Upright BiPed responds

To a post a made back in October 2011, here.  He posted his response shortly after mine, at UD, and I copied into that earlier thread on November 14th, and promised to respond later.  I never did, so here is his response again, in full.

I will make my responses in installments, in the comments, as it is rather long.

Upright BiPed’s UD post is below the fold:

Dr Liddle,

You asked me to respond to a post you made elsewhere. This is that response, but I make it here where you left our last conversation. Your counter-argument is based on a major false premise and several instances of a failure in conceptualization. These permeate your comments. I’ll deal with that false premise, but first a couple of observations about your response.

So UBP’s starting point seems to be that the “information” we say a genome contains is not different from “information” in other senses.

Different information systems are different by virtue of their implementation into different substrates, and also in the types of effects that result, but the physical objects involved in the transfer share the same dynamic relationships.

A musical box is an interesting example, because unlike some other information transfer systems, like the pixels on your screen you are viewing right now and from which you are receiving information about the contents of Upright Biped’s post on UD, the sequence of pins on a music box cylinder are actually instrumental in making something else, in this case a melody, and thus bears a closer homology to the sequence of base pairs on a DNA molecule which, by a series of physical operations, results in the making of a protein.

The pixels on your screen are “making something else” as well. This is evidenced by the simple fact you know the contents of my post. The substrates change, the effects change, but the dynamics of the transfer stay the same.

UPB claims the music box represents “recorded information”, which implies that the information started elsewhere and was “recorded” on to the music box. However, I think he is making the point that without a mechanism to get the “recorded” music box back into the form of music again, the information isn’t truly recorded, which seems fair enough. After all, if I translated my post into unbreakable code, it wouldn’t really be recorded information because there would be no way of getting the information back out again. So in the music box example, the music box is a way of “recording” a piece of music composed by someone, and getting that piece of music back out again, at a different time. A phonograph recording (the old wax cylinder kind) would be an even better example.

If you took the cylinder out of a music box and then lost the box, the representations would still be “truly recorded” even if the box was lost. If you never found the music box, or a replacement, then that would simply be a melody you’ll never hear. That doesn’t change the representation in the cylinder.

Translating your post into an unbreakable code poses some problems. An unbreakable code, as a matter of principle (practicality may differ) is a code without rules, and a code without rules isn’t a code at all. Moreover, translating your post into a code with no rules has nothing to do with the word “translate”. How would you accomplish it? To say that “it wouldn’t really be recorded information because there would be no way of getting the information back out again” is to make an observation about non-existent entities that have nothing to do with the topic (recorded information transfer). It’s fluff.

In my last post to you I made the point that you repeatedly try to smuggle a mind into the conversation. The reason for this is obvious; it primes the pump that the observations are anthropocentric, and therefore flawed. But it doesn’t work. The fact that humans are symbol makers is not a question; of course we are. But even if we weren’t, the dynamics of information transfer among humans (as in non-human transfer) wouldn’t change one iota. The anthropocentric flaw is not being able to remove yourself from the sample.

No, I don’t think that works. For a start, “Lizzie has seen an apple” is not a recording of Lizzie’s thought, it is an inference about what Lizzie was thinking. Lizzie’s hearer has indeed received information from Lizzie, but not exactly the information that Lizzie sent. So it seems to me that language is a very different kind of information transfer system from a phonograph, or a musical box, or, indeed a reproducing organism.

Lizzie is a symbol-maker saying “I’d like an apple” to another symbol-maker. That fact doesn’t change the dynamics of the transfer in any way; it only changes the effect of that information in the hands of the a free-agent receiver. What you describe as a “very different kind of information transfer” is only a very different kind of effect, coming as the result of a free agent being the receiver. But, the dynamics of the transfer haven’t changed. Like I said, you have to remove yourself from the sample.

In these three examples, we start with a physical pattern of some kind (a performance, a melody, an organism) and we end with a recreation of that physical pattern (a rendering of that performance, the sound of that melody, a second organism). In the case of language we do not. There is no protocol that can create an apple from the word apple, although uttering the word may induce someone else to go fetch one.

