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.

…and

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

..and

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”.

Speechless.

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. I’m going to start with this, to get it out of the way:

    [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.

    No, I did not know this.  I want to make something absolutely clear before we continue: I do not lie. If I say something that is incorrect, it is a mistake, not a lie.  I did not intend to misrepresent you (why should I?  I’d invited you to respond, so it’s not as though you couldn’t correct me, as in fact you have).  I still don’t know what your ID argument is, if it is not that.  But I accept that it is not that.

    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.

    No, I have not “used it to smuggle in a mind”.  If you aren’t inferring a mind, I have no issue with your position, but if you aren’t inferring a mind, in what possible sense is your “semiotic argument” an argument for Intelligent Design?  Do you not consider that Design requires a mind?

     

  2. I simply do not know what to make of this section, Upright BiPed:

    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?

    What are you asking here?  I can only think you have completely missed my point, which is that in the domain of semiotics, a signifier evokes meaning in the receiver, it doesn’t create the signified.  So semiotic information transfer (in the sense the word is usually used) is different from your DNA-protein example in a crucial respect: DNA doesn’t evoke the meaning of a protein (except in the brain of a human geneticist who reads the sequence), it initiates the production of a protein.

    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 don’t know what this means.

    I say again, you are a natural symbol-maker. You transfer information. This is what you do.

    Absolutely.  I’ve made this point several times.

    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.

    This makes no sense to me.  As a Martian observing Earth, I see, on the one hand, human beings having conversations about apples in the absence of apples (using “representations and protocols”) and on the other, human cells producing proteins from DNA sequences.  These seem very different dynamics to this Martian.

    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.

    I don’t get your point.

  3. Upright BiPed,

    Elizabeth: “So semiotic information transfer (in the sense the word is usually used) is different from your DNA-protein example in a crucial respect: DNA doesn’t evoke the meaning of a protein (except in the brain of a human geneticist who reads the sequence), it initiates the production of a protein.”

    That UPB, is the point you’re not understanding.

    From the point of view of the chemistry, DNA is NOT a semiotic code, it is a part of the process itself.

    It is we humans who have labeled it a code, for our purposes of understanding it.

    Life doesn’t need or in any way rely on our labels.

     

  4. I think this is important. Humans have envisioned certain very complex chemical reactions in metaphoric terms, in order to simplify the conception and better communicate it to other humans. And the metaphor we have used is that of computer software. But computer software as a set of detailed instructions, can be abstracted and recorded on tape, disk, punch cards, etc. Chemistry can’t. Our metaphor makes no use of the many different protocols for encoding and decoding the information (languages, compilers, etc.) because those mechanics are irrelevant to the metaphor itself.

    It seems that Upright BiPed here has basically assumed that this software metaphor is physically represented in the chemistry. That if we CALL it a code, it must be like software, independent of the physical representation and requiring the protocols of encoders and decoders to translate into and out of the abstracted recording. He just doesn’t seem to grasp that the code metaphor is human conceptual shorthand, and has nothing to do with how the chemistry actually works.

  5. It appears that at least some insight can come of this foray into the labyrinth of pseudo-philosophy; we all seem to be converging on the same points.

    This is where a close familiarity with condensed matter physics and chemistry is really needed.  Those who work with complex systems have little doubt that “codes” – be careful with that word – evolve.  It is the specific needle, or needles in a mountain range of needles that is the research issue; and that research is making progress and is extremely interesting.

    The use of the word “code” in describing the process of molecular construction and evolution is a shorthand metaphor for sequential processes and their constraints leading into other processes and molecular configurations.

    Why is the word “code” used in describing the processes leading to something like proteins more appropriate than using it, say, in describing the processes leading to the production of urea or benzene or any other organic molecule?

    The main reason is that it is a way of keeping track of complex sequences of processes and interactions – along with constraints – and how they follow from or lead to other structures.  Biochemists and physicists are mapping out the actual sequences of chemical reactions and describing what is constrained and what is allowed. It is a detailed description that needs a relatively efficient language.

    Teleological language is common in physics and chemistry, but it doesn’t mean what ID/creationists think it means.  One can unpack the language; but the result becomes so wordy that the overall picture gets lost or simply too boring to write down for lay audiences. Metaphorical and teleological language is efficient when used properly by people who know the details it summarizes.

    The ID/creationist subculture has grown up using exegesis, hermeneutics, etymology, and word-gaming in what they like to think of as “learned discourse.”  And they fail miserably when repeatedly taking metaphor, analogy, and teleological language literally.

