Dietary Chemistry Design

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Quasar
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Dietary Chemistry Design

Post by Quasar » Tue Nov 06, 2018 12:19 am

Just a diagram I mocked up in excel for the future.

Image

I'm looking for feedback on this: anyone who has better knowledge of biochem than I do, please let me know if I'm understating some processes while overstating others, or if any of this is just plain wrong.

Not shown: water and oxygen would be consumed by many of these processes.

(Edit) In case you are wondering how this all ties in with the evolution system: P. Specium will start with only the "digestion", "protein synthesis" and "glycolis" processes activated. Everything else will have to evolve.

Also worth noting, creatures will expel resources they cannot process, meaning P. specium waste will be full of Pyruvate and NADH, both easily processed into ATP by a creature with the right digestive system.

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White parrot
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Re: Dietary Chemistry Design

Post by White parrot » Tue Nov 06, 2018 4:04 am

I won't be able to help much, as biochemistry is one of my nemesis. :o

That being said, I feel like lipogenesis needs to be included so that lipids can be properly used as energy storage (and insulating protective tissue?)(well, if the ability is evolved of course). They have to come from somewhere, after all.

Not relevant to the diagram itself, but how will enzymes be represented, in the context of Species? Consumed to "power" metabolic processes?
More generally, I assume actions such as growth and healing will consume "enzymes" and lipids (... cell membranes are made of lipid, aren't they?). I'd add notes on these "product molecules" on the graph to keep track of their use.

Do you think you'll have a simplified, "mirror" diagram for decomposers and plants so as to know exactly how each possible waste products will impact fertility? If there are proper metabolic pathways, substances could potentially be decomposed into others and so on rather than be directly converted into fertility... Possibly overkill though.
At this point, we shouldn't be surprised by anything nature does. She's like a meth addict whose drug-fueled rampages unfold in slow motion and span millions of years.
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smjjames
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Re: Dietary Chemistry Design

Post by smjjames » Tue Nov 06, 2018 4:38 am

Quasar wrote:
Tue Nov 06, 2018 12:19 am
(Edit) In case you are wondering how this all ties in with the evolution system: P. Specium will start with only the "digestion", "protein synthesis" and "glycolis" processes activated. Everything else will have to evolve.
Heh, you've opened up a can of worms here, what about alternate pathways? I'm thinking alien life forms here though since the metabolic pathways for Terran life were likely already more or less locked in by the time multicellular life came around and most of that are basic cellular proccesses.

Also, the metabolic pathways are another strike against the way the gills-anaerobic-lungs is set up because anaerobic proccesses are still used alongside aerobic proccesses.

Also2, how complex do you want the system to be? Because theres a huge amount of complexity and you'll also have to make consequences for too high or too low of some of these. Not to mention that your starting point with just digestion, protein synthesis and glycols may actually be too simple for an organism like P. Specium. I mean, it's a pretty simple creature, sure, but on the scale of things, it's actually still pretty complex, we aren't talking sponges here, we're talking something like tiny little wormlike creatures that were around during the Edicarian period, and even before that.
Quasar wrote:
Tue Nov 06, 2018 12:19 am
Also worth noting, creatures will expel resources they cannot process, meaning P. specium waste will be full of Pyruvate and NADH, both easily processed into ATP by a creature with the right digestive system.
Poo everywhere, okay. A thought though, could they spontaneously evolve photosynthesis? Not that theres a simulated Sun to get energy from anyway.

You probably should put this up on the Steam forum, get more eyes on it that way. Or put it up in the blog.

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Re: Dietary Chemistry Design

Post by Quasar » Tue Nov 06, 2018 5:17 am

White parrot wrote:
Tue Nov 06, 2018 4:04 am
That being said, I feel like lipogenesis needs to be included so that lipids can be properly used as energy storage (and insulating protective tissue?)(well, if the ability is evolved of course). They have to come from somewhere, after all.
... lipogenesis...
Wikipedia wrote:"Lipogenesis is the process by which acetyl-CoA is converted to triglycerides (i.e., fat)."
Oh, of course. The process by which carbohydrates become fat. [smacks face] I'm an idiot.

Triglycerides are already on the chart (simplified to "Lipids"), so this would be a process directly between Acetyl-CoA and Lipids. Which, of course, are on opposite sides of the diagram.

