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Quarian ecosymbiotic physiology, feat. Mordin Solus (long read)


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#26
Steelcan

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Phatose wrote...

Steelcan wrote...

that 1% of differences is at least hundreds of thousands of nucleotides


Yes, but if the plants on Rannoch aren't all dead then the important bits aren't in those hundreds of thousands of nucleotides.

Edit:  Just to be clear, since the entire ecosystem is built on this symbiosis, this is not a recent evolutionary divergence.  All, or nearly all, animals on Rannoch will have the relevant sequences.  This is something as vital to all life on Rannoch as, well, the Kreb's cycle is to life on earth.  This will not be in the 1% that separates Quarians from space-chimps.  It will be in the code common to all life on Rannoch.

It's just a matter of close examination of that ecosystem, which the Geth have to have done if they've actually preserved Rannoch for the Quarians.

This symbiosis is likely important and integral, but I doubt its as universal as the Kreb's cycle.

#27
Spartanburger

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I like what I read and I agree with the solution, but there's a few things that made me think.

[quote]DeinonSlayer wrote...
"put Geth in their suits" is one of the biggest science handwaves in the series short of Synthesis. First off, we're talking about envirosuits mass-produced by and for one of the poorest races in the galaxy. Secondly, if the answer were as simple as uploading a VI to "simulate disease," wouldn't the galaxy-renowned tech experts have thought of it at some point in the last three hundred years?
[/quote]

I completely understand what you're saying, and I had that very question myself. Why couldn't the Quarians, who despite their difficult situation in the galaxy are incredibly adept at VI development (they made a semi-sentient network of VIs ffs) develop VIs to do simulate the diseases, infections, microbes and other material? (One speculatory answer is that, to simulate a lifeform in such a way that the immune system would actually respond as if real would require an adaptive consciousness only attainable by AI). And that is assuming that the suits are advanced enough to do that. (Okay, they are called environment suits for a reason. They're designed to create and maintain an environment that's survivable for the long-term, so perhaps even a low grade model would be capable of something. Plus, then there’s how Quarians generally have extensive cybernetic augmentations, some of which would likely be able to aid in the restoration of the immune system).

At the same time though, I don't think that the “why not VI?” plot hole is enough justification to count simulating foreign matter out as a potential solution.

I think of it less as "simulating diseases" and more like a virtual and adaptive vaccination. My body is unprepared to fight a disease? Inject dead or harmless versions of the disease into my body to help train it to fight said disease. (It’s been years since my last class that dealt with it but IIRC it had something to do with having the immune system essentially “train” to fight the specific disease. A quick google tells me that it’s lymphocytes that are built up to “remember and recognize previous invaders and help the body destroy them”). Over time, my body's immune system becomes far stronger in fighting that disease. Defenses against various other microbes would be built up in a similar fasion. This is, mind you, just what I've heard of how it works. I'm not a medical or biological specialist, though I've grown up in a family filled with PhDs who all work in the medical field.

The VI/AI/Program in questions would generate minor amounts of foreign material, perhaps using the minifabricator in the omni-tool, and introduce it into the suit environment. The amounts would be kept small, and over time the immune system would get stronger, similar to how the vaccination would help in fighting that one disease. For more complicated material, like bacteria or a virus, a more intelligent system would have to be in place. Either nano machines connected via a network with the capabilities to mimic those organisms, or fabricating dead cells to use as a more literal vaccination. The latter would likely take a more advanced fabrication suite than what comes in a omni-tool. Something a high-end hospital or research lab, or university would have.

Some might say that a vaccination wouldn't really work since the Quarian immune system is supposed to have a symbiotic relationship with pathogens on Rannoch. Pathogens alone are rare on Rannoch, and most of what remains is partially beneficial, but that does not mean that nothing on Rannoch is harmful. It’s not absolute; there are still deadly diseases on Rannoch and the immune system would need to check all foreign material to filter out and identify those rare pathogens that are harmful. It would screen foreign material and microbes for ones that are symbiotic and attack those that are not. Mimicking these symbiotic microbes is likely one tactic used by the harmful Quarian pathogens. Immune system thinks it's a good microbe and it gets further into the system with far less in its way to stop it.

