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
- There is no information in living systems.
- There are no codes in living systems.
- 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.
So, stitching the apparent argument together from threads found floating on the breeze, is it Mung’s contention that replication is impossible without protein, and that protein translation is impossible without protein?
I’m not. I was just including myself possibly belonging to the group that Mung characterises as “TSZ code-denialists”.
He thinks there is as group of us (see his plural) and I suspect I am one.
That’s why I want to know what he thinks we are denying?
I don’t think that’s it, exactly, William, although I think I know what you are referring to.
My take is that frequently ID proponents or supporters (e.g. you and Mung) make terribly vague and not easily comprehensible points into which we do read some kind of theistic argument because they seem to be couched as anti-atheist arguments.
But if they aren’t – fine. In which case it would be nice for some clarification (as I’m currently requesting of Mung) to know what the point actually is.
I actually think (and that’s my bias, but it may simply be a mirror of yours) that you and Mung have a kind of atheophobia, and read into the comments and arguments of some of us (me, for instance) things that simply aren’t there.
And this happens all the time at UD – perfectly innocent bits of science (multiverses, consciousness, evolutionary biology) are perceived as being some argument against the existence of God. It is most odd.
Questions like this absolutely blow my mind.
First and foremost, that the genetic code is a code. Which is a stand in for the view that codes are not possible absent intelligent agency.
So further, that codes do not entail intelligence.
Thirdly, that symbols and representations are not present in the cell.
How in the world could anyone miss that unless they just were not paying attention?
Let me again post this quote:
The relationship has not been consummated. Would you like to be there when it is?
Please learn your figures of speech.
Actually, Lizzie, the recent comments that I have seen from you about the genetic code give me no reason to believe that you don’t think the genetic code is a code.
So Elizabeth, while I have your attention:
1. Is the genetic code a code?
2. Does the existence of a code entail an intelligent agent?
3. Has the genetic code always been a code, or did it have to wait for humans to come along and put it in writing before it became a code?
Depends on the definition of a code that you are using! By some definitions, yes. By others, no. To me the issue depends how far you want to stretch the analogy with language, or with computer code.
Again, it depends on the definition of code you are using! If by “code” we mean “a series of symbols arbitrarily allocated to agreed referents by a community of code-users” then, yes. But then, by that definition, the genetic code is not a code (because that definition actually has intelligent agents as part of the definition). But if your definition of code is something like: “a system in which Physical configuration A locks only to Physical Configuration B which locks only to Physical Configuration D”, then the genetic code IS a code, and I don’t see any reason to think that such a system has to have entailed an intelligent agent. Unless your definition of “intelligence” includes such a system, in which case it does!
Which is why I really want to know what the point of your question is. The answer depends on the definitions used. But if your question is simply: did the genetic code (as it is normally referred to) necessarily entail an intelligent agent, then in my view the answer is no. I don’t see any reason to think so.
Again, it depends on your definition of “code”. There are many. But to answer your question, we need to keep them consistent.
OK.
As I say above, to me, it depends entirely on what definition of “code” we are using whether we call it a “code” or not.
I would certainly agree, however, that the parent cell “sends a message” to the daughter cell in the form of a copy of its own DNA (which it was “sent” by its own parent cell), and that that copy contains at least some of the information the cell will require to function (i.e. persist and reproduce) within the (or as an) organism. But if we go that way with the analogy, the recipient of the message is a cell – and I wouldn’t call the cell an intelligent agent. And the sender of the message is some ancestral organism, again, not an intelligent agent. So the code isn’t a message sent between two intelligent agents, however way you look at it.
So the issue is: does the code itself have to be designed by an intelligent agent? Well, languages are designed over time by communities of senders and receivers, not by intelligent individuals on the whole, so, no – they can be designed by a community of code users. But that wouldn’t take us to an ID argument.
OK, didn’t scroll up far enough, sorry.
Not sure why. It seemed a reasonable enough question to me.
Well, I certainly dispute the view that codes are not possible absent intelligent agency, unless you are defining the cell as intelligent. In which case, I would agree that there is a sense in which DNA is a code sent from one intelligent agent (a cell) to another (its daughter), who then decodes it as required.
