59-reaction solution to challenge 19 (cell)

[calcyman]

The solution below works reliably, but the current bug with the
caustic agent causes the program to freeze whenever it breaks a bond.
The solution works by building a mouth (inspired by the 112-reaction
solution), only this requires much fewer reactions:



// construct mouth

a3e1 => a4 + e1
a2a4 => a7a5
a2a5 => a8a6
a7 + a0 => a9a11
a8 + a0 => a10a12
a11 + a0 => a13a15
a12 + a0 => a14a16
a16 + a6 => a16 + a106
a15 + a106 => a15 + a206



// trap entering atom

x0 + a206 => x1000a1206

a1206a9 => a1206a1009
a1206a10 => a1206a1010

a1009a13 => a1009a1013
a1010a14 => a1010a1014

a1013a15 => a1013a1015
a1014a16 => a1014a1016

a1015 + a1016 => a2015a2016

a2015 + x1000 => a2015 + x2000

x2000a1206 => x3000a2206
x3000 + a1009 => x4000a2209
a2209a2206 => a3209 + a3206
x4000 + a2 => x5000a2
x5000a3206 => x5000a4206
a4206 + a3209 => a5206a5209
x5000a5206 => x6000 + a6206
x6000a5209 => x7000 + a6209
x7000a2 => x8000 + a2



// reset mouth

a6206a1010 => a206a6010
a6209a1013 => a9a6013
a6010a1014 => a10a6014
a6013a2015 => a13a6015
a6014a2016 => a14a6016
a6015a6016 => a15 + a16



// safety mechanism (in case caustic agent breaks bond)

x1000 + a2 => x0 + a2
a2015 + a1206 => a2015 + a7206
a7206a1009 => a6206a6209



// DNA replication

e1 + e8000 => e8008e8006
x8008y1 => x8003y8009
x8009 + y8006 => x8002y8003
x8002 + x8000 => x8004x8005
x8004y8007 => x8008 + y8003
x8005 + y8003 => x8006y8007



// DNA splitting

a3f8008 => a9000f8008
a9000a2 => a9000a9002
f8006 + a9002 => f9000a9003
f8008f9000 => f111 + f111
x8003y111 => x222y111
x222x222 => x111 + x111



// membrane expansion

a0 + a9003 => a9004a9005
a9004 + a9000 => a9006a9007
a9007a9005 => a9999 + a9008
a9006a9008 => a9000a9003



// mitosis

a9999 + a206 => a7001a7002
a9999a7001 => a7003a7001
a7003 + a9 => a7004a7005
a7002a7005 => a7006 + a7007
a7006a7001 => a7008a7009
a7009a7004 => a7010 + a7010
e111 + a7010 => e333a7011

[Bertrand Dechoux]

> the current bug with the caustic agent causes the program to freeze whenever it breaks a bond.

That's something I had resolved but it indeed seems like the problem
is still here. (Applet, JWS and download)
I should write a fix soon (tm).
Thanks for reporting the bug.

Bertrand

[Ralph Hartley]

calcyman wrote:
> The solution below works reliably

It doesn't check that the imported atom is of the type it needs. If it
imports too many of the wrong type, internal pressure will keep it from
importing any more, and it will be stuck.

Ralph Hartley

[Tim Hutton]

Calcyman, try the attached JAR file - it doesn't crash any more when
the caustic atom acts. The cell rep definitely works.

Ralph, yes this solution does seem to struggle without manual
assistance. I've just left it running for a while and the cell
absorbed two 'a' atoms it didn't need and then there weren't enough
remaining outside to grow the membrane enough. I'm sure Calcyman could
fix this issue, with a few extra reactions.

Bertrand, it looks like you fixed the caustic atom issue in the SVN
repository but didn't update the jar - were you working on something
that wasn't finished? I notice that the parsing stuff in Reaction.java
(the repository version) is currently broken. I've fixed it in the
attached JAR but now I'm not sure whether I should go ahead and make a
new JAR release, or whether there are other pending changes I should
know about before I proceed?

There are other bugs that have crept in. The evaluation code on level
19 is failing, for example. On every level it looks like a successful
evaluation just gives the message that you completed every level. A
failed evaluation doesn't tell the user anything, which is confusing.
I'll try and sort these issues out.

Thanks everyone!

Tim

2009/5/28 Bertrand Dechoux <dech...@gmail.com>:

--
Tim Hutton - http://www.sq3.org.uk

Take the Organic Builder challenge -
http://www.sq3.org.uk/Evolution/Squirm3/OrganicBuilder/