The big question is if this would be enough for an individual to go suitless in their lifetime. One of the things that always annoys me is when people say that Quarians "don't have an immune system." They do. It's been only 300 years. Significant genetic changes take thousands of times that amount of time. What the Quarian immune system is is untrained. Like any other part of the body, it is essentially a muscle. Work it, and it gets stronger. Ignore it, and it wastes away. It's still there, but incredibly weak. You know how newborns have with significantly weaker immune systems? The Quarians are like that, only they never get the exposure, both in-utero and post-berth, that they needed to have a system strong enough to handle out-of-suit exposure. A lot of the immune system strength is also passed down from parent to child, as you said later with the Methyl groups that turn genes on and off in response to stresses experienced through a lifetime.

Tali's estimate of "600" years to adapt to a foreign world seems, in my eyes, a little long but close enough. Her estimate of "60" for Rannoch, a teeny bit short. I think it would likely be the third or fourth generation of Quarians living on a reclaimed Rannoch that would have immune systems that very closely resemble the ones their ancestors had. This, in my solution, would be done by controlled, monitored, repeated exposure. From that point, adapting to other worlds would take significantly less time.

Tali adapted to Shepard in a year. She’s been shot and exposed to microbes and material that are non-native to Rannoch. She’s taken off her mask to breathe in the raw air. I think that she’d likely adapt to be able to live suitless on Rannoch, though it might take a few years.

However, the notion that Geth in suits, mimicking diseases can somehow affect the immune system enough to let Quarians go suitless in a matter of weeks or months is ridiculous. The systems might adapt, but not that fast. And that’s assuming that the Geth are able to mimic it in the first place and yadda yadda yadda.

Woah, that turned out a lot longer than I expected. Moving on.

[quote]DeinonSlayer wrote...
Dialogue in ME2 stated that generations of genetic engineering would be necessary to adapt to a new world.
[/quote]
Not in any of my 15 runs of ME2 have I heard mention of genetic engineering. All I've heard is Tali talking about the difference between adapting to a foreign world and to Rannoch: "It's the difference between 60 years and 600. For any Quarian alive today to be able to live without a suit, we have to retake our homeworld" and about Quarians on foreign colonies: "Normally, a Quarian would be sick for a few weeks before adapting to the foreign environment." Given a healthy immune system (pre morning war) and appropriate immunoboosters and vaccines, I think that adaption to the foreign system could take that short a time. It’s adaption from an incredibly weak immune system that would take time.

[quote]DeinonSlayer wrote...
A codex entry in ME3 told us the reason Quarian immune systems broke down is due to them being physiologically dependent on interaction with their native plant life back on Rannoch - which they did not have on the fleet, and which would exist nowhere else.
[/quote]
The online codex does not mention this, but then again it seems to mention nothing of Quarian biology at all.
The wiki, though not a super-reputable source, says a few things that are interesting:

1. Pathogenic microbes were comparatively rare in their homeworld's biosphere.

2. Pathogenic microbes that were native to their homeworld were often at least partly beneficial to them, giving rise to a symbiotic relationship with their environment. (This does not mean that all pathogens were partially beneficial though. There would still be rare few that were harmful. )

A symbiotic relationship, yes, but I do not consider that a "dependent" relationship. Mutually beneficial yes, dependent not so much. Up for dispute though. Scientists still argue over the definition of a symbiotic relationship.


[quote]DeinonSlayer wrote...
Observations
*snip*
These stripes may well play a part in that, allowing seeds to adhere to an individuals' legs as they walk ("Our bodies carried the seeds which spread the desert grass").[/quote]


Although I think this is a neat theory, I have four issues with it.

1. How does having lines/stripes on your legs actually help a Quarian in any way? Sure, they might help carry the seeds and pollen, but how would something from that translate into a benefit for the Quarian? Absorbed through the skin/fur/scales/whatever?

2. For something like this, wouldn't it be better to have it be a solid patch of... whatever it is that picks up and carries the seeds/pollen? Having stripes only covers a limited and inefficient surface area. If the stripes were partially for show (perhaps to aid in attracting a mate?) would we not see something similar on Quarian suits to mimic this? I would also ask that, if it was for show, why would only those parts of the design carry the seeds/pollen and not the whole thing? (like, only the black stripes of a tiger being able to carry pollen with the orange being unable or something) Is the pattern and pattern alone the only bit that carries the seeds/pollen and if so, why not the surrounding bits? It’s an incredibly inefficient use of real-estate. And let’s be honest: They can’t really be for show because believe me they’re not looking at the lower legs ahehehehehehe mmm.

