Hi Hoot, I know this thread has been innactive for a while but I read something that I want to comment on that might make clear what Ringo's objections are.
Hoot Mon writes:
Well, of course. Music is carried by the molecular structure of a CD too, but that doesn’t mean that music is only a condition of structured plastic molecules. The same thing is true for genes.
That isn't true, the music is not in any way imprinted onto the molecular structure of the CD. All that is on the CD is a collection of metaphorical 1's and 0's. There is absolutely no deterministic way to extract any music from that whatsoever. In PC's there is nothing special about any bit pattern at all. You can't take a bit pattern and extract meaning from it.
To illustrate this, delete all the codecs from your PC and then try and play something in Media Player (assuming you use Windows). You'll find that it won't work. The CD is not sufficient to reproduce the music. The music is contained in the codec more than in the bit pattern itself. It's the interpretation of the bit pattern that gets passed to the speakers and turned into acoustic vibrations. Change the codec and exactly the same bit pattern could produce a different piece of music, or it could turn out to be Shakespears Macbeth, or it could be a picture.
A more accurate representation of DNA would be an LP. An LP does have (deterministically) music 'imprinted' on it. The pitts and troughs in an LP are direct representations of the vibrations in music. There is no interpretation required. There is no codec involved at all. There is a one-to-one relationship between the LP and the produced music. A physical relationship, rather than an arbitrary relationship imposed by a codec.
So the question is, can exactly the same sequence of DNA produce different proteins? Does CAG represent on (and only one) protein. If so it fits the record player analogy. Or alternatively, can CAG produce many different proteins depending on some external 'codec', in which case it fits the CD analogy.
And if you still assert that DNA fits the CD analogy, I believe Ringo's question is what is acting as the 'codec' in DNA to interpret which protein CAG should produce.
But do they all carry digital information?
I'd argue that all catalysts carry the same type of information as DNA (because from my limited understanding DNA appears to catylyse protein production). So yes, if a rock has a catalytic property then it would carry the same type of information as DNA.
I don't understand what is "metaphoriocal" about 1's and 0's.
Erm, well unless you can show me some 1's and 0's on a CD then I'd say they're metaphorical....used to represent the patterns the laser made when burning the CD. We could have used A and B to represent the two states if we'd wanted. This doesn't really affect my point though so I'd be happy to ignore the word metaphorical completely.
Hoot Mon writes:
CAG does not "represent" a protein. CAG is a codon of three digital nucleotides, which codes for the amino acid glutamine. It takes many codons to hold the digital instructions of an entire protein.
Noted, but it doesn't change my point. Can CAG code form anything other than glutamine? Does the physical structure of DNA directly determine the chemicals produced via deterministic physical (or chemical if you prefer) processes, or is there something arbitary in there imposed on top?
Hoot Mon writes:
I don't understand what you are saying. DNA certainly does not catalyze a protein. DNA is remote to the chemical production of proteins. (I threw in "chemical for Ringo's sake, who believes molecules are only chemicals and have no way to store digital codes.) DNA is linked to proteins only by way of code translation, which is performed by messenger RNA.
I think you missed the actual point of my post. I know that DNA produces RNA, which then is involved in producing proteins. That still is not in any way an analogy of the production of sound from a CD. It is an analogy of the production of sound from an LP though as far as I can see.
DNA is the pattern of ridges on the LP, RNA is the vibrations of the need/arm structure (which are deterministically produced by the ridges) and the protein is the sound. There is a direct physical link between each step, nothing at all arbitrary. The needle/arm structure can only interpret the ridges etc on the LP in one way, governed by physics.
However on the CD all you have is a bit pattern of 1's and 0's. In a PC every single bit pattern can and does mean different things in different circumstances. When the CD is played it requires something in place on the PC to decide what the bit pattern means, and if you don't get the right codex you'll get the wrong sound (or no sound at all). There is something completely arbitrary about what the bit pattern means, something that is not grounded in the physical world. That is why the sounds you hear are not directly imprinted onto the CD in the same way as they are on an LP.
Now I may be wrong and there may be something about DNA and how it works that is arbitrary. But I haven't seen that presented yet.