The Myth of Biosemiotics

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I recently came across this book:

Biosemiotics: Information, Codes and Signs in Living Systems

This new book presents contexts and associations of the semiotic view in biology, by making a short review of the history of the trends and ideas of biosemiotics, or semiotic biology, in parallel with theoretical biology. Biosemiotics can be defined as the science of signs in living systems. A principal and distinctive characteristic of semiotic biology lies in the understanding that in living, entities do not interact like mechanical bodies, but rather as messages, the pieces of text. This means that the whole determinism is of another type.

Pardon my skepticism, but

  1. There is no information in living systems.
  2. There are no codes in living systems.
  3. There are no signs in living systems.

Biosemiotics is the study of things that just don’t exist. Theology for biologists.

I had a hunch that the idea of codes in living systems would be resisted here at “The Skeptical Zone.” I had no idea though at the time just what might be the extent of that opposition. Apparently Code entails Goddidit. God must not exist, therefore codes cannot exist.

The idea of what a code is that I am trying to follow comes from Information Theory/Coding Theory. I was not particularly concerned with whether the application of information theory and coding theory to biology ought to be taken seriously, I thought at this point that was a given. I was wrong before, I’ll probably be wrong again.

Do the Semiosis Skeptics and Code Denialists here at TSZ reject the concept of biological information?

If so, why?

Warning!: It’s a trick question.

230 thoughts on “The Myth of Biosemiotics”

  1. Mung:
    Richardthughes, our conversation was not about codes, it was about biological information.

    I thought I was pretty clear that I think that every domain including biology has information.

  2. keiths: Before we die of boredom, please tell us what your point is, if any.

    Don’t you get it? I’m waiting for you to die of boredom first.

    Or you could retract that claim of yours that you never supported with any actual evidence. Doesn’t that bother you in the slightest, hanging a claim like that out there and never backing it up with a shred of evidence?

    You know, what with you being so righteous and all.

  3. Richardthughes: I thought I was pretty clear that I think that every domain including biology has information.

    Indeed. But the OP is about information in a particular domain. Biology. You know, that whole biosemiosis thing. Information, Codes and Signs in Living Systems

    Here’s how one author puts it:

    Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of a species…Thus, information about the environment eventually becomes implicit in the genome of a species.

    Now the author admits that the species doesn’t have a genome, so let’s not let that distract us.

    If this information resides in the genomes of the members of the population, and if it is in fact about something external to the genome, then it must be by way of representation.

    Focus, grasshopper.

    And it’s not because that information represents anything to us, as humans. This must have been the case before humans ever appeared.

  4. Meh. The information is about the organism. If the organism is complementary to the environment it will have improved chances of reproduction.

  5. Mung,

    The danger of representationism appears to lurk in your approach. The philosophy of mind people are well ‘represented’ in that discussion. 😉

    I think Lizzie, though of course I disagree with her current worldview, has made some valid points in this thread:

    “the intelligent agents in human communication are missing from the cell version.” … “the reason we think of human codes as entailing intelligent agency is because intelligent agents use them (and think them up) to communicate with each other.”

    Much of this is echoed in the claim that IDism indeed is a kind of neo-creationism, given that it univocally predicates from intelligence to Intelligence according to the heart of its ‘strictly scientific’ theory. But I don’t consider you a ‘creationist’, at least not of the YEC variety. The distinguishing factor of ideology marks the difference between a person who believes in divine Creation and one who is a ‘creationist.’

    There is, however, an easily seen over-simplification in much of the IDist ideology, which boils down to informationism; that *everything* is about information. And then the IDist slides off the cliff simply by saying information requires Intelligence means ‘strictly scientific’ inference of a Designer. At the end of the day, that’s what your argument re: “the myth of biosemiotics” is really about, isn’t it (the hidden intention at least)?

  6. Richardthughes: Meh. The information is about the organism. If the organism is complementary to the environment it will have improved chances of reproduction.

    Actually, you are saying that the information is about the relationship between the organism and it’s environment.

    Explain how that can be the case without representation, when all you have in DNA is a sequence of the same four nucleotides.

  7. Gregory, perhaps you are impressed by Lizzie’s tautological statements, I am not. I think I gave them the attention they deserved.

    “the intelligent agents in human communication are missing from the cell version.”

    No freaking kidding. Unless cells are intelligent agents. Do cells communicate?

