Lots of heat surrounding this question.
My take is that a code must be a system for conveying meaning.
In my view, an essential feature of a code is that it must be abstract and and able to convey novel messages.
DNA fails at he level of abstraction. Whatever “meaning” it conveys cannot be translated into any medium other than chemistry. And not just any abstract chemistry, but the chemistry of this universe.
Without implementing in chemistry, it is impossible to read a DNA message. One cannot predict what a novel DNA string will do.
DNA is a template, not a code.
Go to it.
But your position cannot account for what it does. Hence the debate.
Mindless repetition of your same nonsensical IDiot claims won’t make them true Joe. After a decade you still haven’t learned that.
Then get to your sooper-dooper IDiot lab, make a codon out of modeling clay and sticks, have it produce a stick and modeling clay amino acid. Should be easy if codons are just arbitrary symbols as you say.
I hope you find them useful. For the newer one especially, I have to admit it gets a bit technical and I did skim some of the stuff at the end. I have not attempted the research papers he references, of course.
Moved some posts to guano. Just a reminder that the rules demand you address comments rather than the commenter. Comments can be reposted minus personal attacks or spats can continue in the noyau thread where rules that apply to all other threads are relaxed.
I agree with you, Allan, and I appreciate the technical expertise you bring to the table with your posts. I learn something from trying to understand them.
But let me play devil’s advocate.
The first issue I’d bring up is that there is something special about the genetic code as implemented in DNA: it serves a purpose for the organism. And it can fail to achieve that purpose due to transcription errors. That is different from a purely physical, causal process which could be read by us as a mapping, such as measles and spots. The spots don’t serve any purpose for measles.
The second issue is the one you bring up about where to draw the line. Why is the DNA code something that we must be involved-in to call a code whereas the bees example is considered to be something that is a code without us. Aren’t they both just biochemistry?
And finally, one can extend that last point. How does involving us solve the issue? After all, we are “just” biochemistry (or are we?). So how can we have maps and languages and DNA cannot? Saying that we have brains does not help: that is just more biochemistry.
Now I believe the first two questions do have answers and they are based on applying evolution. But filling in the details of those answers is still very much a work in progress.
We can start on the third by recognizing the brain’s natural ability to learn associations and then using evolution to explain that.
But that is just a start. Further issues remain. For example, how do our languages have meaning/intentionality, and does that intentionality differ from the animal intentionality of actions towards the world? One could write a whole book on that last issue alone.
I may not have been as clear as necessary about what I am getting at.
My understanding of the word “code” — which may not be the only possible one — is a system of transferring information such that an arbitrary reader can discover the meaning of the message.
This applies to human languages, including encrypted ones or extinct ones.
I think it also applies to musical notation, including mechanical notations, such as music box cylinders.
One thing that distinguishes such symbol systems is grammar and syntax. The notation has elements that can be rearranged to form alternate messages, and such alternate messages can be understood.
DNA does not have anything analogous to grammar and syntax. Altering a bit or rearranging a sequence can scramble the meaning. If you are given two unknown sequences, you cannot tell if either have any meaning or usefulness, except by inserting them into a living system. Even then, you do not know whether a negative finding means the sequence can never have meaning in another context.
For this reason, you cannot design DNA the way aircraft or houses are designed. There are no modules that fit together by rules and by attributes. (A minor exception might be protein domains, but these are already large sequences, almost stand-alone genes.)
The question I’m addressing is not a dictionary duel. It is the question of whether biological design is possible.
I await any demonstration by ID advocates that design is possible.
Moderation issues should be discussed in “Moderation Issues”.
How can you have intententionality if you cannot predict the results or consequences of an action?
If I rearrange the phrase, “the dog bit john” to “john bit the dog”, we understand the two sequences.
If I make a small change to a DNA sequence, there is no way other than trial and error to determine how the meaning has changed.
This goes to whether evolution could be a result of front loading, or to whether a super intelligent being could be twiddling with genomes to produce new species. or new adaptations.
I await a demonstration by Doug Axe or someone that there is a way to know the meaning of a DNA sequence without cut and try.
