the fact that you have not been able to clarify what analogous roles to those played in a human semiotic transfer system are played by which players in a cell, or population of cells. Indeed, you have regarded this question as “not relevant”. And so I remain at a loss to know what your semiotic theory actually means.
What I would like, at this late date, is for you to present a coherent theory in which you actually lay out what you mean by “semiotic” in the context of biological information transfer, in, for example, the instances I have given above.
Well, not exactly. But I did hope it would host that conversation, as well as many others.
Upright BiPed, it seems to me that you are massively missing the point of my posts. I am not disputing the physical facts of what goes on in a cell. I am disputing your analogy with semiotic information transfer between intelligent members of a shared symbol-using community. I do hope you will engage with this point. In the mean while, I would ask you to stop casting aspersions on my willingness to engage with you, not to mention my integrity.
It is my view, Upright BiPed, that the phrase “semiotic state” as applied to protein synthesis is bullshit. I will remain of that view until you can lay out for me exactly how the relationship between two intelligent agents communicating information to each other using a shared symbol-system maps on to the relationships between biochemical entities.
You are not presenting “evidence” at all. You are presenting an analogy coupled with a non-sequitur, in my view.
And were I as ungenerous as you, I would regard your refusal to engage with my question as “evasion”. As it is, I honestly believe it is because you haven’t seen my point.
But I’d be grateful if you would try.
Stickied this for a bit, as Upright BiPed is back in town 🙂
Elizabeth,
You are not presenting “evidence” at all. You are presenting an analogy coupled with a non-sequitur, in my view.
I absolutely agree.
From my encounter with UB on another forum:
He did not reply.
OK, let’s try to lay this thing out.
Upright BiPed is talking, it seems, about the process by which the nucleotide sequence in a DNA molecule results in a specific protein being synthesised.
There are several stages to this process, but I will simplify: Firstly, the DNA acts as a template, essentially, on which a strand of messenger RNA is constructed. Leaving aside the editing of the mRNA strand, the mRNA bonds to a certain set of tRNA molecules. The tRNA molecules are themselves formed on the same templating principle as the mRNA, i.e. they are the set they are because of certain DNA sequences.
One end of each of these tRNA molecules binds to a specific triplets of mRNA and the other end binds to to an amino acid. Some members of the set of tRNA molecules share the same amino acid end, but have different mRNA triplet ends.
The result of all this is that we have a strand of mRNA bearing a sequence of tRNA molecules each carrying a specific amino acid, so we have a string of amino acids, the order determined by the sequence of nucleotide triplets in the mRNA, which in turn is determined by the sequence of nucleotides in the DNA. An RNA catalyst (the ribosome) then separates the amino acid string from the tRNA and outputs a connected folded protein.
Upright BiPed wants to describe this as a “semiotic” system, because many sets of tRNA molecules would do the job, as long as there was only tRNA molecule for each possible triplet, and that each tRNA molecule could only attach to one amino acid. It doesn’t matter, of course, if more than one tRNA molecule binds to the same amino acid, and that is in fact what we have.
So the system of tRNA molecules is a bit like a symbol system – each tRNA molecule “represents” an amino acid. Not only that, but the mRNA molecule also “represents” an amino acid, but that representation, like a human symbol system, is arbitrary – any triplet could “represent” any amino acid; the fact that any one triplet “represents” any one amino acid is simply an epiphenomenon of the particular set of tRNA molecules that the DNA molecule templates for.
An equally good system could work with a completely different set of tRNA molecules as long as the rule that there has to be only on tRNA molecule for each triplet, and each tRNA molecule has to be specific to one amino acid.
So let’s grant that such a system can be described as “semiotic” on the grounds that the mapping is arbitrary, not a matter of necessary chemistry.
In principle we could alter the DNA of a cell so that a different set of tRNA molecules was produced, and recode the protein coding portions of the genes into the new mapping, and get a perfectly well functioning cell. So in that sense the “language” of the cell is the “language” of a community of “shared symbol-users”, so that as long as the DNA in a community of cells conforms to the community symbol system, i.e. each cell’s DNA generates the same set of tRNA molecules, each cell’s DNA will be “read correctly” correctly by the cell’s tRNA molecules and the correct protein produced at the correct time.
