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


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#1
DeinonSlayer

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*glances around nervously*

For the last few days, we've had a thread going on about Asari mating habits. The thread has since metamorphosed into a rather clinical and intelligent discussion of anatomical features and evolution (into which, naturally, I crapped a couple of TVTropes links and scurried off - sorry, guys :unsure:).

A more careful review of that thread got me thinking.

A while back, something in my anthropology course actually got me thinking about how Quarian immune systems could have broken down, and what would be needed to fix them. After playing around with the idea for a bit, the pieces started falling into place. I know that the whole "Tali's sweat" thing has practically become a meme on this site, and I don't want to be lumped into it. Still, this is going to get a bit technical.

Quibbles
As to why I wrote this: I maintain that, after spending three games emphasizing the difficulty associated with fixing Quarian immune systems, "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. Tali's suit in ME1 had hoses conspicuously sticking out of it. How much could these suits realistically do? 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?

Dialogue in ME2 stated that generations of genetic engineering would be necessary to adapt to a new world. 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. Taking in those facts, along with the vid I saw in my anthropology class, I put together the below dialogue sequence between Mordin and Shepard, taking place on the Normandy at some point in ME2.

Let me be clear: I don't want this to turn into yet another Quarian/Geth debate. I just figure I'd get another discussion going, kicking around ideas on alien physiology. Speculation follows:

Observations
Posted Image
Look at the legs of this Geth trooper. Every non-Armature variant of mobile platform has legs shaped like those of a Quarian, sporting stripes like those seen above. Assuming they were roughly modelled after their creators, it stands to reason that the Quarians themselves would have these stripes on their legs. We're told that they (Quarians) have an ecosymbiotic physiology. Plant life on their world evolved a symbiotic relationship with large animals, instead of insects, to spread seeds or pollen. 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").

The plants benefit by having their seeds propagated, while the host animal in turn absorbs something vital from the seeds in the course of transporting them. Something the host animal cannot do without. Take that away, and health problems begin to accumulate.

Mordin Solus on Quarian physiology
I wrote up this dialogue sequence for a fanfic which I doubt I'll ever get around to actually writing (What can I say? I'm a nerd with too much free time on my hands). Still, I don't want it to go to waste. Given the above framework, it outlines the cause of the breakdown (and the cure for it) in whole. Takes place some time after recruiting Legion in ME2:

Mordin: "Three hundred years insufficient for microevolution to weaken Quarian immune system. Cause of breakdown, environmental. Lack of exposure to symbiotic flora, resultant chemical deficiencies during fetal development led to stunted adaptive capabilities."

Shepard: "Come again?"

Mordin: "Example. Human adult height determined by multitude of genetic and environmental factors. Malnutrition will cause stunted growth. Same for quarians. Development and maintenance of healthy immune system depends on exposure to multiple chemicals in pollen produced by plant life native to quarian homeworld. 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. 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."

Shepard: "So if they had their native plant life back, their immune systems would rebound?"

Mordin: "No. Child of human mother who suffers from vitamin D deficiency likely to be born with rickets. Quarian immune system weakened during fetal development by mother's lack of exposure. Epigenetic changes compounded over generations."

Shepard: "Elaborate."

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. Changes are passed from one generation to the next. Human example: if grandparents suffered malnutrition, grandchildren likely to develop diabetes on account of inherited epigenetic changes. DNA unchanged, but genes switched on or off in reaction to stress. Generations of 'malnutrition' caused quarian immune response to grow steadily weak as effects compounded."

Shepard: "So, in addition to the plants, they would need some sort of gene therapy too? Is there any way that can be fixed?"

Mordin: "Can extract DNA, 'unwind' and apply corrections to specific methyl groups. Use tailored retrovirus to re-insert corrected code. Multiple applications necessary to rewrite epigenetic code of entire quarian organism. AI assistance very helpful in gene analysis, fabricating virus... still, expensive. Time-consuming. Anti-rejection medication needed to alleviate risk of autoimmune response to treated tissues until treatment is complete. Must be done on individual basis, but would reverse generations of breakdown. Restore immune systems to pre-exile strength. In optimal scenario, patient could be rid of the suit in weeks. Permanently, so long as healthy levels of exposure to symbiotic flora are maintained."