There’s a nice question here whether “animal intentionality of actions towards the world” really counts as intentionality.
If we think of sensorimotor abilities as teleologically organized towards affordances rather than towards discrete objects, it’s much less clear whether we’re talking about intentionality at all.
Tomasello urges us to recognize that chimps (and possibly gorillas) have “individual intentionality”, prior to the emergence of “shared intentionality” on which language and culture depend. I’m trying to figure out whether the concept of “individual intentionality” really makes sense. I’m worried that Tomasello’s reliance on Searle exposes his views to criticisms grounded in Hegel and Heidegger.
Does that mean you are repudiating your book? Or is there a subtlety in the book I missed?
Well, let me amend that. There are lots of subtleties in the book I am sure I missed. But I thought a central theme was to posit those two types of intentionality.
Playing catch-up:
Petrushka in the OP writes: DNA is a template, not a code.
Exactly! And the point that there is no way (currently) to predict what properties a protein synthesized from an unknown DNA sequence might have without synthesizing it and testing it cannot be repeated too often. (So I did!)
Just to be clear, I’m using intentionality in the philosophical sense of aboutness. Not in the sense of purpose.
In that sense, intentionality is usually applied to mental representations.
But I’ve seen it applied to actions. At least I have a clear recollection of seeing that. But I may be mis-remembering. I’ll try to dig up a reference.
Also, KN points out there may be issues with that usage, even if I am remembering it correctly.
To be honest, I only stuck that in the post you link as a sort of easter-egg shout-out to KN.
I don’t think our ability to predict matters to this issue. Saying that DNA has a meaning by implementing the code is enough for the ID folks, I suspect. In any event, we if assume the code is being used to transcribe a protein, we can predict the meaning of an instance of the three letter code.
I don’t think the ID proponent’s claims are about the meaning of the whole genome. Nor are they about the entire development of the phenotype. I understand the claims as solely about the mapping of three letter codes to proteins.
Morse code doesn’t convey meaning, but just translates dots and dashes to letters, regardless of any underlying meaning.
That’s a template. There’s no meaning in such a template. Just chemistry. It’s a mold.
The problem for the Design Hypothesis is that if you have a small flaw in the [DNA] mold or template, you change the meaning entirely.
It’s as if a small flaw in the stamper for a coin changed its denomination. Or turned a silver coin into rubbish.
That exposes a flaw in my writing. Which is why I keep trying to qualify my statements by talking about what is important to my thought.
I’m not repudiating it entirely. I still think I was onto something. But I now believe that there are subtleties in the problematic that I overlooked in the account that I offered there.
Zachriel,
Then it’s wrongly called a code. It should be called a template. 🙂 Seriously Morse isn’t really a code. The dots and dashes are representations that map to letters of the alphabet. Unless we’re calling alphabets codes!
Templates are about physical reproduction. I agree that physical DNA can be viewed as a template.
The claim is not about physical DNA.
It is about the code mapping 3 letter sequences to proteins. The claim is that that mapping constitutes semantic meaning, and not merely a conventional mapping like Morse code or a simple causal relation like spots and measles.
Now maybe it is only us that assign that meaning. I would tend to go along with that explanation.
But playing devils’ advocate, one could say that the claims for meaning are based on the purpose the mapping serves for the organism in continuing its life. That would include the recognition that failure to properly implement the meaning has detrimental consequences for the organism. Under that point of view, the hardware failure in transcription or failures in the DNA implementation would support the attribution of meaning.
Regardless, Morse Code is comprised of dscrete units that can make up words and sentences, and the words and sentences can convey novel meanings that can be understood.
The part of this that I find interesting is that with language, one can encounter a completely new phrase, sentence or paragraph and understand it.
With DNA, any rearrangement makes gibberish, or a new meaning that cannot be understood except by doing the chemistry and testing the result.. There is no abstract level of meaning.
This is part of what is implied by emergence.