Well, we need a definition of intelligence here. Is the capacity to decode a message enough to qualify an entity as “intelligent”? If so, by definition, intelligence is entailed by codes.
I would not call a codon a “symbol”, unless we also want to call a lineage of cells a community of symbol users who have, in some analogous sense, agreed collectively on the mapping of symbol to referent. And that seems a stretch.
Because it doesn’t make sense?
I would dearly like to know what Yockey actually meant by that, and what you think it means. Because I probably disagree with Yockey, and I do not see how he gets there from Shannon. Yes, all those, I would agree, are reasonable terms to use, but I think they are indeed analogies. And they break down when we try to map those terms on to a human messenging system. Who is sending a message to whom? Is it parent cell to daughter cell?
For instance:
Information: fine: there is information, in the Shannon sense, in DNA, and we can quantify the amount of information that can be carried by a given length sequence of DNA. And that information is transmitted from parent cell to daughter cell.
proofreading: again, fine: there are systems in the cell that ensure that the message is received with fairly high fidelity.
So who is the “messenger” here? The “messenger” here is the process of cell division. So already the mapping is getting sloppy, now, because normally the word “messanger” in biochemistry is used to refer to “messenger RNA” which is not the daughter to cell transmission but nucleus to cytoplasm transmission.
So let’s try again. Perhaps Yockey means that the cell, having received its DNA from its parent, receives a chemical signal that it needs to produce a protein. That signal makes its way to the nucleus via a series of chemical reactions (not especially symbol like) which triggers the expression of a protein-coding gene. So do we say that the nucleus now sends a message to the cytoplasm in the form of an mRNA string? Or to the tRNA molecules? Or to the amino acid molecules? Or to the ribosome?
It seems to me of you (or Yockey) want to say that these processes are directly mappable to information theory as described by Shannon, you need to make the mapping explicit.
Otherwise you accept that while there are similarities in many ways to the kinds of coding and decoding that goes on in human message exchanges, the intelligent agents in human communication are missing from the cell version.
Unless, as I say, we consider that cells are intelligently sending messages to their daughters or nuclei are reacting intelligently to chemical signals by sending messages to their own intelligent cytoplasms.
Neither of which delivers you an intelligent designer of the system.
In light of this distinction, it seems to me that what Mung wants to say here is something like this:
If a system consists of relations of physical configurations such that physical configuration A locks only to physical configuration B which locks only to physical configuration D, then the system consists of a series of symbols arbitrarily allocated to agreed-upon referents by a community of code-users.
I don’t think I’m the only person here worried that this is an invalid argument.
(Needless to say, the invalidity of this argument doesn’t affect the usefulness of biosemiotics as a theory of organism-environment transactions.)
Well, the point I keep making, is that if we want to infer intelligent agency from the observation of something we want to call a code, then the next step is to define the community of code users who have “agreed” (in however tenuous a sense) to use that code. You could define (in a tenuous sense) all cells of all terrestrial organisms as a community of shared symbol users, passing down information through the generations.
But that isn’t usually the sense in which the “code” is interpreted. Instead, the relevant “message” seems to be from DNA in the nucleus to the various molecules in the cytoplasm to construct the right protein at the right time. So where is the shared community of symbol users? There isn’t one, because as far as we know (That stupidly termed “dogma”) the code is only used in one direction (nucleus to cytoplasm not cytoplasm to nucleus), and there’s no terribly good reason to pin the role of “sender” on the nucleus anyway. It’s only doing what it’s been told to do by whatever chemical signal triggered it into “asking for” a particular protein.
And in any case – 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.
So the analog to the intelligent agent in the genetic code is either the cell (parent to daughter) or nucleus (nucleus to cytoplasm). Not some external code deviser.
Unless we want to think of the code not as human language but as computer code.
But then the Yockey quote doesn’t map at all well on to that version of the “genetic code as code” thing.
I would not agree with that.
Languages evolve in communities of senders and receivers.
The first step would be to demonstrate that the code system did not evolve without external guidance. Otherwise, you are assuming your conclusion.
In the case of the genetic code, the best that IDists can do is point out that we do not yet have the pathetic details of how it evolved.
A gap that keeps narrowing.
OK, I’ll buy that. I certainly don’t think languages are often intentionally designed (though there are a few weird exceptions).
