DNA ei ole ohjekirja, se on sovellus

http://www.forbes.com/sites/anthonykosner/2013/12/13/seven-ways-to-look-at-the-double-meaning-of-dna-code/#fb22339109ae

Kun ymmärrys DNA-koodin monimutkaisuudesta lisääntyy, alkavat ihmiset tehdä mielenkiintoisia havaintoja. DNA:n metadatasta, eli kahdesta päällekkäisestä koodista, koodin käyttöohjeista, kirjoittaa Anthony Kosner osuvasti:

1. DNA As An App
For so long we have considered the genetic code to be something like a book to be read, a recipe for making proteins. This new discovery makes me think that DNA is actually less like a document and more like an app. These transcription factors bind to to specific sequences of DNA right next to the genes that they regulate. So we can think of these TFs as kinds of functions that employ certain logic to turn the transcription of genetic material on and off and to regulate its speed. This reminds me of the reactive data bindings in the JavaScript app framework called Meteor.

Siis DNA muistuttaa enemmän sovellusta kuin ohjekirjaa. Transkriptiotekijät ovat geeneissä sidoksissa sellaisiin kohtiin, joissa ne voivat vaikuttaa geenin toimintaan ja säätelyyn loogisen kytkimen tai säätimen tavoin. Siis geenin sisällä on mekanismi jolla solu voi säädellä geenin toimintaa. Nerokasta.

2. DNA Contains Puns
On of the most startling things about the dual nature of the duons is that it makes us wonder what else could be hiding within those double helixes? The duons are like words or phrases within the “text” of our DNA that mean two different things, depending on context. And yet, as in human language, not all words have this double meaning.

Jotkut DNA-jaksot merkitsevät kahta eri asiaa. DNA sisältää sanoilla leikittelyä. Osoittaako Jumala huumorintajuaan DNA:ssa? Siltä näyttää.

3. DNA As Zappos
Another concept of DNA has been that it is a factory for making proteins. But in the present context DNA appears to be more like Zappos or Amazon’s distribution hubs or the UPS Sort. DNA contains the instructions for making all of the proteins that a body needs, yes, but it also choreographs the elaborate logistical dance that delivers the right proteins to the right location at just the right time.

DNA on proteiinien jakelukeskus. Amazon Zappo on sopiva vertaus.

4. DNA As Playing Battleship
The dual-functioning nature of some DNA code puts us in a curious position when trying to determine, for instance, genetic factors of disease (think of the troubles of 23andMe.) In the present scenario, it is as if we have been playing a game of Battleship looking at the known position of our pieces (the genes), but not of the positions of the duons that contain the code of the TFs. And it turns out that the correlation between genes associated with a given disease and co-located TFs will be likely spots for aiming the big guns at.

5. Genome 2.0
We have just gotten through the human genome and perhaps we need to start again! Hidden within what scientists have already decoded is at least one more layer of code. It is interesting that at the time that Wilson and Crick came out with their discovery, another DNA researcher, Rosalind Franklin, argued that other structures could satisfy the x-ray data for DNA and wondered if their’s was ”the solution or a solution?” More than 50 years later it seems that perhaps they were all part right.

Juuri kun ihminen on lähes selvittänyt ensimmäisen koodikerroksen merkityksen, niin paljastuukin toinen kerros. Meneekö toiset 50 vuotta metadatan selvittämisessä. Löytyykö joskus vielä kolmas kerros? Tai vielä useampi kerros?

6. DNA As Language
Intriguing for those with a familiarity with quantitative linguistics and current work on natural language processing is how the instance of a dual-functioning code in DNA begins to make genetics seem more like a language with all the messiness that entails and less like a pure instruction set. If certain sequences have an ambiguous identity and shift modes between description and process, there is room for many errors and chaotic recursions to arise, just like in human language.

DNA:n kieli on monimutkaisempi kuin mikään maailmalla puhuttu kieli.

DNA As Scaling Mechanism
Finally, DNA is a model of natural economy. There are a limited number of sequences that can be generated from the base amino acids and a limited number of transcription factors that can be deployed in combinations to yield all of the complexity of a living breathing human being. Nature, I think, is simplicity scaled. And what the inclusion of the TFs within the DNA code looks like to me is that code contains both the description of the proteins it can create and the methods to scale those proteins up from a zygote all the way up to an adult and through an entire life cycle. These two processes, specifying and scaling, integrated together into the same nucleotide sequences is a conceptually elegant way of tying together DNA’s dual nature. I wonder how that would work with software?

DNA todistaa suunnittelusta