Author Topic: Metabolism v.1.0  (Read 6034 times)

Offline shvarz

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« Reply #15 on: March 23, 2005, 05:24:23 PM »
What do you mean no other Co-A?  What about fat-CoA?

8.  Well, everyone else seems silent, so I guess we can just hook up and go for it (when PY is not looking our way :) ).  One important thing that is missing from current metabolism is NADH.  Do you know what it is and what is it for?  If yes, do you think we need to implement that?
« Last Edit: March 23, 2005, 05:24:50 PM by shvarz »
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Offline Numsgil

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« Reply #16 on: March 23, 2005, 05:30:16 PM »
fat-CoA!  Damn.

CoASAC doesn't sound as cool.

How about Acetyl ASH.  We just refer to any coenzyme A as ASH.  That still sounds cool and Acetyl ASH isn't too ahrd to remember.

Offline Numsgil

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« Reply #17 on: March 23, 2005, 05:33:00 PM »
Yeah, I know about NADH/NAD, etc.

Since we're not modeling mitochondria in any way, we can just assume that anything that produces NADH, or FADH2 really produces the amount of ATP that would normally be produced by the mitochondria.

I don't feel bad about this level of abstraction at all.

Offline Numsgil

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« Reply #18 on: March 23, 2005, 05:41:40 PM »
Okay, this is the beginnings of my look into photosynthesis:

The Calvin Cycle.

Offline shvarz

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« Reply #19 on: March 23, 2005, 05:44:53 PM »
well, it is not just energy.  Here is an example from glycolisis:

you break glucose anaerobically - you get 2 ATP and 2 NADH and 2 pyruvates, so seems like you got 8 ATP (NADH = 3 ATP)

but then bacteria actually convert pyruvate to alcohol and spend these 2 NADH.  WTF?  Why do they do that?  It is because the amount of NAD is limited, so if you keep splitting glucose you run out of NAD.  Normally NADH is converted to ATP by giving H to oxygen.  But without oxygen you can't get even the 2 ATP that you were able to get before, because all your NAD is NADH.  So they have to waste 2 perfectly good NADH.
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Offline shvarz

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« Reply #20 on: March 23, 2005, 05:48:13 PM »
Yeah, essentially it is already there - last diagram with photosynthesis there is an arrow from CO2 to glucose.  That's Calvin cycle.  I guess you want it more detailed :)
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Offline Numsgil

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« Reply #21 on: March 23, 2005, 05:51:57 PM »
Hmmm...

I guess we could add a simple NADH + O2 -> ATP (not balanced.  That's right, isn't it?) reaction that enzymes can be develop for.

Same for any other molecules that are produced that are generally used to produce ATP via the mitochondria.

Offline Numsgil

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« Reply #22 on: March 23, 2005, 05:54:13 PM »
Quote
Yeah, essentially it is already there - last diagram with photosynthesis there is an arrow from CO2 to glucose.  That's Calvin cycle.  I guess you want it more detailed :)
Yeah, every step should be modeled with an enzyme.

I don't know enough to say much more than I think we have:

Photosynthesis II -> Photosynthesis I -> Calvin Cycle
edit: had it backwards

Might as well model each step in every one of those.  Talk about difficult to evolve photosynthesis...

But not impossible, since you can earn energy for completing parts of it.
« Last Edit: March 23, 2005, 05:55:18 PM by Numsgil »

Offline shvarz

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« Reply #23 on: March 23, 2005, 07:06:50 PM »
I am still inclined in starting with a smaller system first and working out the bugs with it.  Then we can expand later.  You know, this looks like a big project.  What if we don't include metabolism in v.3.0 and keep working on metabolism on our own.  
I am guessing we'll run into quite a few problems.  And no one else seems to be interested in contributing to that anyway.
"Never underestimate the power of stupid things in big numbers" - Serious Sam

Offline Numsgil

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« Reply #24 on: March 23, 2005, 08:52:52 PM »
I've been thinking of releasing about what I have right now as 2.36, and saving up all these big things for 3.0.

3.0 should be whatever version has atleast one of these:

specialization,
digestion and enzymes,
metabolism,
etc.

Offline PurpleYouko

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« Reply #25 on: March 23, 2005, 10:35:53 PM »
If that is the case then we need to fix those ties and stuff before we worry about these new things.

I am working on the mutations module now so anything else you want to change, please go ahead and make 2.36.

 :D  PY  :D
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Offline Numsgil

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« Reply #26 on: March 23, 2005, 10:38:49 PM »
Yeah, a few things here and there.  I'll probably disable the env grid for 2.36, since it's still such a work in progress and doesn't actually do anything.

A few other things.  What modules are you in PY?

Offline PurpleYouko

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« Reply #27 on: March 24, 2005, 08:52:24 AM »
Sounds like a good idea to disable it for now.

All my present work is in mutprob, mutations and MDIform1.

If I get back to graphics at some point then this will include main.frm too

Shouldn't cause any problems for what you are working on.

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Offline Numsgil

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« Reply #28 on: March 24, 2005, 09:42:53 AM »
Alright, I'll work on a few loose ends and probably release 2.36 by the end of the week.

Offline PurpleYouko

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« Reply #29 on: March 24, 2005, 12:20:42 PM »
Did you get the ties sorted yet?

I am pretty sure they are going wrong because of your bubble sort. Something is getting crossed somewhere between your new robotlist and the old nodes.

 :D  PY  :D
There are 10 kinds of people in the world

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:D PY :D