Trying to fit all this onto the same chart without it becoming a complete flustercluck is going to be fun. Also, I'm reminded that one possible input for glucinogenesis is lactic acid, so that will need to be included as well.

You've pretty much nailed the plan for enzymes. Each energy cost will be classified either as Movement and taken from the yellow "Stamina" meter we already have (which will be synonymous with ATP), or it will be classified as Growth and taken from Enzymes. I was thinking lipids would be treated specially, only used to grow specific insulating or energy-storing body parts, but being able to produce them from Acetyl-CoA might change that.

I don't think we'll have decomposition chemistry, except maybe as an extension of dietary chem (ie. creatures using decomposition processes to make molecular energy).

-----
smjjames wrote:
Tue Nov 06, 2018 4:38 am
Heh, you've opened up a can of worms here, what about alternate pathways?
Before I even look at going alien, there's terrestrial waste-eaters and decomposers, photosynthesis and plant biochemistry, plus the weird kinky stuff extremeophiles get up to when nobody's looking.

At the moment this entire diagram basically only encompasses human biochemistry, because that was by far the easiest to research on wikipedia.
Also2, how complex do you want the system to be?
ALL OF THE COMPLEX.

But also simple. The diagram will be laid out on a single page when you click on the creature, and as the creature does it's thing in the world, you'll be able to watch resources drop into the buckets at the top, and travel through the system, being converted, utilized and expelled.

Finding a way to set it up so that it's not a complete mess will be essential (I'm picturing it laid out something like a pipe network in Oxygen Not Included).

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Re: Dietary Chemistry Design

Post by Natural_20 » Tue Nov 06, 2018 11:30 am

Quasar wrote:
Tue Nov 06, 2018 5:17 am
White parrot wrote:
Tue Nov 06, 2018 4:04 am
That being said, I feel like lipogenesis needs to be included so that lipids can be properly used as energy storage (and insulating protective tissue?)(well, if the ability is evolved of course). They have to come from somewhere, after all.
... lipogenesis...
Wikipedia wrote:"Lipogenesis is the process by which acetyl-CoA is converted to triglycerides (i.e., fat)."
Oh, of course. The process by which carbohydrates become fat. [smacks face] I'm an idiot.

Triglycerides are already on the chart (simplified to "Lipids"), so this would be a process directly between Acetyl-CoA and Lipids. Which, of course, are on opposite sides of the diagram.

Trying to fit all this onto the same chart without it becoming a complete flustercluck is going to be fun. Also, I'm reminded that one possible input for glucinogenesis is lactic acid, so that will need to be included as well.

You've pretty much nailed the plan for enzymes. Each energy cost will be classified either as Movement and taken from the yellow "Stamina" meter we already have (which will be synonymous with ATP), or it will be classified as Growth and taken from Enzymes. I was thinking lipids would be treated specially, only used to grow specific insulating or energy-storing body parts, but being able to produce them from Acetyl-CoA might change that.

I don't think we'll have decomposition chemistry, except maybe as an extension of dietary chem (ie. creatures using decomposition processes to make molecular energy).
When you design your biochemistry, don't forget about effects on buoyancy. Right now you have creatures buoyant by default, when in reality an animal without a store of something less dense than water should sink. Good examples are air, blubber, and shark liver oil.
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White parrot
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Re: Dietary Chemistry Design

Post by White parrot » Tue Nov 06, 2018 2:39 pm

smjjames wrote:
Tue Nov 06, 2018 4:38 am
Quasar wrote:
Tue Nov 06, 2018 12:19 am
(Edit) In case you are wondering how this all ties in with the evolution system: P. Specium will start with only the "digestion", "protein synthesis" and "glycolis" processes activated. Everything else will have to evolve.
Heh, you've opened up a can of worms here, what about alternate pathways? I'm thinking alien life forms here though since the metabolic pathways for Terran life were likely already more or less locked in by the time multicellular life came around and most of that are basic cellular proccesses.

Also, the metabolic pathways are another strike against the way the gills-anaerobic-lungs is set up because anaerobic proccesses are still used alongside aerobic proccesses.

