Saturday, 11 January 2014

Updating cells through Horizontal Gene transfer: An idea for a game

My interest in biology runs so deep I enjoy coming up with my own theories. If you've read my blog you'll find many. Of course what is most exciting is when I find that a theory I have developed from my own experience and logic turns out to be real. The process of horizontal gene transfer is just that and is becoming more widely understood as a far greater force for evolution than sex.

 “The human genome includes sequences derived from viruses.”  Page 135 of The mathematics of life

Not only did an understanding of software development and thus code help me understand this most basic aspect of allowing a cell to upgrade its DNA but I feel it has great potential to express science concepts particularly biological ones.

That's the reason I have been exploring HTML 5 and 3D technologies including unity for the last few years.
From what I have learnt I think I can now show the concept of horizontal gene transfer in ways it hasn't been shown before.

The challenge I face is one of resources, time and money being a big issue and skills. I don't know the 3D virtual worlds arena well enough yet. So I thought I would simply describe the basic specification for the small game or app I would like to develop. If you would like to help in some way please let me know. I have so many of these ideas that aren't really that hard to put together but other constraints get in my way. It's the bain of our lives isn't it. Hopefully this is of use to some one.

Plugins

The basic concept is that human code like PHP, Javascript, C etc already has many of the characteristics required to demonstrate Horizontal Code Transfer. If you consider the concept that many pieces of software like moodle, wordpress or web browsers allow plugins. The plugins work because they are designed for the target code base. They do what is necessary in the target code base to achieve their ends. That is pretty much how viruses work. They are targeted for a particular species and have a specific mechanism by which they adjust the target DNA code.

Simplicity

To keep things simple lets just focus on a cell, ignore the other cell components for now just have a nucelus and a virus. The virus contains the new code the nucleus. contains the target code base. The virus gets into the nucleus and delivers its code.  The concept is simply that the new code is a script/plugin written for the target code base.

In Unity3d this is actually quite a simple game to create. I've done most of the work already but the time to put it all together hasn't arrived. If you want to know more just ask. I want to be able to teach this to my son when he is older because it is such a fundamental way that our bodies work. Now that I understand it I can't tell you how useful it has become.

An experiment

I would create an experiment. Have a cell with a nucleus with a script attached that controls the nucleus and cell. A virus gets through. It has a script attached. It attaches it to the nucleus. The new script adjusts the existing configuration of the cell. Using the existing nucleus as a code base. It then creates more of itself.

It's an experiment to show It's possible in code and the mechanisms behind horizontal gene transfer. An added bonus is that a knowledge of software creation is can help understand it. I would then look at ways in which this could benefit a cell. Much like an update for your favourite program.

Modelling evolution

Using the cell model I was building. I would start to assemble the cell through evolution like this. I would then make a game around it. Maybe the player manoeuvre each element into place, or players build up their own cell and lots of viruses try to attach. The player has to get the useful viruses in place while avoiding the bad viruses .

This could be an open source game like a cell manager. You play the cell security. Choosing which viruses get through.


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