Bacteria and replicase accuracy

Hey

First of all, I wanted get some programmers opinion on how hard it would be to make a Bacteria cell playable once the microbe stage is up (i would like to simulate metabolic pathways in Bacillus for educational purposes, plus I think that most people would learn much better playing a game then looking at a chart like this http://www.genome.jp/kegg-bin/show_pathway?bsu00010)

I don't know much about programming, but i can learn and would like to know how hard it would be to simply add ATP and amino acid values for certain simulated genes that go into your bacteria. Like once you get a certain pathway your ATP or amino acid or nucleotide uptake levels go up, but the cost for the protein production is also calculated.



Also I have a question on "replicase". How will this be calculated? Simply by ATP or protein and nucleotide levels combined with ATP. In addition, would it be realistically simulated (which could be problematic because last time I did calculations (I was gonna post em, but the page screwed up and died. i will redo the calculations later) the High energy bonds (ATP) required to multiply was about 70 million) or would the "ATP" be a simulation for, lets say, a million ATPs?

On the idea of replication, since the cell will begin as Eukaryotic (because they make best gameplay cause of organelles and mutlicellularness) Perhaps evolution at this level could be initiated by mating.( http://en.wikipedia.org/wiki/Mating_of_yeast). A pathway to evolve?

Anyway, just some ideas I am coming up with. (kinda been lurking) Anyone think that modifying the code will be easy/and or hard?

-Koeng

I'm no programmer, but I can answer some of your questions. Normally I would merge this with the Misc thread, but since there is an active discussion there now (or two) we can keep it separate for now, and then archive it when finished.

Metabolism in Thrive will definitely not be that complicated. We are using the simplified balanced chemical equations for things like glycolysis, aerobic respiration, etc. Also, bacteria will not be playable since they don't have a nucleus, don't have organelles, and cannot form multicellular organisms.

Also, I don't know where you got that idea, but the microbe stage won't be looking at such charts (By the way, both of your links are broken. You need to remove the brackets at the end of each one).

Again, DNA and genes are too complex for this stage of the game.

If by replicase, you mean reproductase, then it just is a way to track the cell's progress to cell division. Also, cell division will be how cells divide, so mating is not needed.

We're attempting to simulate metabolism in an intermediate level of detail in order to make the game playable and possible to implement. Adding bacteria doesn't add to gameplay in any discernible way, and simulating the metabolism of, say, E. coli or bacillus in its entirety just doesn't help people engage with the game, which is what we want on the surface level. Our metabolic plans are already fairly complex, and adding in real bacterial pathways just doesn't make sense to do on any level, as cool as it would be to have them.

NickTheNick wrote:

I'm no programmer, but I can answer some of your questions. Normally I would merge this with the Misc thread, but since there is an active discussion there now (or two) we can keep it separate for now, and then archive it when finished.

Metabolism in Thrive will definitely not be that complicated. We are using the simplified balanced chemical equations for things like glycolysis, aerobic respiration, etc. Also, bacteria will not be playable since they don't have a nucleus, don't have organelles, and cannot form multicellular organisms.

Also, I don't know where you got that idea, but the microbe stage won't be looking at such charts (By the way, both of your links are broken. You need to remove the brackets at the end of each one).

Again, DNA and genes are too complex for this stage of the game.

If by replicase, you mean reproductase, then it just is a way to track the cell's progress to cell division. Also, cell division will be how cells divide, so mating is not needed.

For the charts, I just meant thats how they NORMALLY look. I wanted to know how hard it would to be to code for similar reactions. And for bacteria being playable, some do have organelles, and couldn't it be possible to just take out the visible organelles but keep function?

In addition, mating is not a form of replication, it is... mating. Diploid cells undergo meiosis/spore when conditions are tough, making 4 haploid cells. When these awake, they tell each other to make surface proteins. Once they have 2 complementary surface proteins, the cells can fuse and share genetic information(chaning back into diploid). Meaning which it is an optimal time for exchanging genetic information. A similar idea is with animals, we don't just replicate ourselves to make a new creature, we mate. That way there is more genetic information exchanging, which leads to evolution.

Also, the metabolic pathways aren't that different then what you would be using, just more numbers. Metabolic systems can be modeled so they simply add to a certain value, and these values are used to do stuff like replicate the cell

-Koeng

No - like all prokaryotes, bacteria do not contain organelles.