Shepard: "So a technique exists. But..."

Mordin: "All living quarians afflicted with weakened immune system. Causitive epigenetic changes. No 'healthy' baseline exists from which to determine proper methyl group settings."

Shepard: "So, you could fix it, but you have no idea what it's supposed to look like? I take it you can't simulate what changes would be needed?"

Mordin: "Genetic code not a toy, Shepard. Change one gene, change entire organism. Educated guess could lead to improved immuno response, also increase risk of heart failure. Genetic Paradigms already conducts procedure without baseline. Sixty percent mortality rate. May have seen commercials on Illium. Blind rewrite poses unacceptable risk. Unethical. No, no, no, no. Need healthy, pre-exile baseline to model appropriate changes - would prefer more than one sample, but medical records no longer exist."

Shepard: "They might in one place. I need to talk to Legion."

Modifié par DeinonSlayer, 15 juin 2013 - 02:28 .


#2
Steelcan

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Give me a bit to read this over...

#3
Dextro Milk

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Interesting read. You have my full attention.

#4
DeinonSlayer

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The video I was referring to from my anthropology class was focused on the Överkalix study. I included a link in Mordin's dialogue above. They found that, while the actual genetic material stays the same, individual genes in an organism switch on and off during the course of one's lifetime in response to different stresses. These changes are then inherited by one's offspring. Several diseases have been identified in humans which can be inherited on the basis of epigenetic changes.

So, yeah - if someone has a screwed-up diet, they might be cursing their future kids with health problems.

Modifié par DeinonSlayer, 15 juin 2013 - 02:08 .


#5
Steelcan

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Well to get to the point about quarian/geth interfaces. Cerberus and subsequently the geth did develop organic/synthetic interfaces. Both of these devices allowed for organics to enter synthetic consciousness and interact with the geth.

One possibility is that the geth have developed the reverse technology as well. Allowing synthetic entry into an organic consciousness, this is hinted at by Javik in his dialogue about the Zha'til.

However, this is where things get complicated. Once they have entered the suits/consciousness (ignoring the possibility of numerous minds in one body) how do they "mimic infections"? Infections, either bacterial or viral, are a physiological issue. The geth could not interact with quarian tissue. However Javik again brings this up, he mentions how the AI could alter the physiology of the Zha. The geth could perhaps be doing something similar, altering the quarian genetic code. This is not something particularly difficult to do. Viruses add in their own genetic information to infected cells, it is how they reproduce. The geth could be altering quarian genes to make up for their reduced immune system.

This carries several issues. First and foremost in order for this to be effective, billions of cells would need to be affected. The entire immune system would have to be altered to not only produce anti-bodies, new WBC's (white blood cells), etc... But the immune system would also need to recognize this as a non-foreign tissue so it is not rejected.

SO for currently living quarians the effect might take a very long time for.

That said the geth could alter the gametes. If these cells are altered the offspring of immune enhanced quarians would bear these modifications like any other gene therapy.

"quarian children will grow up healthy and strong, thanks to the geth"

#6
His Name was HYR!!

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I read this.

I have nothing to contribute apart from this temporary bump.

Cheers! [& refer to top-half of sig.]

#7
DeinonSlayer

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@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.

Modifié par DeinonSlayer, 15 juin 2013 - 02:34 .


#8
Steelcan

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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.)

#9
DeinonSlayer

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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.)

It wouldn't surprise me if that was the intent. Evidently the Prothean cycle had their own Illusive Man, and everything... personally, I think that particular trope has been overused in sci-fi in recent years.

Modifié par DeinonSlayer, 15 juin 2013 - 02:45 .


#10
Steelcan

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DeinonSlayer 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.)

Evidently the Prothean cycle had their own Illusive Man, and everything... personally, I think that particular trope has been overused in sci-fi in recent years.

Javik DID say not to trust them, citing the Zha'til as the example from his cycle.

I'm also not a fan of cyclical time patterns, the Prothean VI had me rolling my eyes. 

But a Prothean TIM?  That'd be something to see.

#11
Big Bad

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Well done, OP. I read the dialogue in Mordin's "voice" and it sounded to me pretty much exactly like something he would say.

#12
Steelcan

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Also the issue of side affects.