    The “genetic code” is another one of those concepts that ID/creationists hijack, take literally, and use in ways that the scientific community did not intend; it’s the same pattern as with the second law and entropy.  ID/creationists will insist on foisting their usage off onto others in debates.

    Yet, no matter how much pseudo-sophistication ID/creationists pour into their expositions, a few probes into their understanding of fundamental concepts usually reveal that they have little more than a middle school education in science; and even much of that is wrong. What they lack in understanding they try to hide in mountains of pseudo-philosophy.

     

  6. I think we already discussed reifying a metaphor. That describes most of what ID theory does.

  7. I suggest a prime example would be “complex specified information” – a concept that has proved somewhat elusive to definition and impossible to quantify.

  8. Elizabeth,

    1. Always ask, “Does the word data work here?” If so, then insist on using it instead of information.

    2. The article on biological information in the Stanford Encyclopedia of Philosophy is easy to read, and well worth it.

    3. Floridi’s article on semantic conceptions of information in SEP is demanding. But, given the work you’re putting into this, I recommend that you study it closely. (I’ve gone at some of it several times, and am about to work through the whole thing again.)

  9. Mike Elzinga: The use of the word “code” in describing the process of molecular construction and evolution is a shorthand metaphor for sequential processes and their constraints leading into other processes and molecular configurations.

    Or literally, when used explicitly to mean simply a correspondence (many-to-one) between sets. It’s the conflation between the two meanings that befuddles ID advocates.

    Having some troubles with Upright Biped’s longish essay. The basic point seems to be that information in genomes is expressed and transmitted into proteins, while information in the mind is expressed and transmitted as ideas. Both exhibit a correspondence. Is that correct?

    What does that have to do with Intelligent Design other than drawing a weak parallel?

     

  10. the function of UPB’s “theory” is to decorate the longstanding question of how the system arose. It’s a layer of flowery verbiage superimposed on irreducible complexity.

  11. What indeed does UB’s theory have to do with ID?

    It’s been asked a few times now, and the answer would be the more intriguing following UB’s apparent insistence that his theory doesn’t need a “mind”

    What is ID without an Intelligent Designer, which most of us would think would have to possess something that could be called a “mind”?

  12. Indeed, mappings among sets are described quiet precisely in mathematics.  One can have many-to-one mappings (often referred to as functions), one-to-one mappings (invertible functions), and one can make mappings which are probability functions, i.e., a number in a domain maps to elements in a subset with specified probabilities (e.g. the Schrödinger equation).

    “Codes” are usually understood as one-to-one mappings of things like letters onto letters, or diagrams onto diagrams (structures onto structures), or instructions onto actions.  However, this works for chemical systems only if the binding energies are quite large relative to kinetic energies; in which case bonding, such as in crystals, leads to highly regular and reproducible results.  One can describe a crystal in terms the spatial repetition of a small subset of atoms called a “unit cell.”

    In the case of quasicrystals, however, while regularity is usually the rule, the regularity can be highly dependent on contingencies.  A number of regularities can be “good enough” to continue building on, but small perturbations that crop up in the evolution of a developing system can change the trajectory of the system evolution.  The “genetic code” generally refers to just such a situation.  And, of course, less tightly bound structures built on top of underlying structural patterns can also be the grist for selection in an organism.

    ID/creationists take metaphors like “code” and “information” literally; and because they see codes and information coming from humans, they immediately jump to the conclusion that anything that involves “codes” or “information” originates with intelligence.

    Just looking at the conversations over on UD reveals just how ingrained those literal interpretations of “code” and “information” have become. To ID/creationists, they have become axioms. To question them is to “reveal ignorance and stupidity.”

  13. Over at UD, Barry Arrington just amped up the metaphorical nonsense to a whole new level with his announcement of the winner of the “Describe the Cell” contest.  The winning entry by nirwad:
     

    “A ‘cell’ is a bio-cybernetic chemical automaton able to self-replicate, self-organize, and perform metabolic functions by means of nano-level molecular machines controlled by internal digital software stored in information rich polymers.”

    “Bio-cybernetic”?? What a load of crap.

  14. People often seem to want to write “bio-genetic” or “biogenetic” too.  As if just having “genetic” implies that it isn’t biological.

  15. Joe Felsenstein on May 31, 2012 at 11:24 pmsaid:

    People often seem to want to write “bio-genetic” or “biogenetic” too.  As if just having “genetic” implies that it isn’t biological.