And, it seems, all living things have (roughly) the same “symbol” system. In practice this means that all living cells have a stretches of DNA that form templates for the same set of tRNA molecules.
So far so good.
But UBP then draws two conclusions that are IMO quite unsupported. He says that:
which I will provisionally accept on the assumption that the “semiotic state” of “the transfer of genetic information” simply means that translation from mRNA sequence to amino acid sequence is achieved by means of a specific but arbitrary set of tRNA molecules templated by the DNA,
“and therefore requires a mechanism capable of creating it.”
Sure. There needs to be a mechanism by which that set, or an equivalent set, of tRNA molecules came to be templated by the DNA, and not some useless set in which one triplet could result in any one of a number of amino acids.
So?
Why shouldn’t evolutionary mechanisms result in such a set?
It’s an interesting challenge, and one that I would still like to rise to (although I am much shorter of time than I was when this conversation started). So perhaps someone else would like to take it on.
So here is my proposal to UBP:
If someone were to produce a virtual GA environment in which, evolved, starting with a population merely of self-replicating virtual organisms that produced no “proteins”, a coding system by which the virtual genomes coded for a set of “symbols” that in turn resulted in a “reading” of other parts of the genome to produce reproduction-enhancing “proteins” – would you accept the result as evidence that evolutionary mechanisms can result in the evolution of a “semiotic” system of information transfer?
I’m not saying I can, or will, do it, but I’d at least like to get agreement on what would constitute contradictory evidence for your claim.
Elizabeth, I’m a little confused by your use of the word “arbitrary” above. Doesn’t seem to fit, somehow.
Perhaps it’s the wrong word. “Fortuitous” maybe? What I mean is that any set would do as long as the set itself has certain properties.
The properties don’t lie in the molecules themselves, but in the set.
Like the arbitrary mapping of the symbol “b” to the sound “buh”.
Any symbol would do. So the mapping is arbitrary. Whereas the mapping of a left hand button to a left hand stimulus and a right hand button to a right hand stimulus isn’t “arbitrary”.
You repeated claim that any part of the relationship required for the recorded information contained in my posts is immaterial is not evidence or justification for that actually being the case.
Really? I don’t see an answer anywhere in this thread. If you think that you have answered this and actually shown that any part of the kind of information transfer you speak of (e.g bee dance > behavioral response by observing bees) requires anything immaterial, I would appreciate a citation. Otherwise, all you are doing here is handwaving.
Reciprocating Bill,
Well Bill, the fatal flaw has yet to be spoken, hasn’t it? And did I not already mention rhetorical ploys? Nonetheless, I appreciate how you’ve sought to put yourself in the enviable position of not needing any evidence to support your position. You’ll no doubt begin to wax institutionally about empiricism next. The irony will then be complete. 🙂
The flaw in Thorton’s counter-example, as stunning as it was, is that there are many ways in which the ground could become wet, none of which has anything to do with rain. I find it amazing that neither of you grasped this before typing. This is elementary stuff. On the other hand, if every single time we found the ground wet, throughout all existence, and in no circumstance did we ever find a single instance of wetted ground that did not occur as the result of rain, and we even understood why that it must be this way – then we would have a completely legitimate inference to suspect it had rained if we found the ground wet.
You’ve tied your argument to an example that has nothing to do with reality, or our written and compiled knowledge of reality. We know thousands of ways that the ground could become wet; we can make them up as we go, over and over again. We would never run out of ideas of how the ground could become wet. Yet you don’t know a single way to record and transfer information that doesn’t entail the physical roles and dynamic relationships as given in the argument you wish to refute. This fact alone demonstrates the distinction between our two positions.
Then is it also a tautology to define heat dissipation as ‘the transfer of heat from a hot object to a cool object’, and then suggest that demonstrating heat dissipation also demonstrates a tenet of the Second Law of Thermodynamics.