3. Although I really like the idea of having Geth resemble their creators, why would they deal with tiny details like stripes on the legs when they have completely different faces and heads? Why, when designing a labor machine would they add those stripes there? It would be like adding hair to the arm of a car-manufacturing robot. There’s no point. And once the Geth are independant, why continue the design when it provides zero benefit to them (okay, it can be argued that the Geth have done inefficient things in the past, like restoring Rannoch, but still).

4. Those are plate-straps. They’re flat textures in ME1 Geth, but in ME3 Geth they’re physical plates that appear to be about 1-3 millimeters above the normal surface of the Geth leg.



[quote]DeinonSlayer wrote...
Something the host animal cannot do without. [/quote]
If the host animal “cannot do without” it, then they’d all be dead because, well, they could not do without it. This is a symbiotic relationship, not a dependant one. The conclusion, however, that health problems would likely develop after periods without exposure to such a relationship is likely correct, but it still raises a question:

Quarians were able to live in many foreign environments, like various other worlds and the Citadel, and do fine once their systems adapted. In these locations, it is unlikely that they would be exposed to such seeds, pollen, or microbes that provide them with the symbiotic relationship. If they’re able to live in those places fine, perhaps the health problems are not as major as thought.

Another thought that just came up: Microbes in the body would be self sustaining, right? I mean, in some symbiotic relationships, the microbe would be able to live and reproduce safely within the Quarian while giving the Quarian a little something in return. Considering that, for a while the mother and child’s entire systems are one, would some of those microbes be transferred to the child? And if that is true, then wouldn’t the modern Quarians still have those microbes inside them? I don't know for sure. Not really been formerly educated in this.


[quote]DeinonSlayer wrote...
I wrote up this dialogue sequence for a fanfic which I doubt I'll ever get around to actually writing[/quote]

You have no idea how hard I would read it if you did. I’m a sucker for fanfiction. gimmie.



[quote]DeinonSlayer wrote...
Liveships originally designed to allow entire codependent ecosystem - dozens of plant and animal species - to be transplanted on new colony worlds. Liveships each meant to sustain no more than 200,000 colonists. After exile, expected to feed millions.[/quote]

Didn’t see anything on this in the codex or wiki, so I have to assume this is of your own speculation. I like it, actually, though the codex says they don’t contain animals (though that is likely due more to current situations rather than pre-morning war).

I have my own theory on it though. I think the ships were designed and built specifically for the flotilla, post morning war.

The basic idea I have is this. The political hammering has just started to hit the now exiled Quarians, but they were still a major race. They would still likely have massive amounts of assets available. Unable to get enough political play to get a planet or housing (or to keep their counsel species status), they would find themselves knowing that they’d be stuck on the fleet for a while. They knew they’d need huge ships like that, so they liquidated most, if not all, assets outside their fleet to commission four massive ships, getting around dreadnought numbers limits by classifying them differently and having them completely unarmed. This would also explain how such a race would lose so much of its wealth.

Still, you have a nice theory and I like it.

[quote]DeinonSlayer wrote...
Priority shifted to production of staple foods, vital medicines, at expense of inedible codependent flora. Lack of exposure to codependent flora, combined with sterile environment, led to collective weakening of immune systems.[/quote]

Food production on liveships work via nutrient vats that grow plants, which are shipped out to other ships, irradiated on arrival, and then crushed down into paste. If the lack of symbiotic plants weren’t hugely effective, the irradiated food likely was.

[quote]DeinonSlayer wrote...
Mordin: "Genetic code only half of the story in organic life forms. Methyl groups adhere to DNA structure during the life of an organism in response to different stresses, switching genes on and off.

Generations of 'malnutrition' caused quarian immune response to grow steadily weak as effects compounded."
[/quote]
Okay, and when the organism starts to respond to old stresses, stresses not had for some 300 years perhaps, those Methyl groups could then switch genes back on. “switching genes on and off” means that it works both ways.