    Same with “nano-level molecular machines”.  “Nano-level machines” or “molecular machines” would be fine.  Or, simply, “biochemistry”.

     

  16. I don’t propose to go into too much more detail, but to me the whole argument hinges upon an artitrary decision that the modern code – or even some reluctantly-conceded ‘core’ of 9 or 10 amino acids – is an absolute minimum for a worthwhile amino-acid condensation system. If you don’t have a multiplicity of amino acids, you cannot create catalysts, and (runs the apparent argument) without such catalysts there is no means to create the assumed ‘representation’ betwen mRNA and acid. But it is simply the case that you cannot create protein catalysts without that minimum. Non-protein catalysts: no problem. Further, you do not need catalysis before it is worthwhile making proteins.

    The amino acid is a particularly nifty molecule. Having a -COOH group in one direction and a -NH2 group in the other means that you can eliminate an H and an -OH (water) and create long bonded strings for all kinds of purpose. Even the simplest of the lot, glycine, is formed into sheets and helixes by this simple method. Such polyglycine sheets perform many roles in both catalytic and non-catalytic peptides.

    The basic recipe is simple:

    1) attach your amino acids to carriers (in the first instance, this would have to use something other than protein for catalysis, whatever does it now).

    2) Stabilise carriers and growing peptide in an orientation that permits the energy of carrier attachment to be transferred to the peptide bond of the new acid. 

    3) Keeping hold of one end of the growing peptide by its last attached carrier, shift it along, then spot-weld the next carrier’s acid in the same way.

    Bingo. You have a non-semiotic Mark l peptide-bond formation system.

  17. UB:

    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).

    I’m always entertained when a discussant cites a topic regarding which they haven’t the slightest clue in support of their argument, in this case the “dance” system of honeybees. It is still an amazing adaptation, however.

    Foraging honeybees, having discovered a resource that is in short supply within the hive, use two dance forms to convey information regarding the distance, location, and quality of the resource. The first is a “round dance” used to indicate the presence of nearby food resources. The second is a “waggle dance” used to indicate the location of more distant resources. Performed in darkness on a vertically oriented surface within the hive (not “in flight,” for God’s sake), the waggle dance employs two phases: Turns that encode the distance to the food source, and rapid lateral wagging, performed as the bee walks in a straight line, that encodes the direction of the food source relative to the sun’s azimuth in the angular orientation of the waggle pathway relative to the downward pull of gravity. “Followers,” in turn, emit begging signals to request food samples from the foragers. This combination of encoded distance and angle, along with samples that are indicative of the kind and quality of the resource, enable followers to find the food resource with a directional accuracy of plus or minus 20 to 30 degrees and distance accurate to within 10 to 15% over distances of a kilometer or more.

  18. I hadn’t noticed that.  I just saw “bees” and “dance”.

    And actually, nectar is the outcome.

  19. Glycine has been found in interstellar dust clouds and comet dust, and this paper suggests a low energy method for its formation in the absence of a protein catalyst:

    NH2CH2CN could have been formed and protected by icy dust particles, and then delivered through micro-bombardments onto the early Earth, leading to glycine formation upon contact with the primordial ocean.

  20. Actually my interest in Von Frisch was his 1915 demonstration of the sensory perception of insects, specifically that bees can distinguish color. And it was that research which I read fully and spent time with. So you are correct that the exchange of information among foraging bees is not performed in flight. The problem for you remains though, given that my comments were not an exposition of the particulars of the waggle dance, but were an observation of the transfer of information. That the exchange takes place in flight or otherwise does nothing whatsoever to change the observation being made, and you know it.

    I suppose you can afford to be generous with your indignation, given that you’ve had your hat handed to you by the evidence itself.

  21.  

    From the point of view of the chemistry, DNA is NOT a semiotic code, it is a part of the process itself.

    It is we humans who have labeled it a code, for our purposes of understanding it.

    Have humans labeled a base-2 (boolean 1 or 0) system in the use of transistor logic and upward simply for our purposes of understanding it or for engineering purposes as a framework to building complex functional digital systems? A detailed case can be made for the latter. Assuming we merely labeled DNA as a code (and of course we had to in order to understand it as we understand codes. If we didn’t understand codes would we label it as such?) does not eliminate the fact it is a code which was utilized through similar engineering requirements of building complex functional systems.

     

  22. Dr Liddle, on the other threrad you made a comment:

    “Because we have several times proposed examples of information transfer that you have rejected, apparently because it doesn’t involve representations and protocols (like those cosmological examples Mike gave)”. 