Okay, so maybe it didn’t occur to you that the effect of the sound pattern “apple” is not the sudden appearance of an apple coming from the pattern of the sound. The fact remains that the word “apple” has an effect, and the actualization of that effect (from the sound pattern of the word) follows the same dynamics as any other form of recorded information transfer.

Again, remove yourself from the sample. Stop injecting issues that only pertain to you as a symbol-maker. Observations having to do with what a free agent can do with information does not change the physical dynamics observed in the transfer.

This, it seems to me is because the word “apple” is a symbol, or, in Saussure’s term, a signifier that is linked to a signified (aka referent) in this case a specific kind of fruit. UBP appears to want to say that this linkage between signifier (word) and signified (fruit) is equivalent to the link between the sequence on a music box cylinder and the melody that emerges, and that therefore the music box cylinder (and therefore a base sequence in a polynucleotide too) is a symbol for the sound pattern that emerges from the music box in the same way as the word “apple” is a symbol for an actual apple.

But it clearly is not. When I say the word apple, and you hear it, no apple is created, though you may reproduce my image of an apple in your own inner eye. But the referent for the signifier “apple” is not “the mental image of an apple” but an actual apple. So the linkage between signifier and signified in language (the relationship of a “sign”) is qualitatively different from the relationship between a recorded physical object or pattern and its reproduction.

Well, it was obvious from the start this was where you were heading, and you’ve done me the favor of encapsulating your error in a single sentence: “But the referent for the signifier “apple” is not “the mental image of an apple” but an actual apple.” So my question to you is simple:

Do you have an apple in your head -or- Do you have a “mental image of an apple”?

Really, Dr Liddle. Have you been taught that when an animal communicates it doesn’t know it’s communicating, so it expects apples to appear as it gestures? And will you please take special note; none of this anthropomorphism has anything to do with the observed dynamics of information transfer, instead it revolves around a certain (repeating) disciplinary issue.

I say again, you are a natural symbol-maker. You transfer information. This is what you do. Accept that, then to the best of your ability, remove yourself from the sample. Recorded information goes in a lot of different directions. It’s an anthropocentric error to continually describe a particular aspect of being human as if that aspect alters the observed dynamics. It doesn’t. I suspect that you probably know this, but are left to ponder the sudden appearance of apples. This is what the evidence of your rebuttal would indicate.

It seems to me that UBP is defining recorded information as something that requires a discrete protocol, then regards it as noteworthy that all instances of recorded information require a discrete protocol.

This is a question of the structure of the system. In order to make your case, it requires you to deal with what you’ve ignored in your objection. Recorded information is an abstraction (within a system) which is represented in an arrangement of matter/energy. For one thing to represent another thing within a system, it must be separate from it. If it is a separate thing, then there must be something that physically establishes the relationship between the two. That is what the protocol does. The dynamic involved is that all three of these physical things remain discrete, and this has been validated by observation.

And finally, describing the parts of a system does not result in a circular argument.

In other words, the table – an object with pattern – was being replicated with each layer of snow, with sufficient fidelity that an observer could extract from the layer of snow the information that the table had an umbrella hole. By evening there was about 4 feet of snow on the table, but there was still a dimple in the middle, indicating that the information that beneath the snow was a table with an umbrella hole had been faithfully recorded and transferred from snow-layer to snow-layer all afternoon. Yet in this case, the “representation” was also the “effect”.

Your table wasn’t being replicated (or represented); that was just snow. What you say was a representation, wasn’t a representation. A representation is an arrangement of matter in order to cause an effect within a system. It wasn’t a representation you saw outside, it was table covered in snow. It had a hole in the center of it, which left a dimple in the snow. That dimple made you think of the hole. You then end this anthropic adventure by concluding the “representation was also the effect”. It wasn’t. The representation was a neural pattern going to your visual cortex and beyond. The end effect was “There’s a hole in the table”. Those are not the same thing – and – you’ve put yourself right back into the sample, making observations that only matter to a human.

However, that seems to me to be the least of the problems with UBP’s case. The far bigger problem is that there is a qualitative difference between a sign (in the Saussurian sense), namely a linked signifier with signified pair, where the signified can be a physical object, and the signifier a symbol potentially renderable in a number of media, and where the transfer of information using the signifier does not result in the physical creation of the referent, and the information transfer in a musical box or in a reproducing organism whereby a physical pattern is recorded in such a way that it can be reproduced, which, at its simplest, can be layers of snow on a table.