In any case, I didn’t set out to define a semiotic state as a system that demonstrates the listed entailments. If you’ll read the argument as it was presented, I described the transfer of recorded information by its material interactions alone. It was demonstrated that the material interactions within all instances of recorded information transfer have common objects which play specific roles in a specific dynamic process. In those observations, I used descriptive phrases from human information transfer (ie, representations and protocols) because those descriptive phrases are an accurate reflection of the material roles those objects play in any form of recorded information transfer. This is directly equivalent to the accepted standard of describing protein synthesis as a process of “transcription” and “translation”, which are also descriptive phrases taken directly from human information transfer. Each of these terms are legitimate because they accurately describe the material observations at hand – ie transcription is materially one thing and translation is materially another. The transfer of information during transcription is controlled by the material forces of base pairing, but translation is something else entirely. Translation is not controlled by the material state of nucleic acids, but by the material state of the aminoacyl synthetases (and following one of the entailments of recorded information, that action occurs in material isolation). Likewise, the descriptive terms I added are also accurate in describing the material interactions. For instance, for one thing to represent another thing within a system, it must be separate from it (as is the case in nucleic sequences and their resulting effects), and a communication protocol is an isolated formality which establishes a standard for the transfer of information (as is the case with aaRS charging tRNA prior to entering the ribosome).
Having established a valid description of the transfer of recorded information, and having used descriptive terms that are functionally legitimate to those material observations – only then did I even mention semiosis. By my suggestion that a ‘demonstration of recorded information is also a demonstration of a semiotic state’, I make the claim that recorded information is – by necessity – semiotic. I make that claim squarely upon material observation, and I challenge you or anyone else to demonstrate otherwise.
You suggest that by my claiming that recorded information transfer is necessarily semiotic, I have created a tautology. I suggest you view it in other terms in order to test if what you’ve called a “lethal flaw” actually exist – one which you’ve also claimed doesn’t require evidence to support it.
A tenet of the Second Law of Thermodynamics states that heat travels from a hot object to a cool object. ‘Heat traveling from hot to cold’ is to the Second Law of Thermodynamics what the ‘entailments of information transfer’ are to recorded information – at least to the extent that one is an observation and the other is a classification. One establishes the material basis of a described law, and the other establishes the material basis of a described phenomena. If I then define “heat dissipation” as “heat traveling from a hot object to a cold object”, and suggest that a demonstration of heat traveling from hot to cold also demonstrates a tenet of the Second Law of Thermodynamics, then I have established a correspondence between “heat dissipation” and the Second Law by virtue of the material observations. It is very much my intent to establish the same correspondence between semiosis and recorded information by virtue of the material observations. Recorded information must be semiotic in the same way that heat dissipation must travel from hot to cold.
What you’ve failed to recognize in your objection is that I have materially demonstrated that recorded information transfer is necessarily semiotic. You are free to challenge the Second Law by materially showing that heat needn’t travel from hot to cold, just as you are free to challenge my claim by materially showing that recorded information transfer needn’t be semiotic. What is unacceptable is to haphazardly try to slap a logical fallacy on it, and then claim no evidence is necessary.
Ah, you’ve installed the irony without the need to wax about empiricism.
By the way – biology is no different and any other science, in that they are all tasked by the human desire for a rational, systematic search for knowledge and understanding. It has never been a foundational assumption of that search to make valid material observations, then ignore observed causally-adequate mechanisms in favor of ones that we cannot even conceive of.
There’s no need to disparage the armchair, there’s little doubt that it’s played an inspiring role in the history of knowledge. As for settling questions, you may do so by showing the material observations are false, or by demonstrating an unsupported assumption or internal contradiction in the conclusion of the argument.
Here is the misuse of the term entailment to which you refer: “There is a list of physical entailments of recorded information that can therefore be generalized and compiled without regard to the source of the information. In other words, the list is only about the physical entailments of the information, not its source. I am using the word “entailment” in the standard sense – to impose as a necessary result (Merriam-Webster). These physical entailments are a necessary result of the existence of recorded information transfer.”