    “the reason we think of human codes as entailing intelligent agency is because intelligent agents use them (and think them up) to communicate with each other.”

    Um. Yeah. Human generated codes entail humans generated the codes. Who ever thought otherwise.

    The danger of representationism appears to lurk in your approach.

    This comment interests me, but it does not tell my why I should be concerned.

    Information is always information about something. IOW, representation seems to be entailed by the very concept of information. If you think otherwise I am all ears.

    I do not think that information is the end all and be all, “that *everything* is about information.” It’s just the reigning paradigm in biology, probably because it allows other problems to be swept under the rug.

    I don’t know if information entails intelligence. For me that is an open question.

    Frankly I am amused watching everyone else slide off the cliff. As a sociologist, I hope you are taking notes, and I hope you’ll at least give me a mention in your next book. Seriously, we’re talking pure gold here, right?

    I know BruceS thinks I’m in a conspiracy with Elizabeth, but really I’m in a conspiracy with you. Don’t tell anyone.

  8. “perhaps you are impressed by Lizzie’s tautological statements, I am not.”

    Again, at the end of the day, IDists (among which you self-identify in your promotion of “Intelligent Design” theory) are doing the same. “I (Mung, UB, Stephen C. Meyer, William Dembski, Michael Behe, Cameron Wybrow, and whoever else) am ‘intelligent,’ therefore exists (capitalised) Intelligence.” Univocal predication. Simple apologetics, but not ‘strictly scientific’.

  9. Mung: I want to know what definition or definitions of a code you had in mind when you said that the genetic code is a code “by some definitions” of a code.

    If you didn’t mean that just say so and we can move on.

    I mean exactly that. That it is possible to define a code, coherently, in ways that include the genetic code, and in ways that do not.

    On the other hand, if you want me to believe that the definitions you had in mind at the time you made that statement was a definition you were gong to make up three hours later, please say so.

    OK, so we are fundamentally misunderstanding each other about what constitutes a definition.

    I do not regard the definitions of a word as a list that exists “out there” somewhere, and from which I can draw, but to which I am forbidden to contribute. Even dictionary definitions, as I said (and there are many dictionaries, each with a different set of definitions) record usage, they do not prescribe (or proscribe) use. That is, incidentally, what people mean when they say that language evolves culturally, it is not designed. But that is simply an apposite metal issue regarding codes and language, not my point re definitions.

    Instead, I regard words as having a kind of “field” of usage – there are sets of referents for a word that have something in common, but often fuzzy boundaries (there’s a parallel here with the concept of “species” – is a hyena a cat?) And words often expand their coverage – “language” used to mean something that people spoke (from the word for tongue – indeed “tongues” is a synonym). Now we use it to refer to computer languages, sign language, even the language of art forms.

    Same with “code”. It used to have a broad sense being a system of rules (as bound into a “codex”), then acquired a specific narrow linguistic sense, as defined by Pierce (as far as I know). It also came to refer to a cipher, and, more recently, to computer code.

    So if we want to include both human language and genetic code under the same definition, we need first to abstract the things that a genetic code and human language have in common, and then exclude things that we do not want to include (for instance we might not want to call a stamp a code). Then see if we have a coherent workable definition. I think I came up with one.

    On the other hand, if you asked me whether a hyena was a code, I would say that I could think of no coherent definition of code that would include a hyena. I could, however, think of a coherent definition of “cat” that did, although it wouldn’t be terribly standard, and would probably include items we don’t normally think of as cats at all.

    So no, my answer is not tautological at all. I think it is possible to define code, sensibly and coherently, in a way that includes both the genetic code and human language.

    I also think it is possible define code more narrowly (e.g. as a system of symbols and rules shared by a community of symbol users to communicate with each other) that would probably exclude the genetic code.

    But I must return to my original question: why is it important?

  10. Moved a post to guano. If you haven’t anything to say apart from casting nasturtiums on other posters, don’t say it here please.

  11. Mung: Indeed. But the OP is about information in a particular domain. Biology. You know, that whole biosemiosis thing. Information, Codes and Signs in Living Systems

    Here’s how one author puts it:

    Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of a species…Thus, information about the environment eventually becomes implicit in the genome of a species.

    Now the author admits that the species doesn’t have a genome, so let’s not let that distract us.