Here you say there is a difference between:

a) A Saussurian sign [signifier+signified] where the signified can be an object and the signifier can be a symbol.


b) where a “signifier does not result in the physical creation of the referent”


c) a music box or an organism where something can be reproduced, like layers of snow on a table.

I respond:

a) Firstly, a Saussurian“sign” [signifier+signified] is a linguistics concept that does not invalidate biosemiotics or information theory. In any case, a signifier cannot result in a signified without a protocol. That protocol may exist in a living interpreter (such as a human, or a bee), or it can be instantiated in a machine (such as a music box or a fabric loom). In each of these cases, the protocol will be separate from the signifier and the signified, and it will establish the relationship between the two.

b) There is no principle involved which would require a representation to result in the production of a physical object; only a physical effect. This is at the central false premise of your objection. When a bee dances in flight in order to direct the other bees to the feeding grounds, it is not nectar that results from the dance, just a change in flight plan (which is an effect, not an object). And once again, you’ve injected yourself right back into the observation.

c) A representation leads to an effect within a system, and those systems vary, as does their effects. And thoughts of layers of snow becoming a “representation”, is simply anthropocentric.

BIPED: In this instance, the configuration of holes served as the representation, and the configuration of sensors served as the protocol, leading to the specified effects. Each of these is physically discrete, while sharing the immaterial relationship established by the protocol.

Well, yes, but the discreteness is, as I’ve said, only arguably intrinsic to the concept of “recorded information” and in any case, does not render it semiotic.

Here you say that discreteness is not intrinsic to recorded information, but is only arguably so. You also used the word “concept” which is a cognitive term, one which we generally use in order to know anything at all, so I will leave it aside. (If the existence of recorded information is in doubt, then that can be addressed separately).

Now to your objection: Over the course of this conversation I have given many examples of the discreteness observed. These observations have been given in coherent terms. In all of those instances you have never shown that the observation is incorrect. This suggests that the ‘discreteness’ is inherent based upon logical observations, and is only arguably non-inherent (and is therefore falsifiable by any contrary evidence available). I have told you of the physical entailments which are evident in the transfer of recorded information. One of those qualities is a discreteness among the physical objects involved. You then return to me to say “that doesn’t make it semiotic”. But I have already challenged that objection, and am awaiting a reply. You may remember the question:

If in one instance we have a thing that actually is a symbolic representation, and in another we have something that just acts like a symbolic representation – then someone can surely look at the physical evidence and point to the distinction between the two.

BIPED: a) the existence of an arrangement of matter acting as a physical representation

Well, maybe, though it’s a bit imprecise. But sure, information transfer is going to entail physical arrangements of matter. And let’s allow “representation” to be the thing-that-is-read, like DNA, or the cylinder of the musical box, or even the pattern of sounds making the word “apple” and let that representation be of something (a whole organism; a melody; an apple).

…or a neural pattern related to an apple, resulting in a pattern of impulses being sent to the chest and larynx.

BIPED: b) the existence of an arrangement of matter to establish the relationship between a representation and the effect it represents within a system (the protocol)

Well, no. In the case of the linkage between the signifier “apple” and its referent, the piece of fruit, there is no “arrangement of matter”. There is some kind of “arrangement of matter” that links the signifier “apple” to the evocation of the idea of an apple in a hearer, but the “idea of an apple” is not the referent of the signifier “apple”.

Translating first sentence: ‘In the linkage between the word apple and the fruit apple, there is no arrangement of matter.’

If that is true, then each time you say the word “apple” you have the uncanny good fortune of inventing it from scratch. Otherwise, there is a pattern(s) in your brain that maps your knowledge of the fruit to the word and potential downstream effects on your vocal chords. And once again, you’ve plopped yourself right down in the middle of the observations. And still, none of this changes the dynamics of the transfer in any way. The apple is not the word, and neither of them is the pattern in your brain. Again, get out of the study.