Computer languages are not analogous to human languages because they do not have connotation. Except in the form of unintended features.
Synthetic languages have developed small users communities, not unlike Morse code users. They are human languages to the extent they have copied features of human languages.
Human languages are part biologically evolved, part culturally evolved and part mentally evolved.
🙂
LoL.
ok, Elizabeth, let me try again.
Do you think there is any definition of a code according to which the genetic code is a code? If so, what is that definition?
This isn’t about what I think, it’s about what you think. You want to know if you qualify as a code denialist? That is obviously going to depend on whether you think the genetic code meets the definition of a code.
Isn’t it the case, that if there is a definition of a code according to which the genetic code is a code, then the genetic code is a code? Or do definitions not matter?
Sorry, Lizzie, I could have done a better job on that last post. Please don’t take offense. I see that you said that according to some definitions the genetic code is a code. Which definitions then?
I mean we agree that it would be absurd to say that the genetic code does not meet every definition of a code, therefore it is not a code, right?
No problem 🙂
Well, if we were to define a code as something in which a pattern instantiated in some physical medium (beeps and boops; depressions in clay; vocalisations; beads on a string) specifies some outcome, we might say that the pattern “codes for” that outcome, or that the outcome is “encoded in” the pattern. And we might want to reserve the term for scenarios where the pattern isn’t absolutely direct (as in, say, a printing plate). In that sense, the genetic code would be a code.
Hi Mung. I’m not an expert nor have done the reading but it probably doesn’t meet the ‘obsfucatory’ definition of code, but I’m pretty sure that’s not the one you intend.
Good grief. Scientists often use ordinary language as shorthand to refer to complicated matters.
One might also ask, foolishly, “Was the Big Bang really a bang? If so, who made it?”
Or is electric current really a current?
Or an electric field a field?
Elizabeth, I did not ask you to make up your own definition of a code.
I asked: Is the genetic code a code?
You responded: By some definitions, yes.
Now why would you say such a thing if you were not aware of any definition of a code by which the genetic code is code?
When you wrote: By some definitions, yes.
Did you really mean to convey the idea that you could make up a definition of a code according to which the genetic code is a code? Because that’s what it sounds like now.
Why is the question so difficult?
Mung: Is the genetic code a code?
Elizabeth: By some definitions, yes.
Mung: Do you think there is any definition of a code [not including something you just made up] according to which the genetic code is a code? If so, what is that definition?
Oh, right.
What did you want, then, some dictionary definition?
Yes, I assumed you meant that. That’s how operational definitions work. You define a construct for some specific purpose, and you make it clear that that is how you are defining it. The definition I made is quite a good one, in that it excludes things that we would probably generally agree are not codes, yet it is broad enough to include the genetic code as well as other codes that are pretty universally agreed to be codes.
There aren’t a set of prescriptive definitions of words, Mung. Even dictionaries only record usage.
I took some paradigm features of codes, and devised a definition that was inclusive enough to cover the genetic code, as well as human language, but excluded direct templates.
*Runs to Uncommon Descent, starts ‘Liddle doesn’t trust dictionaries, creates own definitions’ post*
The concept of definitions seems to be something that deparates TSZ from UD!
I find it rather odd.
Construct (Philosophy)
Though I’m sure KN and Walto can do better!
Mung,
You are rude and inconsiderate.
You’ve been answered in spades by me and others here.
You don’t like the answers, so you ignore them.
Bad form. You lose.
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.
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.
And here I think I’ve been playing nice with Elizabeth, who ought to know by now what I mean when I say the genetic code is a code, since I created an OP and set it out in that OP.
My post at UD won’t be quite like what you’ve written though.
Pedant,
A simple search shows you’ve had nothing whatsoever to say of any relevance.
Why should she know that since you equivocate over the multiple definitions of “code” with every post?
Interesting comment since you’ve had hundreds of posts with nothing whatsoever to say of any relevance.
It’s a purposeful strategy on the part of the IDiots. If they never define their terms they can’t be pinned down with concrete rebutting examples. Mung’s just a good little foot soldier following the IDiot script.
Actually, Mung has posted hundreds of times jut to remind us that he isn’t willing to say what he has in mind.