Aoccdrnig to rscheearch at an Elingsh uinervtisy, it deosn’t mttaer in waht oredr the ltteers in a wrod are, olny taht the frist and lsat ltteres are at the rghit pcleas. The rset can be a toatl mses and you can sitll raed it wouthit a porbelm. Tihs is bcuseae we do not raed ervey lteter by ilstef, but the wrod as a wlohe.
I don’t understand why you think that is so important. Take sarcasm–a mere look can make a remark mean the opposite of what it otherwise would.
You have also argued that, in the case of DNA, our limited ability to predict outcomes is important. That does seem like a disanalogy with many languages if we suppose the meanings of statements in the latter are ultimately reducible to the meanings of the words in those statements, while the “meaning” of a DNA sequence is not.
I honestly don’t know if that disanalogy with, e.g., English, either works completely, or, supposing it does, whether it’s important to some argument for design or not. Neither of these is obvious, I don’t think.
Grammar, syntax and spelling make it possible to construct novel sentences that have a predictable meaning.
Human language, as opposed to computer languages, have a layer of connotation, which may be the intended layer.
But you cannot construct novel sequences of DNA and know what they mean or what they will do. That is a problem for the Design Hypothesis.
This also distinguished the DNA code from any designed code, such as writing or musical notation or computer languages.
If DNA is a code, it is an evolved code, not a designed code. It lacks important attributes of designed codes. Its primary attribute never occurs in designed codes.
It’s like writing a book where the meaning of the last word in the book is affected by the first and the 15,000th. Like BA77 says, there are “layers of overlapping codes”. How can a designer consciously design in a system like that?
They can’t, it’s obvious. So trial and error is all that remains.
I would say it’s like a language in which — even to native speakers — changing a single word can make Money Dick indistinguishable from Fifty Shades of Gray.
I will change my mind about this if and when we find a good shortcut to protein folding. If that becomes easily computable through rules rather than trial and error, the maybe we sign is possible.
So it is a code! Or could be one.
But that is Frankie says, except he also asserts that it could never evolve. So it is really on the second assertion that you disagree with him. And for good reason, I believe.
That is getting awfully close to a god-of-the-gaps argument.
The god-of-the-gaps argument says that science cannot explain this yet, therefore it will never be able to explain this.
And your argument says that just because we cannot design something yet, or compute something yet, without using trial and error, then we will never be able to design it or compute it. And further, no entity could exist that could design or compute it without trial and error.
I don’t accept the god-of-the-gaps argument. Why is your argument different?
(One answer might be to show the problem is NP-complete. Perhaps it has been shown to be that?)
Seriously, Morse code should be called Morse alphabet.
It’s just an alternate “typography” for alphabetic letters and digits.
I don’t think you even need to say it “maps to” letters of the alphabet. I think it IS letters of the alphabet.
Which doesn’t say much about whether DNA might be a code, or not; except if the IDist argument is that DNA is a code exactly in the same way that Morse is a code, then their argument is pointless.
You’re right. I just wanted to sound sciency! 😉
🙂 🙂 🙂
This issue relates to the issue of rarity of functional proteins in sequence space. There are 20 amino acids coded for in the “standard” genetic code. Proteins are linear sequences of amino acids (the median length being around 360 aas). The theoretical possible number of proteins of any given length is
which gives astronomically large numbers. The ID argument (Axe, Durston etc) is that functional sequences among unknown proteins are rare. The evolutionary argument is that we don’t know but there are hints that functionality is not rare. The computing power needed to predict spacial orientation of short sequences is as yet unattainable.
BruceS,
@ BruceS
Thanks for reminding me about Nick Lane. I’m sure someone linked to a book or video of his before. I’m downloading the Kindle version of The Vital Question now. Perhaps I can compare notes with Frankie when we’ve both had a chance to read it.
If the leopard thinks of it as a meal rather than as an antelope, why would that make a difference?
I would agree with that, though I would not limit it to primates.
I am not relying on Searle at all. However, I have not read Hegel or Heidegger, so I don’t know about their criticisms.
So you’ve said before, but I don’t see why it must be the case for it to be possible to construct novel sequences and know what they mean or do. Why must this be so? And, even if this capability of being reduced IS deemed essential, our inability to understand new sequences with testing could simply be a matter of insufficient knowledge or brain power and not a fact about the putative language at all, couldn’t it? I can imagine the same problem occurring with some natural language like Etruscan, e.g. What would follow from that?