So let’s add it up: I used the word, then stated I was using the word in the standard dictionary sense, then stated the definition of that word from a standard dictionary, Merriam-Webster, then I coherently restated the sentence using the Merriman-Webster definition in place of the word itself – and you refer to this as “misuse”.
It is hard to parse here if you are referring to material evidence in the sense of an observation or in the sense of material reality. It is certainly not true that until we defined, and proposed, and theorized about heat dissipation, heat transfer from hot to cold was not a physical entailment of heat dissipation. I hope you don’t mind if I consider these material realities to be more important that your rulings as to what can be what, and when.
That is true, but it does not follow that each male you encounter will be a bachelor. This is the same error you made earlier with regard to the rain-soaked ground, you’ve simply moved it to a definitional battleground. Your counter-examples simply do not reflect the argument in front of you.
Is the observation (that heat always transfers from hot to cool) an observed entailment of heat dissipation? In other words, is it “imposed as a necessary result” of heat dissipation?
Is the observation that heat always transfers from hot to cool, at best, a description of a characteristic of heat transfer? Is it also true that the more interesting part of this exercise is whether or not the observations are valid?
I have already stated that a primary goal of the argument was to describe the issues by their material characteristics alone. In doing so, tribal skirmishes over the use of ‘words’ can be kept to a minimum because it is the physicality of the objects that are at issue.
Given that the observations are about their observed physicality, I wouldn’t have it any other way.
Of course it’s a claim. It’s also a claim that heat dissipation must transfer from hot to cool. It’s a claim that sound waves reverse directions at the boundary of a horn. We do not speak physical regularities into being. The question is not whether it is a claim; the question is whether that claim is supported. I have supported my claim, and you cannot show a flaw in the material observations, nor can you provide a method of recording and transferring information that doesn’t entail the roles and relationships described in the observations I’ve provided.
I’ve already answered your first sentence here. As for what compels us, there remains the simple fact that you can’t refute the observations.
Again, your assertion will require evidence, not repetition.
To parse this: there are characteristics of semiosis that are most often exemplified by human information transfer, and these are absent from the entailments which are exemplified by any other form of recorded information transfer. So, the question is therefore straightforward. Which of these characteristic of human information transfer nullify any of the material observations made? If that answer is none, then please explain how this helps your case?
The conclusion of the semiotic argument is that the transfer of recorded information is demonstrably semiotic, and therefore requires a mechanism capable of creating a semiotic state. If that is not a valid conclusion based upon the material evidence, then state the specific reason it is invalid.
The paragraph you cite was a challenge to your implied claim that semiosis is a human phenomenon alone. Is the relationship between “a bee flying off in a particular direction from the hive (in response to seeing a pattern in the flight of a returning bee)” an “inherent material property of that particular pattern in flight” – or – does it require “a physical protocol to establish the relationship between the two?” If it requires a physical protocol to establish the observed relationship, then it is in complete material agreement with the entailments provided. Consequently, it is not an unsupported assumption, but is instead backed up by material observation. This nullifies your earlier implication that semiosis is a purely human phenomena. Your position is indefensible from a material perspective.
You’ve now had your say.
In the course of one post, you’ve tied your argument to a ridiculous non-sequitur about rainstorms, you’ve laid out a position that can only be substantiated by evidence that no one can even conceive of, and you’ve claimed that your position has the unique quality of requiring no support. I doubt that in the long run you will consider this the decisive beat down of the semiotic argument you had been promising.
Hello Allan,
Agreed, for the sake of argument. But, cutting the code in half renders it all but worthless judging by the functional load required of it today. Cutting in half again renders it all but worthless by virtually any standard. Cutting it in half again renders it worthless regardless of our imagination.
