A Programmer Unimpressed with Biological "Design"

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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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/*DNAunion*/ I think the analogy is already broken.Let's start with the assumption that DNA is the machine code of the cell. "Genes are assembler" is then wrong. The idea is that "Genes are to DNA as assembly language is to machine code". But...(1) Assembly language is based on mnemonics -- short 3- or 4-letter English-like instructions that represent longer, binary (0's and 1's) machine code: the two languages use completely different coding systems.(2) Genes are basically just stretches of DNA, which, of course, use the same coding system.The correct analogy would be "Genes are to DNA as (processor) instructions are to machine code".Then there's the last part: "Cells are like processes". That's incorrect too. Perhaps way back before OOP (object-oriented programming) days that might have been a decent analogy, but for the past decade and more the correct statement would be "Cells are like objects in an OOP".

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Percipient: Processor instructions and machine code are pretty much synonyms.

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/*DNAunion*/ As are DNA and genes.As used by the author, the term DNA in general would represent a genome or at least a relatively large portion of the genome under investigation: a gene is a single segment of that DNA.When someone refers to machine code in general they are referring to a series of processor instructions (opcodes) and data, both represented in binary, that constitutes a program, module, function, or other compound unit of logic.In such contexts, a single processor instruction is to machine code as a gene is to DNA.[This message has been edited by DNAunion, 11-01-2003]

/*DNAunion*/ I think the analogy breaks down at the very first statement: that DNA is like machine code.DNA performs no real function itself, it basically just stores information for the rest of the system. Probably the most analogous component of a computer system is a secondary storage device, such as a hard drive, CD-ROM drive, etc.Both in a computer system and a cell, the information stored is useless until it is moved out of its storage medium to a location where it can be processed. Copying of DNA information (and loosely, the subsequent tranporting of it to where it can be used) is trascription. This is analogous to retrieving information from a hard drive and storing it in main memory.And so on.

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/*DNAunion*/ Probably the most analogous component of a computer system is a secondary storage device, such as a hard drive, CD-ROM drive, etc...Copying of DNA information (and loosely, the subsequent tranporting of it to where it can be used) is trascription. This is analogous to retrieving information from a hard drive and storing it in main memory.

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Percipient: I think you're forgetting that machine instructions in memory are copied to the processor where they are executed.

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/*DNAunion*/ Nope. Having a 4-year degree in CIS I am well aware of that.But YOU seem to have forgotten about the same RNA machinery you reference. Otherwise, you would have seen more deeply into the analogy and realized your objection was wrong.First, let’s look at this quote and note how good my analogy between DNA and secondary storage is.

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6. Secondary storage unit. This is the long-term, high-capacity warehousing section of the computer. Programs or data not actively being used by the other units normally are placed on secondary storage devices (such as disks) until they are again needed, possibly hours, days, months, or even years later. (Dietel & Dietel, C++: How to Program: Fourth Edition, Prentice Hall, 2003, p6)

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/*DNAunion*/ One could almost translate that directly into molecular biology (DNA is the long-term, high-capacity, information warehousing component of a cell, where information is read as needed by other components of the cell, etc.).So back to my analogy, with another step added (the one that Percipient was incapable of determining).(1) Secondary storage devices store a computer’s information as symbol sequences but are not what interpret that information
(2) The information stored in the secondary storage devices is read into main memory as needed
(3) The binary sequences in main memory are moved into the CPU where they are interpreted/processed(1) The cell’s DNA stores information as symbol sequences but is not what interprets that information
(2) The information stored in DNA is read into mRNA (and other RNAs) as needed
(3) The nucleotide sequences in the mRNA are moved to the ribosome where they are interpreted/processedOf course, although cells and computers share many similarities they also have many differences. You’re not likely going to find any analogy that fits 100% accurately and covers 100% of both systems. As far as this one goes, it’s about as good as one can be.[This message has been edited by DNAunion, 11-02-2003]

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/*DNAunion*/ When someone refers to machine code in general they are referring to a series of processor instructions (opcodes) and data, both represented in binary, that constitutes a program, module, function, or other compound unit of logic.

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Percipient: 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). ... 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.

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/*DNAunion*/ Let's look at the definition you linked to in Machine Code1 and read their paragraphs. I’ll highlight some things.

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MACHINE CODE Computer Dictionary
Definition: The representation of a computer program which is actually read and interpreted by the computer. A program in machine code consists of a sequence of machine instructions (possibly interspersed with data). Humans almost never write programs directly in machine code. Instead, they use a programming language which is translated by the computer into machine code. (Forbidden)

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/*DNAunion*/ By that dictionary's usage, which you linked to,a single processor instruction is to machine code as a gene is to DNA.By the way, even when looking at your preferred interpretation of the term machine code my generaly analogy still holds, since it is just as correct to say that an organism's genes are made of DNA as it is to say that an organism's DNA is made of genes.[This message has been edited by DNAunion, 11-02-2003]

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Percipient: One might be able to build a workable analogy by comaparing machine code to DNA nucleotides,

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/*DNAunion*/ No, nucleotides, being the symbols used by the coding system, would be analogous to bits, not machine code.

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/*DNAunion*/ So back to my analogy, with another step added (the one that Percipient was incapable of determining).

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Percipient: 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.

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/*DNAunion*/ Oh good grief! In the future I'll keep in mind that you read what you want into others' statements and then claim they are wrong.