Give the quarians better nutrition and some things for their immune system to actually respond to and Quarian immune response would grow steadily stronger. Would take time and explosure to occur naturally.

quote]DeinonSlayer wrote...
but medical records no longer exist.[/quote]

I’m going to call BS on this.

The Quarians, what was one of the most technically advanced races at their peak, don’t have medical backups with them? They don’t have genetic baselines of their own species? Other races, the Salarians in particular, never grabbed them? They’re not in medical archives in the Citadel, which would store information on all the races?

Yeah right.

They weren’t in the dark ages when the Quarians were given the Geth boot from Rannoch. They had technology and connectivity that dwarf anything we currently have. Hell, their omni-tools alone probably out-compute our supercomputers. Digital storage in that age would be unimaginably immense. The galaxy was connected. Genetic research on Quarians would likely have been done on various worlds, not just the homeworlds, and the data would have been sent to various institutions and organizations. To say that all of those copies were somehow destroyed is illogical.

The Geth are not needed to attain a genetic baseline of the Quarians. Such information would be available to one with STG access, or one with Citadel medical archive access (some medical personnel, and all spectres).

All that said, your solution makes sense, and would work. But it would be expensive and take up resources used both in the Reaper war or in the repair and recovery from said war.

The solution of simple limited and controlled, yet repeated exposure would also likely work, but would take far longer.

Here’s one semi-related subject I thought of while writing this.

Volus. Would they not also have a weakened (though nowhere near as weakened as the Quarians) immune system? I would imagine that housing at their natural pressure would be expensive, so they’d likely wear their suits more often than not. In doing so, they’d be in the sterile suit environment for most of the time. I think this would somewhat reduce the strength of the Volus immune system. This would likely be more apparent in Volus families that have grown up outside of their natural pressures, like a family a few generations long that have lived only on the Citadel.

Then again, I’m nowhere nearly as educated in Volus culture and biology than I am in Quarian, so perhaps not.


And it's still alien biology we're dealing with here. Nothing is really certain.

Modifié par Spartanburger, 15 juin 2013 - 07:20 .


#28
TheWerdna

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Steelcan wrote...

DeinonSlayer wrote...

@Steelcan
I c/p'd Mordin's dialogue from an older version. I just edited the newer version in - the stuff on retroviral injections and anti-rejection medication is new.

Perhaps that's how the Geth could do it. Still, elaboration in the form of a codex entry or something would be easier to take seriously than "rewriting suit functions to simulate disease."

I think the writers were going for a Battlestar-style "all of this has happened before, all of this has happened again" mantra with the Geth integrating in Quarian suits. The implication was that the Geth would do to the Quarians what the Zha'Til did to the Zha.

:blink:  As I recall that DID NOT work out well.  I'm not sure BioWare wanted this message to be carried through.  Remember our cycle is "special", but what do I know?

(I think the ITers are actually big on this in their thread.)



If you bring Javik on the geth dreadnaught mission he reveals that the Zha'Til thing was working perfectly fine until the Reapers shows up and took control of the synthetic half of them. So ya, basically it was a case of Starbrat causing thing to happen to support his own theaory "Oh look, peaceful syntheitcs and organics interacting?!?!? I can't let tht happen, it would mean my theory is wrong and stupid!"

#29
DeinonSlayer

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It would take a while to get through all of your post, Spartanburger (you brought up some good points - expect a more thorough response to follow), so for now I'll just address two of your points.

Spartanburger wrote...

DeinonSlayer wrote...
Dialogue in ME2 stated that generations of genetic engineering would be necessary to adapt to a new world.

Not in any of my 15 runs of ME2 have I heard mention of genetic engineering. All I've heard is Tali talking about the difference between adapting to a foreign world and to Rannoch: "It's the difference between 60 years and 600. For any Quarian alive today to be able to live without a suit, we have to retake our homeworld" and about Quarians on foreign colonies: "Normally, a Quarian would be sick for a few weeks before adapting to the foreign environment." Given a healthy immune system (pre morning war) and appropriate immunoboosters and vaccines, I think that adaption to the foreign system could take that short a time. It’s adaption from an incredibly weak immune system that would take time.

I had thought it was dialogue from Tali's loyalty mission; it turns out it's actually dialogue on the Normandy in ME2 (been a while since I played it, had to look it up). In the discussion on Quarian immune systems, choose the option "Quarian evolution" under Investigate, followed by "What about other planets?"