The ribosome is an interesting object to contemplate. Along with the (already discussed) requirement for a stable system of protocols, a sequence of nucleotides (carrying encoded information) requires a spatial and temporal mechanism in order to execute the required translation into amino acids, which the ribosome provides – a nucleoprotein that itself requires an intricate process of synthesis, modification, component assembly, quality control, and maturation in order to come into being. And as I understand it, it also requires an enormous system of regulation and energy management after assembly in order to provide proper ribosomal activity. Not only are ribosomes critical in terms of fatal damage during cell reproduction, but they have been characterized as “very expensive” to construct in terms of cell resources; so expensive that quality checks are not conducted just upon the final product, but during the maturation process of individual components so as to throw out any malformed products prior to final assembly. Again, as I understand it, the contemporary two-subunit E. coli ribosome is made up of a ribosomal RNA consisting of 1540 nucleotides, as well as 21 individual ribosomal proteins in the small subunit. The large subunit is made up of two ribosomal RNAs, one with 2900 nucleotides and the other with 120 nucleotides, plus 33 ribosomal proteins.
I suppose the point I’m driving at, is that (not disparaging the work of researchers who have postulated a simpler code to build a simple protein) simply imagining a smaller code is a little like the immovable object meeting the unstoppable force. Take a person like Vetner who is trying to define a minimal organic system, then when he gets there, tell him that he must accomplish it with only 6 or 8 amino acids. At some point this is not about unwarranted incredulity or a lack of imagination, it is that it must be functionally possible. To say that a ‘one acid system can become a two acid system’ is to say that there are no limits to biochemistry, everything is possible.
Thorton,
Is this the powerhouse “valid point” you think I am avoiding:
Okay, I’ll respond to it.
Go find any person on the surface of the planet. Pick anyone you wish. Sit down and explain this entire issue to them. Take your time. Tell them everything I have said and everything you have said. When you’ve finished, ask them these two questions:
a) can you think of any reason the ground could become wet that doesn’t include a rainstorm?
b) can you think of any way to record and transfer information that doesn’t include an arrangement of matter to represent an effect within a system, as well as an arrangement of matter to establish the relationship between the representation and the effect within that system?
Madbat,
The letter “a” represents the “ahh” sound that people make in speech. In cursive writing it is made with a loop and a tail at the top of the loop coming from the right side. Some people write the letter “a” starting at the tail and looping down. Others make a straight line a then pick up their pen, reposition it, and then make the loop. Others do it the same way, but in reverse order. Some start at the bottom of the letter and go up, while some start at the top of the letter and go down. Some make their “a” with all curved lines while others have a mixture of straight and curved. Some even mimic the curve by using straight lines at various angles.
Do you think the letter “a” represents the “ahh” sound as a matter of material law? In other words, do you believe the “ahh” sound must be represented by the letter “a”?
If it isn’t a matter of material law that the “ahh” sound must be represented by the letter “a”, then it must be arbitrary to those material laws. Is that correct? If it is arbitrary to the material laws, then the relationship between the “ahh” sound and the English letter “a” must be…?
Dr Liddle, I will return to respond to your posts at a later date. I am off to the country for the weekend.
Nice illustration of genetically, developmentally and/or environmentally induced behavioral variation. Not sure what your point is, though.
Of course. Lots of different material laws are involved in that representation. The ones you seem to be interested in here are the alphabetical ones. Like you said earlier, all the components needed here are perfectly material *arrangements of matter* – some on paper, some in brains, some in air pressure.
In context of the English language, and most languages more closely related to it: of course! If the laws of English allowed the “ahh” sound to be represented by, e.g., the writer’s favorite icecream flavor instead, communication would be practically impossible. And communication is, after all, the usual goal of using language.
Are there other languages that use other symbols than the letter “a” to represent the sound “ahhh”? Of course! There was and is obviously a lot of environmental and random variation influencing how the laws of a language arise and evolve. That obviously does not render the laws that currently govern the language all of a sudden immaterial. They are still in all components relying on perfectly material *arrangements of matter*. So I must assume that it is the variation influencing the exact content of the different language laws that you think is immaterial? How so? All I see in operation when observing the ongoing evolution of language, i.e. changes in the exact contents of language laws, is perfectly material, random or systematic intrinsic (to the user of the language), and random or systematic environmental variation at work. The vast literature on linguistics, especially historical linguistics, is a good testimony to this assessment.
Upright BiPed:
Scenario 1a
Let’s say that 50% of the time the ground is wet, we know it was sprinklers.
