I would not consider every digital code immediately a program, and even treating DNA just as a digital code can be confusing, since there is so much chemistry and physics happening until DNA is expressed as a protein, that you can't just expect that whatever you encode will really come out exactly as encoded. The nice simple mathematical models and metaphors we use for man-made artifacts fall on their face when applied in biology.

One can understand this better by looking for example at the difficulties encountered by people who do actually base computations on the DNA:

http://en.wikipedia.org/wiki/DNA_code_construction

stiff, you've got multiple people who are experts in either fields (including people like me, who are experts in both fields) telling you your posts are full of crap.

It's not clear to me what your link about the DNA code construction really means.

Consider instead:

1) people can encode terabytes of digital information in DNA and retrieve it using molecular techniques. To do so accurately enough requires coding.

2) Crick, who helped figure out many of the basic information coding mechanisms, widely acknowledged being influenced by the theory of information as proposed by Shannon.

3) both computer scientists and biologists frequently use the theory of control mechanisms (feedback, etc, also known as 'cybernetics' when I studied under David Huffman) to understand how their systems work, and engineer new ones.

4) you can make a computer out of DNA< and you can put computers into biological systems; they interact according to the laws of information theory, entropy, thermodynamics, etc.

The relationship between computing theory- as practiced today- and what biology has managed to spontaneously developed- are intimately related at the most basic levels of physics. Understanding that is KEY to being a productive biologist or computer scientist, and escpeially so for bioinformaticians.

Do you understand the difference between a digital code and a computer program? I know information theory and coding theory can be used for studying DNA, when you make the models account for the physical and chemical complications that arise in biology, but the models used are way more complex than the ones used in traditional CS, so it doesn't make sloppy metaphors like the ones from the OP worthwhile for people who only know CS and no biology. Specific techniques from CS of course might be useful in understanding biology, but not metaphors of the kind OP uses, like calling introns comments. Also, while people do base computations on DNA, it doesn't work vice versa, e.g. none of the computational approaches to studying biology views DNA as a description of any sort of computation, as far as I know, it only treats it as a (often quite complicated) digital code or as a discrete stochastic process, as in the case of using hidden markov models for modelling DNA.

Yeah, I worked on hidden markov models with David Haussler 20 years ago. HMMs are really a massive simplification of the underlying process of evolution, of course (I think that's what you're trying to say).

I'm not defending the original poster's use of analogy between introns and comments. Those are naive, simple analogies.

What I am responding to is your categorical statement that there are no legitimate analogies between CS and biology, and that's patently false.

I'm certainly not claiming - without evidence - that biological systems perform computation. I strongly suspect that biological systems carry out computation- quorum sensing being a canonical example- and in some sense, any sufficiently complex biological system can be considered an analog computer of some sort, with goal-seeking computational behavior.

One of my interests in some time has been building a digital circuit in DNA; one that can compute, using state, a taylor series approximation of an interesting constant, such as pi, using feedback circuits, error correction, and other "digital" approaches. None of this is impossible, it's just technology. People have already started doing this. That the underlying systems are capable of being turned into computing systems is just an outcome of the fact that biological systems are sufficiently complex that they can be used to instantiate simpler digital computing systems.

I think it boils down to what you consider an "analogy", is a markov model really an analogy between computer science and biology? I would consider that simply a mathematical concept that finds applications in both Computer Science and Biology, and it isn't even that related to computations or computers, it's just an useful mathematical tool. I don't deny concepts from CS or Mathematics can be applied to biology.

On the other hand, I think there are lots of CS people who apply blindly oversimplistic models to complex biological situations without understanding the biology, and that's what I was trying to protest against.

I agree with your last sentence. But you made a categorical/general statement upthread, and I called you on that.