    These examples of “information” suggest that information exist merely as the result of an object having a material state. If a thing exists, it contains information. This is an unsustainable reification of the word “information”; sustainable only to the extent that objects become calculable to human observers.

    If everything that exists “contains” information, then you will need a new word for those things that exist which share an arbitrary relationship to other things, resulting in the unambiguous observation of function among living things.

    In other words, an ant’s pheromone is an arrangement of matter having a specific chemical composition, which following physical law determines how that composition exists. You call this “information” because you observe it. But it also has a quality that that is neither reducible to its chemistry alone, nor to our observation of it. Within the system of the ant, its results in unambiguous function.

    Physicists should not conflate the anthropocentric concept of “physical information” with the source-neutral observation of form and function being induced within living systems by the arrangement of matter. 

  23. This is a most marvelously clear example of reifying a metaphor. It’s “like” certain codes in certain ways, therefore it IS a code. And some codes are used by humans to build complex systems, DNA can be labeled a code, therefore it IS a code, therefore it IS an engineering requirement for building complex systems. Therefore biology is an encoded engineering project. [Applause!]

    While we’re at it, birds’ nests are like human houses, houses have plumbing, therefore birds are obviously plumbers. Otherwise, it would make no sense to say that birds live in nests.

    And meanwhile, lest it be lost, DNA is not a human “code”, it’s an organic molecule. The code metaphor is kind of like a gamble – we are betting that seeing DNA as a code will be a useful enough analytical parallel for some purposes, to counteract the potential misunderstanding that it IS a code itself, misleading those who reify metaphors into completely mistaken intellectual cul de sacs.

       

  24. Upright BiPed,

    Upright BiPed: “If a thing exists, it contains information.”

    No, things simply exist, period.

    The rings we see in a tree stump is “information” to us in that we can use it to determine the age of the tree, but the tree did not put this information into its wood to “inform” us as to its age.

    The tree did not use the “information” in its rings as “codes” in order to calculate growth rate or anything else.

    Ditto with claims other processes in biology leaving us “information”, they didn’t.

    All the “information” in biological processes result from our attempts to describe them.

    If I’m wrong, and a thing is a “semiotic” state of matter, you should be able to make helium atom from a hydrogen atom simply by adding the right information.

    Has anyone done that?

     

  25. This is a most marvelously clear example of reifying a metaphor. It’s “like” certain codes in certain ways, therefore it IS a code. And some codes are used by humans to build complex systems, DNA can be labeled a code, therefore it IS a code, therefore it IS an engineering requirement for building complex systems. Therefore biology is an encoded engineering project. [Applause!]

    DNA is a code not that it can be labeled as such, but because it is a code as codes we know of are defined with the purpose which they serve ie: building and maintaining complex systems. But ofcourse, DNA base-4 system isn’t merely a code, its a rule, a rule within the context of biological systems which everything else follows. 

     

    And meanwhile, lest it be lost, DNA is not a human “code”, it’s an organic molecule.

    Codes can be represented with an electrical charge/electric-state or a molecular state or something else entirely. The underlying representation doesn’t negate the code aspect itself.

     

  26. computerist29,

    computerist29:”Codes can be represented with an electrical charge/electric-state or a molecular state or something else entirely. The underlying representation doesn’t negate the code aspect itself.”

    That still does not make a “coded representation” of DNA an equivalent substitute for DNA.

    One is a “code” for DNA and the other is DNA.

    You have not made a case that DNA was originally meant to be a “code” by an intelligent designer simply by claiming that we can map a “code” onto physical objects.

     

     

     

     

  27. NO. DNA bears some cosmetic relationships to human-devised codes, and this makes the metaphor useful for those who do not insist that if it LOOKS like a human-type code, it must BE a human type code, and therefore was Designed for human-type purposes. It’s just not the case. It’s not a human code, and it’s not a rule. It is an organic molecule.

    Yes, I agree human codes can be represented in many ways – as mathmatical formulas, as computer programs, as holes in punch cards, as patterns woven into a bedspread! But this is not true of DNA. It can’t be abstracted out and stored in some arbitrary conventional way. DNA is NOT a “representation” of the actual DNA. It IS the actual DNA. There is no symbolic representation here, no human-style code.

    You are reifying a metaphor. DNA doesn’t “encode” itself any more than oxygen “encodes” oxygen. There is only one possible way to “represent” DNA, which is the DNA itself.   