And the other 50% of the time the ground is wet, we don’t know what it was.
Are we entitled to conclude that 100% of the time it was sprinklers?
Scenario 2a:
Let’s say that 50% of the time the ground is wet, we know it was sprinklers.
And the other 50% of the time the ground is wet, we don’t know what it was, but we know the sprinklers were turned off.
Are we entitled to conclude that 100% of the time it was magic sprinklers?
Scenario 3a:
Let’s say that 50% of the time the ground is wet, we know it was sprinklers.
And the other 50% of the time the ground is wet, we don’t know what it was, but we know the sprinklers were turned off. Moreover, we notice that on this 50% of the time the humidity is around 100%, whereas on the other 50% of the time the humidity is around 50%.
Are we entitled to conclude that 100% of the time it was magic sprinklers?
Compare:
Scenario 1b:
We observe at least two classes of object that seem to exhibit some kind of information transfer.
A subset of these are human communications.
The remain instances are unknown in origin.
Are we entitled to assume that the remaining instances are human communications?
Scenario 2b)
We observe at least two classes of object that seem to exhibit some kind of information transfer.
A subset of these are human communications.
The remain instances are unknown in origin. We know they are not human communications.
Are we entitled to assume they are magic communications?
Scenario 3b:
We observe at least two classes of object that seem to exhibit some kind of information transfer.
A subset of these are human communications.
The remain instances are unknown in origin. We know they are not human communications. We also notice that these remaining communications occur in self-replicating objects, whereas the communications between humans do not occur in self-replicating objects.
Are we entitled to assume that the remainder are magic communications?
Look forward to your return 🙂
Upright BiPed,
Agreed, it must be functionally possible. At some point we must drag ourselves back to the real world. The current thinking is that the protein system was preceded by an RNA world. You may have reservations about that hypothesis, but if there was, that is the system that preceded our genetic code. The main actors in the protein transcription/translation system are RNAs. Protein itself has a very small role to play – except in the critical matter of the aminoacyl tRNA synthetases, which are all protein.
So of course, you cannot make protein aaRS’s without a protein-manufacturing machinery. But, this is the modern system. And we come back to my original point, that it suits the general ID argument to say that the minimal requirement for a functional cell is the modern system – the code and the OoL are placed very close together. You might allow a few fewer acids, but you feel there must be some. But there don’t have to be any.
The fact that protein synthesis is today used for catalysis does not mean that protein synthesis has always been ‘for’ catalysis. It is well-established that RNA has catalytic ability. That is what a ribosome is – catalytic RNA, perhaps one of the most critical catalytic functions in our arsenal. If ribosomes can do what they do, with no direct involvement of protein in the chemistry of their action, this suggests a potential for a world that had no fundamental need for protein. Although less effective, RNA-only life would only have to compete with other RNA-only life.
From such a system of RNA catalysts, a ribosome could readily emerge. RNA clearly has the chemical capacity to condense polypeptides. The original protein product was almost certainly not a catalytic enzyme – if it was a simple repetitive polypeptide, it cannot have been – but proteins do have other functions, structural or as cofactors and regulatory molecules. It is from this simple precursor that I envisage the system arising. More complex peptides are made possible by subdivision of the code, as I noted – with the likely result from chemical constraint that codon neighbourhopods will have the apparently ‘designed’ character they have today.
I think there is likely to be an ‘alphabet’ threshold below which direct protein catalytic activity is not possible. You appear to need a mix of hydrophobic and hydrophilic, charged and uncharged side-chains to form the right kinds of structure. Once that threshold is crossed, the superior catalytic abilities of protein begin to take over – including the function now taken by protein aaRSs. And ancestral RNA life would likely have been obliterated under the onslaught.
And I freely admit that this is largely speculation (with, however, some circumstantial support). But the point is to provide a biochemically plausible pathway by which a code may arise, without needing to invoke a designer. Being plausible is, granted, a long way from being actual, but the fact that one can imagine plausible ways by which modern, apparently IC, systems can arise should be a caution against pinning too much on their actually being IC.