Also2, how complex do you want the system to be? Because theres a huge amount of complexity and you'll also have to make consequences for too high or too low of some of these. Not to mention that your starting point with just digestion, protein synthesis and glycols may actually be too simple for an organism like P. Specium. I mean, it's a pretty simple creature, sure, but on the scale of things, it's actually still pretty complex, we aren't talking sponges here, we're talking something like tiny little wormlike creatures that were around during the Edicarian period, and even before that.
smjjames has a point here: it may confuse viewers on when metabolic pathways evolved relative to anatomical changes.
Quasar wrote:
Tue Nov 06, 2018 5:17 am
Also2, how complex do you want the system to be?
ALL OF THE COMPLEX.

But also simple.
But of course. :roll:

* Processes could evolve in a continuous rather than discrete way, with an evolvable % chance of going right per unit of time (depending on how cruel you are, failure could mean simply having to retry later or wasting the energy to heat loss).

* Technically each process (... I'm tempted to say "enzyme", but those are a different thing in the context of Species. Confusing?) could have an efficiency linked to temperature, but this sounds like overkill.

Temperature, right.
* Reactions could be endo- or exothermic, what have you, so that being warm-blooded or not is folded into metabolism.
(Trivia: lipids are used as energy storage, but as usual some energy tends to leak into heat during the tapping. Also as usual, evolution used the bug as a feature. Human babies are warm-blooded, but due to their small size they lose heat relatively quickly; to compensate, they have a unique kind of fat tissue, "brown fat", which deliberately flunks its energy tapping to directly generate large amounts of heat.)

* Molecules could have a limited lifespan -or half-life, depending on what is easier to implement (even though these substances aren't radioactive... OR ARE THEY?!?). This is, after all, why there are storage molecules: because others deteriorate faster.

* As for when the processes trigger, I'm thinking of doing it on an as-needed basis, with a lack of product triggering a consumption of the reactants, mimicking a system with equilibrium constants but in which end results are constantly consumed. Though... Now that I think about it, beta-oxydations and lipogenesis are antagonist reactions in which both concerned molecules should be common, so we may need to directly use some form of equilibrium constant to determine what the system does... Yes, this sounds better: some evolvable factor that indicates when the reaction is triggered and when it isn't.

* I feel like some trade-offs need to be present so that evolution isn't just accumulating new processes until the perfect metabolism is completed. Some costs for metabolic pathways, equilibrium constants forcing to strike a balance between two substances, circumstantial pathways that can only be used in special cases (typically aerobic, but perhaps if some processes are optimized for a given temperature, or if they risk overheating the bearer)...

Quasar wrote:
Tue Nov 06, 2018 5:17 am
The diagram will be laid out on a single page when you click on the creature, and as the creature does it's thing in the world, you'll be able to watch resources drop into the buckets at the top, and travel through the system, being converted, utilized and expelled.

Finding a way to set it up so that it's not a complete mess will be essential (I'm picturing it laid out something like a pipe network in Oxygen Not Included).
My spontaneous vision is made of whitish rectangles for molecules, more or less filled with a pale coloured liquid (depending on the molecule), with a thin vertical "waterfall" when and where the vat is refilled. The name is written in black over the rectangle (invert if the background and liquids are dark). Meanwhile, processes are lines with bulges travelling through when active (also possible: vibration, steam effect, colour change, all increasing with the frequency of the process. The last one is probably the most visible and suffer the least from poor FPS.); they may be too thin and numerous to be titled though... Ideally, they should be positioned so that content only ever travel downward or at least horizontally.
In any case, both elements could be clicked on or hovered over to reveal name, numerical details and infos in an adjacent window.
At this point, we shouldn't be surprised by anything nature does. She's like a meth addict whose drug-fueled rampages unfold in slow motion and span millions of years.
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Re: Dietary Chemistry Design

Post by Therminator » Thu Nov 15, 2018 1:32 pm

More than two years ago I made a suggestion post about metabolism. Sorry I haven't been active on here for so long.

I think you're trying to make it too complicated, and you can get enough detail with a simpler system.
Especially since each rate in the metabolism will need a gene, with a bunch of regulatory genes on top of it.
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Therminator
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Re: Dietary Chemistry Design

Post by Therminator » Thu Nov 15, 2018 1:41 pm

My chart is not that terribly different from yours by the way, mine looks simpler because in all the cases where a pathway is linear, you can sum all the reactions and treat them as one big step. It is only at branches where intermediates can go both ways that you need to explicitly model the intermediate.

For example NADH doesn't need a separate store I think.

I also wonder what the use would be of having a great and complex biochemistry, with just a fraction of a percent of the players actually understanding what the hell is going on, and the rest feeling dumb and confused.

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