  28. Computerist29 says: DNA is a code not that it can be labeled as such, but because it is a code as codes we know of are defined with the purpose which they serve ie: building and maintaining complex systems. But ofcourse, DNA base-4 system isn’t merely a code, its a rule, a rule within the context of biological systems which everything else follows.

    What is the “code” for nucleosynthesis in stars and supernovae?

    Can you write down the “code” for making a water molecule? How about benzene? How about urea? Amino acids?

    What is the “code” for making a salt crystal? What is the “code” for making solid iron?

    Where along the chain of complexity in condensed matter do “codes” take over from physics and chemistry?

    This should not be a hard question; but we can’t seem to get an answer.

  29. There is only one possible way to “represent” DNA, which is the DNA itself.   

    That’s not 100 percent true. DNA can be represented by alphabetical symbols. what can’t be done is manipulate those symbols to get proteins by any means other than chemistry. When yuy say you can;t abstract DNA, I assume you mean that chemistry is the only way to “read” DNA.

    There’s no virtual cell, no way to design coding sequences except to make them in chemistry and test them in chemistry. That is why they are not a code.

    That is related to what is meant by emergence. We cannot predict the attributes of new complex molecules. No prediction, no virtualization, no symbolic code, no designer. That is why I assert that design is impossible without evolution.

    I could be wrong. And maybe it is possible to travel back in time and possible to exceed the speed of light. 

  30. What is the “code” for nucleosynthesis in stars and supernovae?

    Can you write down the “code” for making a water molecule? How about benzene? How about urea? Amino acids?

    What is the “code” for making a salt crystal? What is the “code” for making solid iron?

    These questions indicate a lack of understanding of what a code really is. DNA is nothing like the code as we’ve created. Its much more advanced. We don’t have a code or a system which when translated and transcribed had a direct 3d functional relationship. The closest we have to this is assembly lines which operate on code, but that code is directly related but independent of the functional output. Biological systems show us how a direct relationship between the code and the functional system can be established, perhaps the only way.

    To claim that:

    DNA is NOT a “representation” of the actual DNA. It IS the actual DNA. There is no symbolic representation here, no human-style code.

    …is misleading in the context of a code establishing a direct functional relationship. It would be a code of the advanced kind from an engineering point of view.

    You have not made a case that DNA was originally meant to be a “code” by an intelligent designer simply by claiming that we can map a “code” onto physical objects.

    I agree we can map any “code” onto any object. Humans create a symbolic link of the object, and then define the properties and functions of that object. Systems which run by a universal code that can be read and modified tend to be the more interesting than most objects out there in the universe.

  31. I presume we’re still talking about “semiotics” here. And that involves abstracting meaning according to some protocol that is devised to encode that meaning into some conventional form unrelated to the meaning itself, and then at the receiving end decoding it in such a way that communication has occurred, or “transfer of information” is completed.

    And my understanding is that such an encoding/decoding process doesn’t happen with DNA during replication – there is no abstraction into and out of some arbitrary conventional representation meaningful only in light of some protocol.  There is simply a complex chemical reaction that occurs.

    As far as I can tell, these people are using word games to pretend there’s some sort of gap they can cram their god into. And I think the answer to Mike’s repeated question is, they don’t try to fabricate nonexistent gaps to cram their gods into other physical or chemical processes because their particular religious doctrines are not offended by non-living processes. It’s not a matter of complexity here, I don’t think. I think it’s more a fear that if their god can’t be injected into biological chemistry, their lifes will lose meaning or some such.   

  32. Well, there we have it. If we SAY it’s a code, then POOF it’s a code. If we SAY it twice, it’s twice as code-ish.

    But at least the underlying objective is becoming clear. Start with the Designer. To find Him, we must find something artificial in biology. Codes are artificial, so if we can find a code, we can find the Designer. DNA is complicated, so we can call it a code. Hallelujah, we’ve “found” the Designer we knew was in there all along. Praise Designer!

    Now, I have to try to figure out why go through all of this prima facie absurd song and dance. Why not just present the religious beliefs honestly and straightforwardly? Why go throught the effort of obfuscating and misrepresenting biology in order to TRICK the Designer into hiding in nonexistent gaps? Seems like a lot of unnecessary self-delusion to me.   

  33. You accuse someone of not understanding what a code is and yet in the very next sentences you assert that DNA is a code; in other words, as everyone here has noted, you simply continue to reify a metaphor.

    Crystals and solids are 3-D structures. Tell us why there is no “code” involved in 3-D structures such as crystals and solids, yet, as you claim, DNA is a “code” or “contains a code.”

