A Programmer Unimpressed with Biological "Design"

Hi DNAunion!You quoted this from the Salon article (How I decoded the human genome):

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"DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights."

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I agree that the analogy breaks down pretty quickly, and at the core, not at the margins. It is essentially useless except for pointing out that both software and heredity have a hierarchy of representation.The key flaw in the analogy is where DNA is compared to machine code while genes are compared to assembler. The key advantage provided by assemblers is symbolic addressing and automatic encoding of machine instruction fields (address modes, address offsets, register specification, etc). Assembler instructions have a nearly one-to-one correspondence with machine instructions, while genes in no way have a one-to-one relationship with DNA nucleotides, but rather are collections of many contiguous DNA nucleotides.A more workable analogy would be to compare DNA nucleotides to individual program statements and genes to functions created from many program statements.I don't think I could agree with this: Processor instructions and machine code are pretty much synonyms.--Percy

Yes, I think you're right, that must be how they are defining machine code, but it is a misuse of the term. Since you also find this definition acceptable, I wonder if this use of the term is becoming common. After reading a couple definitions on the net (Machine Code₁, Machine Code₂) I can see how the misimpression might arise that it is an acceptable use of the term to refer to the collection of all processes as "machine code", and since definition follows usage, perhaps this is accepted now, but I hope not. It would be like referring to the collection of metal, plastic and rubber in your driveway as matter - you wouldn't really be wrong, but people are more likely to understand what you're talking about if you call it a car.In the software industry the terms machine code or machine instructions or processor instructions are all synonyms for the bit level representation of instructions that sit at the bottom of the hierarchy of more abstract programming concepts. One might be able to build a workable analogy by comaparing machine code to DNA nucleotides, but it would probably be better to leave machine code out of the analogy altogether and to instead compare nucleotides to assembler-level instructions. Genes could be functions, and the genome could be the entire program that consists of all the functions.--Percy

As does machine code. The DNA code is interpreted by the cells RNA machinery, and the machine code is interpreted by the processor, so I couldn't agree with this: I think you're forgetting that machine instructions in memory are copied to the processor where they are executed.But I think we're over-analyzing this. Getting back to the original analogy:

quote:

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"DNA is machine code. Genes are assembler, proteins are higher-level languages like C, cells are like processes ... the analogy breaks down at the margins but offers useful insights."

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If by "machine code" he actually means all the instructions available to a processor, then this analogy improves but still breaks down quickly. Genes encode for proteins, but assembler does not encode for higher-level languages, except perhaps when you bootstrap onto a new architecture. To me a gene is more analogous to a sequence of assembler statements that carry out a function, so saying that genes are to proteins as assembler is to higher level languages doesn't really hold together for me, though I like the comparison of cells to processes. I think his analogy says more about his misconceptions of computing machinery than it does about the DNA machinery behind heredity.--Percy

Oh, good grief! In the future I'll keep in mind that your posts aren't really ambiguous but are actually clever puzzles with the missing portions left as an exercise for the reader. Turning the focus back to the original analogy, I think he was trying to make things simple by keeping the focus on structures familiar in both biology and CS. It isn't that your analogy isn't an improvement, but it may possibly be at a point where you've left the original audience behind.--Percy

Gee, guy, I don't know how to respond to this. They're no smilies, so you don't appear to be joking, yet what you say seems a complete fiction to me. Tell you what, rather than doing something as silly as trying to figure out who's at fault, why don't we just stick to the Forum Guidelines and avoid the personal stuff. If you have any further comments about the analogies then go right ahead, but otherwise I think we're done.--Percy