Tali: "When the Geth took the homeworld and our colonies, the sterile environment on the Flotilla ruined our immune systems' adaptability. Even if we colonized a new world or reclaimed our own, it would take a long process of bioengineering to recover."

Spartanburger wrote...

DeinonSlayer wrote...
A codex entry in ME3 told us the reason Quarian immune systems broke down is due to them being physiologically dependent on interaction with their native plant life back on Rannoch - which they did not have on the fleet, and which would exist nowhere else.

The online codex does not mention this, but then again it seems to mention nothing of Quarian biology at all.
The wiki, though not a super-reputable source, says a few things that are interesting:

1. Pathogenic microbes were comparatively rare in their homeworld's biosphere.

2. Pathogenic microbes that were native to their homeworld were often at least partly beneficial to them, giving rise to a symbiotic relationship with their environment. (This does not mean that all pathogens were partially beneficial though. There would still be rare few that were harmful. )

A symbiotic relationship, yes, but I do not consider that a "dependent" relationship. Mutually beneficial yes, dependent not so much. Up for dispute though. Scientists still argue over the definition of a symbiotic relationship.

It isn't mentioned in any of the codex entries on the Quarians themselves; it actually comes from the entry on Rannoch itself, which wasn't added until ME3:

Rannoch has no insect life. As a result, its pollinating plants evolved to rely on animals for propagation. This symbiosis between flora and fauna is responsible for the quarians' weakened immune systems, which made colonization of other planets extremely difficult after their exile from Rannoch. For many quarians, reclaiming their homeworld from the geth is a matter of both cultural and physiological necessity.

Modifié par DeinonSlayer, 15 juin 2013 - 05:02 .


#30
Sumthing

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TheWerdna wrote...

Steelcan wrote...

DeinonSlayer wrote...

@Steelcan
I c/p'd Mordin's dialogue from an older version. I just edited the newer version in - the stuff on retroviral injections and anti-rejection medication is new.

Perhaps that's how the Geth could do it. Still, elaboration in the form of a codex entry or something would be easier to take seriously than "rewriting suit functions to simulate disease."

I think the writers were going for a Battlestar-style "all of this has happened before, all of this has happened again" mantra with the Geth integrating in Quarian suits. The implication was that the Geth would do to the Quarians what the Zha'Til did to the Zha.

:blink:  As I recall that DID NOT work out well.  I'm not sure BioWare wanted this message to be carried through.  Remember our cycle is "special", but what do I know?

(I think the ITers are actually big on this in their thread.)



If you bring Javik on the geth dreadnaught mission he reveals that the Zha'Til thing was working perfectly fine until the Reapers shows up and took control of the synthetic half of them. So ya, basically it was a case of Starbrat causing thing to happen to support his own theaory "Oh look, peaceful syntheitcs and organics interacting?!?!? I can't let tht happen, it would mean my theory is wrong and stupid!"


So, starbrat is extremely biased?

#31
in it for the lolz

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Sumthing wrote...

TheWerdna wrote...

Steelcan wrote...

DeinonSlayer wrote...

@Steelcan
I c/p'd Mordin's dialogue from an older version. I just edited the newer version in - the stuff on retroviral injections and anti-rejection medication is new.

Perhaps that's how the Geth could do it. Still, elaboration in the form of a codex entry or something would be easier to take seriously than "rewriting suit functions to simulate disease."

I think the writers were going for a Battlestar-style "all of this has happened before, all of this has happened again" mantra with the Geth integrating in Quarian suits. The implication was that the Geth would do to the Quarians what the Zha'Til did to the Zha.

:blink:  As I recall that DID NOT work out well.  I'm not sure BioWare wanted this message to be carried through.  Remember our cycle is "special", but what do I know?

(I think the ITers are actually big on this in their thread.)



If you bring Javik on the geth dreadnaught mission he reveals that the Zha'Til thing was working perfectly fine until the Reapers shows up and took control of the synthetic half of them. So ya, basically it was a case of Starbrat causing thing to happen to support his own theaory "Oh look, peaceful syntheitcs and organics interacting?!?!? I can't let tht happen, it would mean my theory is wrong and stupid!"


So, starbrat is extremely biased?


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