    If atoms and molecules can line up in highly regular 3-D arrays, why can’t structures continue to be built up on top of other underlying regular arrays; or, even better, on quasi-regular arrays (quasicrystals)?  If solids can exist without codes, why can’t other structures such as liquids and soft matter exist without codes?

    Do you even know how and why solids and liquids exist?  Can you explain their existence without your “theory” of “codes?”  If you can explain other molecular structures without codes, then why do you need codes for DNA (and proteins)?  If not, then explain the codes for other molecules and 3-D structures such as crystalline and polycrystalline solids.  Start with something as simple as salt, or water, or sulfur dioxide.  Then move up step-by-step through more complex structures.

    Do you think that “codes” tell where and how molecules should move?  How do “codes” push atoms and molecules around?  How does “information” push atoms and molecules around?  Why can’t we ever get an answer to those questions?

    Why are “codes” overwhelmed by taking organic structures outside a very narrow temperature range?  Why is growth affected, and even disrupted and stopped, by temperature changes?  Why do gender changes occur in some species if the temperature is changed during incubation?  Do you know anything about hyperthermia and hypothermia?

    At what level of complexity do the physics and chemistry stop and “codes” take over? If we poured hydrofluoric acid on such a complex structure, would nothing happen?  What happens to DNA if we pour hydrofluoric acid on it?

    You have never taken a chemistry or physics course, have you?

    Do any of these questions ever have any meaning to ID/creationist “theorists?”

    Is Flint right, you are trying to hide your deity in the workings of complex molecules?  Why do deities have to hide inside complex structures and not simpler structures?  How complex does a structure have to be to hide a deity?

  34. computerist29,

    computerist29: ” Biological systems show us how a direct relationship between the code and the functional system can be established, perhaps the only way.”

    A “direct” relationship is not an “encoded” relationship.

    An “encoded” relationship needs “codes” while a “direct” relationship, doesn’t.

    Therefore, biological systems, which you say have a direct relationship with their functions, don’t need codes.

     

  35. Crystals and solids are 3-D structures. Tell us why there is no “code” involved in 3-D structures such as crystals and solids, yet, as you claim, DNA is a “code” or “contains a code.”

    Well if a DNA chain can translate into something its not while achieving a higher-order functional state, then that would qualify it as a code.

    Therefore, biological systems, which you say have a direct relationship with their functions, don’t need codes.

    They do need codes, such as to encode a particular amino acid during translation transcription. The process of developing the functional system or output is tightly coupled to the output itself, that is why I stated “they have a direct relationship to the function”, not that the encoding process is absent. The process and output remains within its biological domain.

    DNA is complicated, so we can call it a code.

    We don’t call DNA a code because its complicated. Specified is more like it.

     

     

  36. I can see we’re going to get nowhere. DNA is not a code. CALLING it a code doesn’t make it a code, even if you call it a code over and over and over and over and over. There is no encoding process, there is no decoding process, there is a complex chemical reaction. You seem desperate to project a code where there is none, for reasons you refuse to reveal. Code is a METAPHOR. Do you know what a metaphor is?

    As for “specified”, sheesh. A specification PRECEDES a design, it’s what a design is intended to meet. Not knowing the spec, you can’t look at a design and tell if it meets the spec or not. You CAN NOT! “deduce” a specification from an object. What you can do, of course, is PROJECT a specification where you desperately wish to find one, and then CALL it “specified”, and then call it specified over and over and over and over and over, and hope that if you do this enough, it will come true. 

    “Functional” does not mean “specified”. A chair makes a functional doorstop. Can you deduce the specification of a chair from its utility as a doorstop? THINK! 

  37. computerist29 asserts: Well if a DNA chain can translate into something its not while achieving a higher-order functional state, then that would qualify it as a code.

    Water is something that hydrogen and oxygen are not; so is hydrogen peroxide. Both water and hydrogen peroxide have many functions. Water is a really universal solvent. Hydrogen peroxide can bleach things.

    Does that mean that hydrogen and oxygen encode for water or for hydrogen peroxide, both of which are “higher order states?”

    And we haven’t even gotten to benzene yet.

    I am guessing you are just playing word games. You don’t really know.

  38. computerist29We don’t call DNA a code because its complicated. 

    We touched on this above. Code can be described simply as a correspondence or mapping between sets, e.g. the genetic code is a many-to-one mapping.

    What do you mean by “code”? 