    If this information resides in the genomes of the members of the population, and if it is in fact about something external to the genome, then it must be by way of representation.

    Focus, grasshopper.

    And it’s not because that information represents anything to us, as humans. This must have been the case before humans ever appeared.

    Let us for now, grant you all this (i.e. grant that to use words like “representation” in this context is reasonable).

    What do you infer from it?

  12. Mung: Here’s how one author puts it:

    Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of a species…Thus, information about the environment eventually becomes implicit in the genome of a species.

    Now the author admits that the species doesn’t have a genome, so let’s not let that distract us.

    I don’t recognise the quotation (could you provide a citation?) but I would agree with it. The uncredited author makes the very important point that the ID chestnut: “how did the information get into the genome” has a simple answer – it is transferred from the environment into the genome by natural selection.

    Or at least information as to what a cell must do to enable its owner to have a good chance of surviving and breeding in that environment is transferred from the environment to the collective genome by natural selection.

    And by collective genome, I would mean (and I assume the author means): the sequences shared by a population that lead to phenotypic features that promote reproductive success.

    That information is, of course, also transferred longitudinally down the lineage, even after the information is no longer relevant (e.g. the environmental challenge or opportunity that caused it to be so widely shared is no longer present), together with random information in the form of sequences that don’t do anything much, or do stuff that doesn’t affect reproductive success.

    So that’s yet another information transfer channel: from environment to population genome. We can add that to parent to daughter-cell transfer; multicellular organism to offspring transfer; nucleus to cytoplasm transfer; internal and external environment to nucleus transfer.

    Lots of information transfer! Do we call it all “code”? Is there any point in doing so?

    And what are its implications for what we apparently disagree on?

  13. Patrick,

    Layman’s language is insufficient at this point.

    Pretty much my point all along. Having some knowledge of the details leads me to consider it not a code according to my understanding of what a code is. An enzyme is not a rule, so 20 of them is not a set of 20 rules. Those enzymes have clear signals of common ancestry, in 2 groups of 10. So perhaps, rather than obsess about ‘code’, we could look at what that tells us about how the system may have evolved.

    My opinion on ‘code’ may be challenged, because I am not particularly expert in codes (though I write code and send messages, sometimes cryptic ones!). But apparently Crick, Yockey, Avery, Uncle Tom Cobbley – they are expert both in the biochemical detail and in the linguistic aptness of the term ‘code’. So rather than pursue the argument directly, a high percentage of Mung’s posts are simply these people ‘agreeing with him’ (only one a biological scientist, incidentally. I’m not sure of Uncle Tom Cobbley’s area of specialism).

    Anyway, I thought we’d moved on from codes?

  14. Mung,

    Explain how that can be the case without representation, when all you have in DNA is a sequence of the same four nucleotides.

    On first appearance, a particular string cannot possibly have any information about the environment – they have not been in contact. Only by ongoing differential copying and frequency change can that ‘information’ accumulate in a wider set of individuals, as the less successful form of the ‘information’ falls by the wayside. It’s not clear at which point a sequence which itself is unchanged from inception would suddenly start to ‘represent’ the environment.

  15. Mung,

    Frankly I am amused watching everyone else slide off the cliff.

    So that’s both sides smirking at the other, then. Everybody’s happy!

  16. The paradigm case of a “representation” is something like this:

    I walk into a classroom and say: “Let x represent the IQ scores of the sample”. In other words, I, an intelligent agent, choose an arbitrary symbol, x to represent something totally different – a vector of IQ scores.

    Or a boy scout leader says to his cubscouts: “if I leave the path, I will place a pair of crossed twigs on the ground, so”.

    In both cases, we can then use the assigned symbol (x, crossed twigs) to communicate information from one intelligent agent to another.

    But information is also transferred between non-intelligent agents. Information about seasonal weather is transferred to stalactites, layers of snow, tree rings, lake varves etc – and can be retrieved by humans much later to tell us about, say, atmospheric C13:C12 ratios over the millenia (and falsify YEC as it happens).

    And so we can say, in a manner of speaking, that tree rings etc “represent” years.

    But that clearly does NOT mean that the weather was sending a message to the tree in the hope of passing it on to us.

    So as far as I am concerned, the language itself tells us nothing. Demontrating that information transfer has occurred, does not “prove” that it must have been done by means of a “representation”. Rather, it is simply that “representation” presents itself, sometimes, as a suitable word to use to describe the transfer o information, by analogy with “let x represent IQ scores”.