Translating second sentence: ‘There is an arrangement of matter that links the word apple to the thought of an apple in the hearer, but the thought of an apple is not what lead the speaker to use the word.’

Again, do you have an apple in your head? You are going in circles, Dr Liddle, and I am feeling rather done with this.

What links the word “apple” to apples is shared agreement among a community of speakers that “apple” means apple … And even if we allowed this as the “protocol” UBP refers to, no amount of cultural agreement that “apple ” means apple will make an apple assemble itself when someone says the word “apple”.


The problem seems to be entailment b, as it always has been. A semiotic system relates a signifier to a signified so that two members of a shared linguistic community can communicate ideas – i.e. one member of the community can evoke in the mind of another member the idea s/he is currently entertaining.

When a “semiotic system relates a signifier to a signified so that two members of a shared linguistic community can communicate ideas” they exchange arrangements of matter (voice patterns) that represent effects within a system (an evocation: apple) and those arrangements of matter will achieve that effect by a second arrangement of matter – a neural pattern – which is the physical instantiation of an agreement among the participants that the sound of the word “apple” represents the red fruit with the white center and the little black seeds.

So, the voice is not the thought, and the agreement is neither of those. Either that, or there is zero physical distinction between knowing what an apple is, and not knowing what an apple is.

The thing you need to acknowledge Dr Liddle, is that this same dynamic happens in any transfer of recorded information, not just among members of a “shared linguistic community”. Again, remove yourself from the observation.

The referents of my signifiers are not my thoughts, but real-world objects, and abstract concepts. Those real world objects and abstract concepts are not brought into actuality when I utter a word. Unfortunately.

This is becoming silly. You apparently think that when you speak the word “apple” there is an apple in your head prompting you to say the word. This ridiculous deduction comes directly from someone who specifically disavows that neural patterns prompt her words – only, she says, real-world objects can accomplish that task. Well, I am a different person. I only have my sensory/cognitive systems prompting my words.

Moreover, this is simply wallowing in an anthropocentric malaise. My background in research is certainly different than yours (we are humans measuring humans, so we tend to get out of the way). Consequently, this is not something I will continue to do. I now need to find a stopping point.

In its entirety, your argument is based a false premise.

You believe that you have identified a distinction in the effects of information transfer, and somehow by virtue of this distinction, the semiotic argument (based on observed physical dynamics) fails. So let us put your distinction in play and follow it to its logical end. Let us say that only information transfer that produces objects is semiotic. That would mean that the exchange of words is not semiotic. Obviously that is incorrect. So let us say that only information transfer that does not produce objects is semiotic. In that case, there is no such thing as machine code (as machine codes are specifically representations and protocols which produce things). This second view suggest that machine code cannot have anything to do with representations, protocols, and effects. In other words, 01100001 is not a representation of the letter “A” and will not result in the letter “A” in a system where 01100001 is the protocol for the letter “A”. Obviously, this is incorrect as well. So your distinction first fails at the observed real-world level, but the question remains “does it change the dynamics of the transfer”. It completely fails here as well. So as I said earlier, there is no principle that information transfer must or must not result in the production of an object in order to be considered semiotic. It’s only required to have a physical effect within a system following the dynamics as set out by the observations themselves. Therefore the underlying premise in your objection has entirely refuted.

If I should choose not to continue engaging you in this dialogue, I would like you to know one of the reasons why. In my comments I said …

Demonstrating a system that satisfies the entailments (physical consequences) of recorded information, also confirms the existence of a semiotic state. It does so observationally. Yet, the descriptions of these entailments makes no reference to a mind. Certainly a living being with a mind can be tied to the observations of information transfer, but so can other living things and non-living machinery.