     

  39. What do you mean by “code”?

    The information in DNA is a code with 4-states per individual unit. The genes which constitute units of DNA are the instructions. We are obviously dealing with two different types of code here. The code to determine how the instructions are to be read, and the instructions themselves. Digital systems are based on boolean algebra. The design and programming of circuit components all function on a 2-state system. A 2-state system is obviously not happenstance, it was selected as a basis for engineering simplicity. The selection of a base-4 system obviously had merits onto subsequent evolution, but that was before evolution could “select” anything. Hence, questions of selection and replication comes up.

  40. You’re getting ahead of yourself here before answering Zachriel’s question:  What is your definition of the word “code”?

    All you’ve done is assert again that DNA is a code.  It may be, according to your definition, but until you articulate that definition, there’s no way for anyone else to determine if DNA meets it.

  41. I think there are problems in regarding DNA as a “four state” system.  Sure, there are four “letters”, but it seems that DNA, considered as a code, is an “alphabetic” system, rather than a boolean system.

    However, gene expression is governed by a boolean system, and it’s essentially binary – a gene is either switched off or on.

    I’m perfectly happy to call it a “code”.  It’s the leap to an ID inference I have trouble with.

  42. The problem with being “perfectly happy to call it a code” is, as has been already asked many times, how you can tell code-based chemical reactions from non-code-based reactions. Just where on the spectrum of compexity does code kick in?

    The only answer provided so far is that code kicks in when it seems “specified”. But then, when does specification kick in, what is the dividing line and how can anyone tell?

    I doubt you’ll get any glances in the direction of your request for the ID inference. After all, ID is the axiom from which the rest is derived. We’d just be back to Behe on the witness stand saying life is designed because, well, because it JUST IS, because just LOOK at it, how obvious can you get? What’s to analyze? There it is!   

  43. I don’t think code “kicks in” abruptly.  It seems to me that there is a continuum of complexity, from simple to highly nested decision-trees.

    And, being a continuum, evolvable.

  44. But computerist29 has already said that it’s not a matter of complexity. He writes:

    “We don’t call DNA a code because its complicated. Specified is more like it.”

    Hopefully, this gives you a bit more insight into where ID comes into play. Clearly genetic processes are specified, just LOOK at them, it’s obvious. And who else but the Designer could have specified them? 

    Now, just where along this continuum we decide specification becomes obvious, even Dembski fears to tread.   

  45. It is not so much a “continuum” as it is a mixture of systems of varying complexity.

    Yes, it is true that as molecules become more complex, potential wells become shallower and more complex.  This means that if a complex molecule is to become a “template” for subsequent evolution, there are many more directions that subsequent developments can go.  Perturbations become more and more significant in nudging further development in different directions.

    In most cases, complexity reaches a point where a sudden major jump in complexity of behavior of the system kicks in and new properties emerge.  These kinds of jumps occur at every level of complexity.  Two hydrogen atoms combine with a single oxygen atom giving something entirely different from either a hydrogen atom or an oxygen atom.  A collection of copper atoms in the solid state has a myriad of properties that are not predictable from just looking at a single copper atom or even a few dozen copper atoms.

    The metaphor of codes comes out of the complexity of organic chemistry.  It is common to talk of building up complex molecules on the backbones of other complex molecules; e.g., one talks about removing an atom or a structure of atoms from a particular site along a hydrocarbon chain and tacking on another structure – a structure that has a name and may be complex as well – at the location of the removed atom or structure. The discussion begins to take on the character of assembling Tinker Toy or Lego parts.

    Once the discussion gets to that level, it is but a small step to see the various combinations of sites, where pieces get plugged and unplugged, as patterns for which code becomes a metaphor. Some pieces will fit, other pieces will not.  It’s analogous to lock and key, hence, code.

    The reason this works finds its roots in quantum mechanics where orientations and orbitals are quantized.  Quasicrystals or aperiodic crystals such as DNA are very interesting templates onto which subsequent structures are built.  These kinds of quasicrystals and aperiodic crystals provide a robust template yet allow for far greater ranges of development of patterns that don’t continue to replicate the underlying patterns.

    But one should not forget that living organisms are mixtures of complex systems that more or less can work together.  The big clue lies in the effects temperature variations have on various systems and subsystems.  Hard structures such as shells and bones can withstand fairly large temperature variations.  Soft tissues in various organs work within narrower temperature ranges.  The nervous system of most animals appears to work within the narrowest temperature ranges of all the systems making up a living organism.

    Much of the research in attempting to understand complex living organisms involves detailed understanding of subsystems followed by detailed study of how subsystems interact and support each other.  Those interactions are often quite a kludge, the only thing going for them being that they work well enough to persist for a while.