    So, as Allan says, if there is to be any dialogue between those who think that the genetic code is evidence of an intelligent designer and those of us who don’t, we need to get beyond arguments about what words mean. Words mean what we agree to let them mean. Giving a thing a name does not change what it is, and the fact that we can redefine a word so that it includes more things does not mean that those things thereafter share all the attributes of those things previously covered by it.

    Would you agree, Mung?

  17. A thought that strikes me when I’m out running: a path has information. Some paths are designed and constructed, others just arise. A sheep wanders through some wet grass and leaves a trail, some other sheep follow that trail – because they’re sheep! Before you know where you are, there’s a decent path worn by their feet. I can read the information – the general way they tend to traverse the hillside, the little round balls of shit, the hoof marks – and in some sense, the path is representative of the sheep. Where they went frequently stands out from where they went less frequently. I can tell it’s not a designed path, but it still has information – both for me and for the sheep.

  18. Elizabeth:

    [quotes Mung quoting ?]Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of a species…Thus, information about the environment eventually becomes implicit in the genome of a species.

    I don’t recognise the quotation (could you provide a citation?) but I would agree with it. The uncredited author makes the very important point that the ID chestnut: “how did the information get into the genome” has a simple answer – it is transferred from the environment into the genome by natural selection.

    I agree with it too. Could be a description of my alternative phrase for “natural selection”, “environmental design”.

  20. My favorite example is Chesil Beach. On Chesil Beach, the pebbles are exquisitely sorted in size order from coarse sand at the far western end to big boulders 18 miles to the east, going through pea-sized to cherry sized, to plum sized, to orange sized etc on the way.

    The sorted sequence would clearly have CSI, if the definition of CSI didn’t exclude patterns that arise from material mechanisms! And the sorted sequence also contains real usable information. The local story goes that fishermen, landing on the beach at night, could tell where on 18 mile stretch they had landed by rolling the pebbles in their hand.

    Where did that information come from? Well, it came from the system as a whole – wind, tide, current, shore topology, transferred in to the sequence of pebbles.
    And it was there long before there was an intelligent agent to make use of the information for their own purposes.

  22. Quoted by Mung, agreed by others …

    Evolution is essentially a process in which natural selection acts as a mechanism for transferring information from the environment to the collective genome of a species

    Moran (and others) would have a fit! Evolution and NS aren’t synonyms.

  23. Allan Miller,

    Layman’s language is insufficient at this point.

    Pretty much my point all along. Having some knowledge of the details leads me to consider it not a code according to my understanding of what a code is. An enzyme is not a rule, so 20 of them is not a set of 20 rules.
    . . .
    Anyway, I thought we’d moved on from codes?

    I hope we can. This is just yet another example of creationists trying to define their god/designer into existence. Apologetics and “bible study” seems to have a profound corrupting effect on theists thought processes.

    So how about it, Mung? Lay out your argument, whatever it may be, in terms of the biochemistry of the cell. Let’s end the semantic nonsense.

  25. Patrick: This is just yet another example of creationists trying to define their god/designer into existence.

    But the resistance to codes has nothing to do with creationists. Isn’t that what you said in the Telepathic Boy thread?

  26. Information is a key concept in evolutionary biology. Information is stored in biological organism’s genomes, and used to generate the organism as well as to maintain and control it. Information is also “that which evolves”. When a population adapts to a local environment, information about this environment is fixed in a representative genome.

    – Christoph Adami

  27. Mung,

    This is just yet another example of creationists trying to define their god/designer into existence.

    But the resistance to codes has nothing to do with creationists. Isn’t that what you said in the Telepathic Boy thread?

    You mean this?

    So all the code denialism going on here is just to tweak the noses of the creationists. Not because code entails designer. Right?

    Wrong. It’s because those of us who have been on this ferris wheel for a few revolutions can smell a big, heaping pile of equivocation coming whenever creationists, including the intelligent design variant, start using words like “code” and “information” without committing to a definition and presenting their argument up front.

    My two comments come from the same experiences. Creationists do seem to think that playing word games is a substitute for actual evidence. Very often those word games hinge on equivocation, both subtle and blatant.

    I’m not saying that’s what you’re doing here, but once bitten twice shy.

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