DNA is object code
eyeondna.com
eyeondna.com
There are about 30,000 human genes, spread over 3 billion base pairs, coding for tens of millions of different proteins. Given how proteins and RNA interact with DNA, and DNA interacts with itself, the language for describing molecular biology usually isn't discrete math, it's statistics.
I think this is why Yates is accusing biologists of treating DNA as the abstraction that represents proteins, when really, it makes more sense the other way around. It seems like in the past couple of years the best fundamental research has been in proteomics, rather than genomics, probably for this reason -- bioinformaticians are recognizing that analyzing the expressed proteins, done efficiently, can give better information than raw DNA about what's actually going on in a cell.
People have been studying "bio-compiler/machine code" for decades. The difficulty is that there are many different compilers at work. Just to name a few: protein folding, chemical gradient regulation, inter/intra-cellular signaling, etc. All of which "compiles" chemical composition into actual physical function. But each of the process alone is so complex, it takes years to un-cover a small portion of the black box, not to mention most of these "compilers" are inter-dependent with each other. So it is close to impossible to use the limited knowledge we have un-covered to predict other novel code -> function compilation. I worked in a protein folding lab before. Just to be blunt here, no one really has a clue.
For it to be object code, it would have to be compiled from something. If anything, DNA is the thing compiled (and modified) several times from the ACGT form down to the protein form. Nature doesn't operate on the "hidden abstraction layer", it modifies directly the DNA, which is a very very strong clue that the meaning is there, not elsewhere. Why does cross-over mixes large sequential swaths of chromosomes? Because genes (the meaningful units) are sequential, and are relatively unlikely to be messed up by such an operation. The requirements of evolution impose much structure on DNA.
I wouldn't call DNA source code either.
Furthermore, while the idea of building higher abstractions sounds nice in theory, it fails, because it's not an engineering problem. It's a science problem, and anyone who has some experience with physics or chemistry knows that models have to remain simple for them to work at all. Meteorological models suck. Climate change models suck. Modelling a single cell is super hard. I wish we could get better models for biology, but it just seems really unlikely. The current approach to discovering gene function seems very reasonable to me.
Nope. In fact, object code doesn't even have to be assembled from something.
It just has to be made available to an execution engine.
And yes, folks modify object code.
And, even if there was some source somewhere else, that doesn't imply that the meaning isn't in the object code. (Meaning can be in multiple places.)
The point comes down to science vs engineering, induction vs building from parts. Biologists are already building models (model != programming language!). Models are the holy grail. They are just damn hard to get right.
Well here's the thing. You are completely right. DNA interacts with its surroundings. It forks, splits, mutates. It is not at all like static source code. However, if you take the software analogy to the limits of our current understanding, you might be able to model it as polymorphic code that is also a quine that runs in a massively multithreaded, multiprocessor environment.
Good luck using that analogy for anything useful.
Might be a bad example. You couldn't use the source even if it wasn't secret. That probably protects windows' copyrights more than the other.
Some of it is code, some of it is data, some of it is macros.
And it's all the self-modifying output of random genetic algorithms.
And sometimes a page happens to turn into another monkey, typewriter or page. Actually, I can't think of an analogy that come close to describing the hairiness of biology. It's the origin of all hair; it eclipses all else.
I like the DNA-as-code analogy. Getting the 'source code' is not the stumbling block - this is becoming far easier with high throughput sequencing methodologies. The real difficulty is writing the code. I have spent the last 3 months constructing 15kb of DNA by classical molecular biology techniques - and this was largely acheived by cut and pasting from existing DNA sequences. The cost of synthesizing large DNA fragments is currently >1 dollar / base. When this falls to trivial levels I think we will really start to see DNA programming taking off.
I don't really know anything about biology, but as a programmer, the article's suggestion that DNA is "byte code" and not source makes sense. To get actual high-level human comprehensible source, I think we'd need to build abstractions on top of DNA object code. Not that I have any idea what these abstractions might look like.
The article compares genomes to Windows, and I don't really know anything about biology, but it might actually be easier to reverse engineer ourselves than Microsoft's operating system, since (as far as I know) our "binary" is much smaller :)
I would say that the object code is the set of RNAs present in the cell and the program is the state of all of the macromolecules in the cell - proteins, lipids, carbohydrates etc. Essentially the program is running on the organic chemistry virtual machine.
When it comes to 'writing' artificial DNA the complexities are that firstly we do not understand the intricacies of how genes are turned on and off, although there is not reason that we should not come to understand this. This is the area that I am working in. The second major problem is that we cannot 'invent' new proteins as we do not how to predict the 3D shape and chemical behaviour 'folding' from the protein sequence. With massive increases in computational power and clever algorithms it is possible that this difficulty will be overcome.
(Poor humans, they will never be able to stop God from smiling about their relatively poor scientific investigations...)
;)