Code center > Suggestions
Codules
Trafalgar:
--- Quote from: gymsum ---I dont think any rael life DNA has a skip in it, its all write, read, stop commands.
--- End quote ---
On the contrary, real life DNA is actually closer to codules:
Quoting from http://www.sciam.com/article.cfm?id=regulating-evolution, from page 3 :
--- Quote ---Most important to our discussion here is the fact that some genes have many separate enhancers. This is particularly true for genes that encode proteins that shape anatomy. Each enhancer independently regulates the expression of the gene in different parts of the body and at different times in the animal’s life cycle, such that the complete expression of a gene is a patchwork of multiple, independently controlled sites of expression. These enhancers enable the same gene to be used many times in different contexts and thus greatly expand the functional versatility of individual genes.
A gene involved in coloring the body parts of the fruit fly illustrates the modular logic of this gene regulation system. The somewhat confusingly named Yellow gene encodes a protein that promotes the formation of black pigmentation (mutant flies without this protein are Yellow). The Yellow gene has separate enhancers that activate it during the development of a variety of fly body parts, including the wings and abdomen.
Because the Yellow gene plays a role during the development of so many tissues, mutations in the gene itself could be disastrous if they alter or disable the function of the protein; they would affect the function of the Yellow pigmentation protein throughout the organism. In contrast, changes in just one of the gene’s enhancers will affect only the function of that enhancer and only the Yellow gene expression governed by that enhancer, leaving the expression and function of the protein in other tissues unchanged.
The evolutionary implications of the modular regulation of body-patterning genes are profound. In theory, mutations in enhancers would allow individual body traits to be selectively modified without changing genes or proteins themselves. And in the past few years, direct evidence has emerged that this is frequently how the evolution of various body parts and patterns has occurred.
--- End quote ---
However, it isn't quite the same.
(Same source)
--- Quote ---We have found that in spotted species, the Yellow protein is produced at very high levels in the cells that will make the spot and at low levels in the rest of the wing cells. In unspotted species, Yellow is made only at low levels throughout the wing, generating just a light dusting of black pigment.
[...]
In unspotted species, there is an enhancer that drives Yellow expression in a low uniform pattern in the wing. This wing-enhancer activity generates the fly wings’ light-gray color. When the corresponding piece of DNA was analyzed from a spotted species, we found that it drives both this low-level pattern and the intense spot pattern of gene expression. What has happened in the course of evolution of spotted species is that new binding sites for transcription factors made in the wing evolved in the Yellow wing-enhancer DNA sequence. These changes created an expression pattern—wing spots—without altering where the Yellow protein is made or how it functions elsewhere in the body
--- End quote ---
Have a look at this: http://www.sciam.com/media/inline/2A5F4661...AA704DF19_5.jpg (if the link works from off-site)
Numsgil:
If you look at DNA strictly from a computer science/language standpoint, it's missing functions. That's basically what a codule is: a way to write code that uses functions. Functions are good because they promote code reuse. And of course, if you don't want to use Codules you don't have to, so it falls into the realm of "backwards compatible language enhancement". Which just rolls off the tongue so elegantly I think it might be iambic.
gymsum:
--- Quote from: Numsgil ---If you look at DNA strictly from a computer science/language standpoint, it's missing functions. That's basically what a codule is: a way to write code that uses functions. Functions are good because they promote code reuse. And of course, if you don't want to use Codules you don't have to, so it falls into the realm of "backwards compatible language enhancement". Which just rolls off the tongue so elegantly I think it might be iambic.
--- End quote ---
I understood everything up till the seond sentence. Why do we want to promote codule reuse? I thought thats what mutations got rid of.
Numsgil:
Exactly. Mutations tend to break copy+paste code, so if all the code is routed through a single place, like a codule, then a single mutation impacts all the code.
gymsum:
One function that would be nice would be gene copy, this is what makes human dna so stable, we have a lot of junk to mutate without much effect.
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