Mung,
As my five o’clock shadow shows, I’m not Elizabeth, but I could make an argument that the genetic code meets the definition you provided here (assuming a broad definition of the word “symbol”):
“Definition. Let the set of symbols comprising a given alphabet be called S = {s1,s2,…,sq}. Then we define a code as a mapping of all possible sequences of symbols of S into sequences of symbols of some other alphabet X = {x1,x2,…,xr}. We call S the source alphabet and X the code alphabet.
Definition. A block code is a code which maps each of the symbols of the source alphabet S into a fixed sequence of symbols of the code alphabet X. These fixed sequences of the code alphabet are called code words.”
There are other definitions of the word, though, that don’t apply to the biochemistry observed in living organisms. Do you consider that a contentious statement?
If not, what is your objection to Elizabeth’s comment?
This might be easier and more efficient if you’d just lay out your argument in all its glory so we can discuss it.
I do not. In fact, I have either said so myself directly or have said things which reasonably interpreted convey as much.
Which comment?
Right now I just want to know what she meant when she said the genetic code is a code “by some definitions.”
I don’t think she was referring to the definition you just posted because she has exhibited no awareness of the definitions posted in that OP.
So maybe she is referring to something Alan or Allan posted. They both posted definitions.
I find it most difficult of all though to believe that she made up a definition of a code three hours after the fact, and that definition is what she had in mind when she said that the genetic code is a code “by some definitions.” [Not saying she claimed it was. Just exhibiting advance skepticism.]
But since I have your attention again 🙂
You appear to agree that, given that definition of a code, the genetic code is a code. Any dispute there?
You’ve also expressed doubt that one can get from that definition to an intelligent agent, a point I granted. Are you willing to say that according to that definition of a code, the existence of a code does not entail an intelligence?
ETA: By some definitions. Which ones?
Mung,
I’m sure you won’t disappoint, mainly because of your history / low expectations…
LOL! Mung keeps the IDiot equivocation train rolling right along.
ALL ABOARD!
Meanwhile Richardthughes, your continued absence in the discussion is due to what? Do you dispute the conclusion I made earlier?
If there is information in genome (genetic information), the sequences of nucleotides which contain that information must represent something other than that sequence of nucleotides.
Else, what is the point of calling it information?
Here is a fairly comprehensive set of definitions for “code” from the American Telecommunications Institution
DNA falls under definition 4 which does not require abstract symbolism or intelligence.
In addition to the flow of Gibbs free energy (i.e., thermodynamic information) through living organisms and ecosystems, there is also a flow of cybernetic (or semiotic) information.
– John Scales Avery
This second form of information [cybernetic information], which is associated with the sending and receiving of signals, with communication, with codes or languages, and with biological or cultural complexity, will be the theme of the remaining chapters of this book.
– John Scales Avery. Information Theory and Evolution
That depends on the definition of “information” and not equivocating with the definition of “meaning”.
Mung does lots of the latter but won’t commit to the former.
Mung,
I believe I’m fine with the use of ‘code’ but per Bill’s repeated request I think you should list the entailments of ‘code’, my prediction of this being ID buzzword but dying on the scientific vine has already been made.
Mung,
This is where we get to the edge of the map vs territory distinction, I think. The model that we commonly use for the biochemistry that occurs in a cell seems to meet that definition, barring any disputes over the words used in the definition. If what you mean by “genetic code” is that model, then yes, the genetic code is a code by that definition.
If what you mean by “genetic code” is the biochemical pathways themselves, I’m not sure. Do the chemical reactions “map” nucleotides to amino acids or do they result in a mapping according to our models? It seems to me that this is the level of detail, pathetic as it may be, where we need to focus on what’s actually happening rather than on whether we describe it as a code or not. Layman’s language is insufficient at this point.
As above, I think that if we’re talking about living organisms, our everyday language breaks down at some point, becoming a hindrance rather than a help. I’m not sure where you’re going with this, but if you want to argue that DNA transcription was designed, then you’re going to need to drop words like “code” and talk in terms of biochemistry.
Richardthughes, our conversation was not about codes, it was about biological information.
Yep. You equivocated over and refused to give your definitions of both terms.
Good foot soldier Mung, following the IDiot script to the bitter end. 🙂
Mung,
Before we die of boredom, please tell us what your point is, if any.