    We tend to think about animals when we think of complex living organisms; but things like viruses and plants are important sources of understanding of living systems.

  46. computerist29: “The selection of a base-4 system obviously had merits onto subsequent evolution, but that was before evolution could “select” anything.”

    Eh? There’s no reason to suppose that evolution by natural selection requires DNA. Other molecules can self-replicate with variation.

  47. rhampton: Glycine has been found in interstellar dust clouds and comet dust, and this paper suggests a low energy method for its formation in the absence of a protein catalyst:

     

    Yes (although the synthesis of the building blocks is a different matter from their condensation).

    I think it’s the major amino acid fraction in “MIller”-style spark discharge apparatus too – basically, it is a fairly easy matter to form simple precursors (eg CO2, NH3, H2O) into that dead simple molecule. It is not, of course, easy to generate these in concentration, and I wouldn’t want to appear to gloss over that difficulty. But it boils down again to shaking people out of the preconception that you need proteins to do anything. The fact that glycine forms so readily demonstrates that a non-catalytic method of synthesis is thermodynamically favourable. That being so, catalytic synthesis is a comparative piece of cake – by things other than proteins, as well as by proteins.

    The role of glycine is important for another reason: it is the only non-chiral acid (no L- or D-form distinction), because its ‘side-chain’ is a hydrogen atom. So if one did have a biological means of glycine synthesis, and the side-chain were modified, it would be an initially arbitrary choice as to which hydrogen were replaced by the longer side-chain. Once you have such a side-chain attachment pathway, it can be amended to attach different side-chains, but always in the same orientation. The unavoidable one-handed stereochemistry of biological catalysts generates a whole family of L-form amino acids from that precursor. There is (IMO) no need to invoke some kind of mineral selection process that generates a prebiotic excess of L-isomers in solution.

    And I find this possibility further pushes me in the direction of a non-protein early life. Only when you have a preponderance (and variety) of L-acids can you make protein catalysts out of them

  48. I think there is a potential for further confusion when some refer to the switching-on-and-off of genes as ‘code’, and others the genetic code translating DNA triplets into amino acids.

    The bottom line is quite clearly chemistry, Adenine has an edge-on shape that fits snugly with a Thymine projecting from an anitiparallel nucleic acid strand. Ditto Cytosine and Guanine. Mispairs stick out like a sore thumb, hence mutational robustness (no parity bit – geometry). Separate a DNA base pair and you can create an identical pair of molecules by using each strand as a template. Does Adenine code for Thymine? Or does Thymine code for Adenine? Meh. It’s simply binary complementarity, like the part and counterpart of a fossil shell.

    1 ‘codes for’ 0, 0 ‘codes for’ 1. The only permissible pair is 1-0, where 1 is a purine an 0 a pyrimidine (0-1 is simply 1-0 read upside-down). Split 1-0 down the middle and you can create two instances of 1-0.

    This complementarity controls the 3D folding of RNA. Helical regions can form in hairpins by antiparallel pairing between inverted parts of the same RNA strand. Do the pairs ‘code’ for each other here – or are they not simply subject to physicochemical forces, and respond accordingly?

    As for gene expression, there are groups to one side of each base that project into the major and minor DNA grooves. Sequences of base PAIRS have distinctive knobbles that specific 3D promoters and repressors will bind to. When transcription comes along, bound repressors get in the way, bound promoters encourage. Again, a physical interaction which functions ‘like’ logic gates. The same pair-sequence can be read in either direction, or frame-shifted, or edited, to give completely different peptides as a result. It ‘codes for’ multiple things simultaneously.  

    Then to the more complex genetic ‘code’ that mediates the sequence in which amino acids are bound in the ribosome by stabilisation against a matured mRNA. Again, it’s a simple physical interaction using that same 1-0 complementarity. tRNAs with the appropriate anticodon will bind. A gap in the set will cause STOP. The product is a FOLDED protein. The sequence of amino acids frequently determines this entirely – but it is, again, a physico-chemical interaction between the atoms of the molecuile, causing adoption of the lowest-energy state. The ‘information’ is in the atoms, not the mRNA. One can mimic the process semiotically – write down a DNA sequence, look up the translation, work out the hugely complex interactions in folding and come up with a ball-and-stick representation of the protein. The letters AAGCTTAGTCA ‘represent’, via an algorithmic protocol, the ball-and-stick model. But this is not what goes on in the cell.

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