An organelle is defined as a compartment separated from the rest of the cell via a phospholipid membrane - including a nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus.

Bacteria have an outer plasma membrane (like all cells), but their intracellular contents are all freely diffusable. The only distinguishment made in bacteria is what is called the nucleoid, which is not a nucleus (i.e. not surrounded by a biphospholipid membrane), but simply condensed DNA that is still free within the cell.

Koeng wrote:

In addition, mating is not a form of replication, it is... mating.

Oxford Dictionary wrote:

mating /mat·ing/ (māt´ing) pairing of individuals of opposite sexes, especially for reproduction.

Roget's Thesaurus wrote:

Reproduction:... Replication...

My point is, evolution in the microbe stage takes place through cell division. A cell can divide after reaching a certain threshold of reproductase, and when it does the player can enter the Microbe Editor to "evolve" the replicated cell. Adding mating would hardly change this, so it wouldn't add anything meaningful to the game. Also, genes and DNA will not be in the game.

The compound processes already contribute to that. Check the Microbial Compounds and Organelles thread for a full page of the processes near the final pages.

NickTheNick wrote:

No - like all prokaryotes, bacteria do not contain organelles.

An organelle is defined as a compartment separated from the rest of the cell via a phospholipid membrane - including a nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus.

Bacteria have an outer plasma membrane (like all cells), but their intracellular contents are all freely diffusable. The only distinguishment made in bacteria is what is called the nucleoid, which is not a nucleus (i.e. not surrounded by a biphospholipid membrane), but simply condensed DNA that is still free within the cell.

Koeng wrote:

In addition, mating is not a form of replication, it is... mating.

Oxford Dictionary wrote:

mating /mat·ing/ (māt´ing) pairing of individuals of opposite sexes, especially for reproduction.

Roget's Thesaurus wrote:

Reproduction:... Replication...

My point is, evolution in the microbe stage takes place through cell division. A cell can divide after reaching a certain threshold of reproductase, and when it does the player can enter the Microbe Editor to "evolve" the replicated cell. Adding mating would hardly change this, so it wouldn't add anything meaningful to the game. Also, genes and DNA will not be in the game.

The compound processes already contribute to that. Check the Microbial Compounds and Organelles thread for a full page of the processes near the final pages.

No is kinda blunt. All prokaryotes?

Not trying to make an internet war, but an organelle is defined as "any of a number of organized or specialized structures within a living cell". Specifically, phospholipid bilayers are not required, just they usually are there ( I believe the person in this yahoo answers is mistaken- http://answers.yahoo.com/question/index?qid=20100402145217AAbAM5z ). Some examples of bacterial organelles include cell walls, poteasomes, usually ribosomes, and even the advanced Carboxysomes, which are essentially microcompartments evolved from viral caspids. Here are a few others with similar functions- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272493/figure/F2/ . It seems like the person on yahoo answers who answered that had a narrow education in biology. (or a troll), since inside of bacteria isn't that freely floatin around. How would they have shape then? How would both chromosomes get into the cells? How would they divide? Even going upon that, some bacteria have thylakoid, meaning that the intracellular contents are not freely diffusing. In addition, the DNA is not always condensed, sometimes upon splitting it is free.

Point is that organelle in science usually has a much broader terminology , for if you believe that an organelle has to be separated by a phospholipid membrane, the centrosomes wouldn't be called an organelle. Neither would a ribosome (widely accepted by most as organelle)Neither would that eye spot on some algae. Even the cytoskeleton or cell wall wouldn't be considered an organelle by that definition, which is one of the origins of the word.

Sorry, people claiming wrong facts about my profession really screws with my mind and sets me off :cry: 
-Koeng

The yahoo answer was significant in that it summed up that organelles like the nucleus, mitochondria, ER, golgi bodies, vacuoles/vesicles, and chloroplasts don't exist in bacteria. Why only these are important is because only these are organelles in the game. Therefore, even where the post is incorrect, such as regarding ribosomes, cell walls, centrosomes, etc. those aren't organelles in Thrive so it doesn't matter.

Plus, rest assured, I did not base all of my knowledge on that post, I simply quoted it since it summed up my point sufficiently.