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Topics - vrukt

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Biology / Synthia! SYNTHIA!
« on: September 06, 2014, 05:57:01 PM »
So I haven't seen too many threads around here about Synthia, or

http://en.wikipedia.org/wiki/Mycoplasma_laboratorium

The only one I could find was from years back.

http://forum.darwinbots.com/index.php?topic=2262.0

The tone of that thread doesn't seem very enthusiastic overall.

Now though they've moved onto synthesizing the yeast genome.

http://www.nature.com/news/first-synthetic-yeast-chromosome-revealed-1.14941

http://syntheticyeast.org/

And trying to collect every genome they can from all the brewing companies historic yeast stores.

http://yeastmine.yeastgenome.org/yeastmine/begin.do

So I just wanted to start a discussion on Darwinbots here about synthetic biology

http://en.wikipedia.org/wiki/Synthetic_biology

With all the recent advances I'd expect a lot more discussion around here as Darwinbots is basically a digital version of synthetic biology.

I for one am excited to see what they can learn from a large sampling of yeast genomes. Even though the tools are still relatively crude and costly, there still seems to be interesting things that can be done cheaply, and the toolset is always increasing in size. A lot of companies have failed though for apparently failing to keep their aspirations within the realm of possibility as complexity increases quickly in synthetic biology.

Anyway if you want to get deeper into synthetic biology these are some good sites to start.

http://diybio.org/
http://biopunk.org/
http://openwetware.org/wiki/Main_Page

Otherwise this is more or less an open discussion, to increase awareness, and hear peoples thoughts/criticisms on the field of synthetic biology. :)

2
Suggestions / Tides, as an addition to the weather aspect.
« on: August 21, 2014, 01:38:38 PM »
So I was watching this last night

Dr. David Deamer - "Systems biology, synthetic biology and the origin of life" https://www.youtube.com/watch?v=_SHHfnIHXQI

He talks about the chemistry of early life, and how tidal pools may have moved it along through repeating wet/dry cycles.

Now I know Darwinbots has no "water" but it does have gravity and light.

So my proposal for tides would involve an "increase in gravity < increase in light < decrease in gravity < burst of Brownian motion < decrease in light < timer"

So the water goes out, leaving behind shallow water, increasing the sunlight and gathering all the bots at the bottom of the tank. Then a wave of water rushes back in, stirring everything, throwing bots upwards, and decreasing the availability of the sunlight, then a timer setting to keep the tides flowing (X cycles before next tide, duration of Y cycles)

Just thought a feature like this could be easily implemented, and add more variety to the darwinbots environment.

3
Newbie / Hi! From a new guy, and of course a few questions!
« on: August 20, 2014, 12:39:40 AM »
Hello! Firstly, I cannot say how much I love this program! It is very interesting, and seems to have a ton of potential.

Now for the inevitable question questions.

I've been trying to make a basic bot, I've never made one before, so I thought I would approximate yeast using pondmode.

It's 1 cell, should be simple right? Well I broke it down as; absorbing light instead of sugar, giving off waste (maybe .nrg to), floating to the surface and sinking back down to the bottom, and budding to reproduce.

So everything went smoothly, except for making it sink and float.

I wanted to attach that to light, so when it got under a certain amount of light it floated, and when it got to another percentage it started to sink again.

I tried

cond
*.light 10 <
start
32000 .setboy store
stop

cond
*.light 90 >
start
-32000 .setboy store
stop

I've also tried a lot of differen't combinations based on that, but I've also fiddled with .sun a bit, lower values on the .setboy, playing with the values on the .light, but I can't seem to get it to float and sink based on the light energy.

However as I have no clue what I'm doing, and don't know the values for .setboy or .light, as well as not being able to find much info about them, does anybody know if that is even possible? Or if I'm heading in slightly the right direction?

I know .setboy has a max value of 32000, but to get back to 0," 0 .setboy store" didn't seem to work so I used -32000

My brothers solution was to just tie .nrg to .ypos. When it gets too low on energy it moves up, and when it fills up to a certain point it shoots energy to drop down. Then stops, and starts moving back up. It actually works very nicely, and he's onto fiddling with reproduction.

I'm being stubborn though, so any tips towards the .light vs .setboy would be much appreciated.

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