I agree. petrushka’s argument seems to me to be lacking a couple of premises. Without them I don’t think it amounts to much.
It is not a bulletproof argument, and I have not presented it as one.
But it is not as bad as god of the gaps arguments, because gaps (transitional species) are expected and routinely found. there is no theoretical reason to believe the problem of emergence will be solved by computation.
It might be solved by quantum computers, but they would have to pretty much parallel chemistry in their operation.
Chemistry is and seems likely to be faster than computation when it comes to emergence.
But whether I’m right or wrong, this is the fundamental problem with ID.
Like most of the arguments I’ve seen them give, there’s a fairly big dollop of hand-waving involved. Put the argument simply and forthrightly so it can be examined. What’s a code, exactly? And why does it matter whether DNA sequences are codes, anyhow?
I’m not arguing from premises. I’m arguing from the observation that chemistry involves emergence. You can’t predict the properties of new biological molecules.
This is not based on first principles. I know of no reasoned argument why emergence cannot be overcome. I just don’t expect it to be.
I don’t think so. I think the fundamental problem is that it’s entirely result-oriented–little more than a conclusion waiting for an argument it devoutly hopes just must be there.
Go for it. Do something simple, like demonstrating you can predict the properties of water from the properties of hydrogen and oxygen. That would be a start.
But you don’t explain why you think this alleged failure of predictability is crucial. I don’t see why that’s the case. And, as said above, there are various explanations even if it is.
This is just the same claim in different dress. Why do you think this predictability feature is so important?
Even if you could predict structures, you have the additional problem of predicting biological function. For example, would structure solve the problem of designing regulatory networks? Could you tweak a molecule to modify the way a bird migrates?
What have I said about why I think it is important?
Of course. And you have the problem of predicting a function that no-one has yet thought of or seen the need for. And you have the problem of predicting the co-functionality of a complex of novel proteins.
That DNA sequences and the RNAs and proteins that they encode for do not map 1:1 with phenotypic traits is worth repeating. Especially the conundrum of how innate behaviours are encoded in the zygote.
Deciding whether to call a real phenomenon such as the information contained in a genetic sequence a code or not is semantic except that biologists are merely using the word as a convenient descriptive. What matters is whether we have a glimpse into what is actually going on inside a cell.
Not to speak for Petrushka but emergence springs to my mind.
Because if one has no hope of predicting the outcome of a chemical change (change of DNA base) then in what sense could it be reasonable to say DNA sequences are “designed”?
ID wants to claim that life doesn’t just appear designed, it actually is designed.
But there is no reason to think that any real designer, even with super-computational abilities, can predict the results of mutating DNA sequences, so how can the imagined designer get any desirable results except by pure luck or by cut-and-try, as Petrushka says.
But cut-and-try is already the process we recognize as unguided evolution.
Maybe the IDist’s “designer” is actually a tinkerer, randomly trying things out to see what looks good, without a plan and without any desires to predict the outcomes of its fiddling. But why would we call it a “designer” in that case?
Without some level of predictability, we don’t call it “design”. We might call it “fooling around”.
The ID claim would be much more accurate if they gave credit for life’s appearance to the Chief Fooler. Erm, Chief Fool-arounder.
Design implies foresight. Not just foresight into what attributes are needed, but into what can be done to implement those new attributes.
I don’t know anyone in the ID community who expresses any confidence that this is possible. The honest IDists speak of a designer having omnipotence and omniscience.
Everybody’s favorite IDist academic — James A. Shapiro — says rather explicitly that evolution does not exhibit foresighte. His version of ID involves mechanisms that efficiently “fool around.”
Efficiently fool around. 🙂
Sounds just like something i said when I was high, as a teenager.
Feckin’ eejits. I suppose “efficiently fool around” counts as deep thinking if you’re too drunk on Abrahamic faith to ever grow up and do real experimentation.
Or real design, either, for that matter.