… and I substantiated each of these statements by the observation of evidence. At no time have you been able to show an error in these observations. I then went on to say:

But Dr Liddle, you are deliberately confusing what is at issue. The output of a fabric loom being driven by holes punched into paper cards is “a physical object” as well – an object created by representations operating in a system capable of creating fabric. The nucleotides in DNA don’t know what leucine is, any more than the hole-punched cards of a fabric loom know what “blue thread” is. Or, any more than a music box cylinder knows what the key of “c” is. Observing the critical dynamics does not require any reference to a mind in any way whatsoever, yet you are repeatedly trying (as hard as possible) to inject a mind into the observations so that you can then turn around and claim that its all about a mind. In case you have not yet noticed, you have failed at this position every time you’ve tried it, and you will continue to do so. The reason for this is simple; the observations are correct and you are wrong

So instead of successfully attacking the correctness of the observations, you introduced Saussure’s (specifically anthropic) concept of a “sign” and have used it as a definition that somehow isn’t required to address the observations. This has the net effect of allowing you to introduce a mind without regard to the observations being made. This is, of course, pure obfuscation of the evidence. Yet, having done so, you then go on to misrepresent the argument as if none of the preceding ever occurred. You say:

[BiPed] seems to be saying: cell-reproduction is information transfer, and information transfer is semiotic, and semiotics require minds, therefore cell-reproduction requires minds.

You say this even though you know it is an absolute misrepresentation of the argument I’ve made. The semiotic argument is simply that the information transfer in protein synthesis is not only physical (as in all other forms of recorded information transfer) but is also semiotic (as in all other forms of recorded information transfer). I do not say that semiosis requires a mind in those physical observations, nor do I have to in order to make those physical observations. I do not say so for a specific reason. That reason is because the source of the information is in question, so to make that assumption in the observations is a logical fallacy. In other words, I do not make that assumption as a matter of evidentiary discipline, and you have used it to smuggle in a mind without addressing that same evidence.

Now certainly I have thick enough skin to be misrepresented, and each time I am I will endeavor to straighten it out. But you represent a special case for two reasons. Firstly, we have been talking rather consistently in and around these observations since May of this year. For you to start blatantly misrepresenting me at this late date is, well, uninteresting. And secondly, you present as someone who simply cannot, or will not, remove themselves from the observations. And that is an argument that I must concede; I cannot argue against it.

54 thoughts on “Upright BiPed responds

  1. And here computerist adds another layer of argument by equivocation: most IDists argue that DNA is a ‘code’ in the cryptographic sense of the word because TGG maps to tryptophan, etc. but computerist is also claiming by analogy that DNA is a ‘code’ in the computer-geek sense of the word because it is a hierarchical set of instructions.

    As a former DNA Jock who now ‘codes’, I find this argument by analogy hilarious. DNA program execution is massively, massively, massively parallel and (pace Elizabeth) analog. We are working towards programs that run like biology, but (as noted here previously) it is often easier to just use the chemistry, rather than attempt to model the chemistry in silico.

  2. Actually there are attempts to use chemistry in place of computation due to some advantages in parallel processing.

    Unless we get practical quantum computers, I suspect that chemistry will always be faster than computation for revealing protein folding. 

  3. computerist29: The information in DNA is a code with 4-states per individual unit. 

    That doesn’t really answer the question. Do you simply mean that it’s a mapping of one set to another? That’s how it was used by the scientists who discovered the genetic code.

  4. Using the Wikipedia definition of code:A code is a rule for converting a piece of information (for example, a letterwordphrase, or gesture) into another form or representation (one sign into another sign), not necessarily of the same type.
    is easy to demostrate that the genetic code is a code. 
    The genetic code is a rule that convert e piece of information, the sequence of bases in DNA, into another form a protein.
    That rule not only is useful for cells to produce proteins, biologist uses that rule to know how are the proteins of the different kinds of forms of life. They look at the sequence of DNA and found where the proteins are represented and read the sequence of aminoacids of the protein.
    Also we can make artificial proteins building artificial sequences of DNA that cells will transform according the same rule (the genetic code) into real proteins. Or we can build an artificial protein sintetizer that follow the same code.
    More crucial to this discussion is if it is a “natural” code or and abstract code. And no matter what the materialist can say it is an abstract code. Because there is no chemical or physical reason that relates GAU/C to Aspartic and GAA/G to glutamic.
    The only reason they related in the code is the specificity of the aspartyl-tRNA syntase and the glutamyl-tRNA syntase.
    The specificity of the aminoacil-tRNA syntase is so arbitrary that as Wikipedia explains “Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins” 
    The genetic code is not only a code, but an abstract one. 


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