All this modification could very well cause cancer. I doubt even an AI can accurately predict what the possible fall out of altering nucleotides. Could be a harmless mutation, or it could be disastrous. Some of the worst genetic diseases are cause from just one nucleotide being changed or added/removed. This would be an incredibly risky procedure.

Also the issue of rejection as mentioned in the OP.

The geth/quarians would definitely need an original copy. But DNA degrades rather quickly.

#13
DeinonSlayer

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Steelcan wrote...

Also the issue of side affects.

All this modification could very well cause cancer. I doubt even an AI can accurately predict what the possible fall out of altering nucleotides. Could be a harmless mutation, or it could be disastrous. Some of the worst genetic diseases are cause from just one nucleotide being changed or added/removed. This would be an incredibly risky procedure.

Also the issue of rejection as mentioned in the OP.

The geth/quarians would definitely need an original copy. But DNA degrades rather quickly.

It's certainly not something you'd want to blindly fumble around with. Need a healthy baseline. More than one, then perform an analysis on those to isolate the needed changes to restore immune system function. Even that's an oversimplification - there could be secondary and tertiary effects of trying to apply changes to only that sequence of the genetic code. The needed changes might need to affect every cell in the body, or they might be isolated to whatever their equivalent of lymph nodes would be. Even with the baseline, it'd take a lot of study and trials, but it's better than starting with nothing.

I figure a "gene map" stored on a old computer in the remains of a hospital or medical university on Rannoch, rather than actual preserved genetic material, would likely be the best way to go.

Modifié par DeinonSlayer, 15 juin 2013 - 03:07 .


#14
Steelcan

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DeinonSlayer wrote...

Steelcan wrote...

Also the issue of side affects.

All this modification could very well cause cancer. I doubt even an AI can accurately predict what the possible fall out of altering nucleotides. Could be a harmless mutation, or it could be disastrous. Some of the worst genetic diseases are cause from just one nucleotide being changed or added/removed. This would be an incredibly risky procedure.

Also the issue of rejection as mentioned in the OP.

The geth/quarians would definitely need an original copy. But DNA degrades rather quickly.

It's certainly not something you'd want to blindly fumble around with. Need a healthy baseline. More than one, then perform an analysis on those to isolate the needed changes to restore immune system function. The needed changes might need to affect every cell in the body, or they might be isolated to whatever their equivalent of lymph nodes would be.

I figure a "gene map" stored on a old computer in the remains of a hospital or medical university on Rannoch, rather than actual preserved genetic material, would likely be the best way to go.

The quarians were a space faring race so it is likely they mapped their genome.  However just knowing the nucleotides is only one step.  You'd have to know what is important, what is "junk DNA" what affects what.

Trial and error is obviously out of the question.  Unless Xen becomes the quarian TIW.

Modifié par Steelcan, 15 juin 2013 - 03:10 .


#15
DeinonSlayer

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Steelcan wrote...

DeinonSlayer wrote...

Steelcan wrote...

Also the issue of side affects.

All this modification could very well cause cancer. I doubt even an AI can accurately predict what the possible fall out of altering nucleotides. Could be a harmless mutation, or it could be disastrous. Some of the worst genetic diseases are cause from just one nucleotide being changed or added/removed. This would be an incredibly risky procedure.

Also the issue of rejection as mentioned in the OP.

The geth/quarians would definitely need an original copy. But DNA degrades rather quickly.

It's certainly not something you'd want to blindly fumble around with. Need a healthy baseline. More than one, then perform an analysis on those to isolate the needed changes to restore immune system function. The needed changes might need to affect every cell in the body, or they might be isolated to whatever their equivalent of lymph nodes would be.

I figure a "gene map" stored on a old computer in the remains of a hospital or medical university on Rannoch, rather than actual preserved genetic material, would likely be the best way to go.

The quarians were a space faring race so it is likely they mapped their genome.  However just knowing the nucleotides is only one step.  You'd have to know what is important, what is "junk DNA" what affects what.

Trial and error is obviously out of the question.  Unless Xen becomes the quarian TIW.

It's not necessarily the kind of thing one thinks to grab in the course of fleeing for their lives. We're already making significant strides in that area with our own genome, though. A species several hundred years more advanced than us would probably have that mapped out to a greater extent for diagnosis of genetic diseases and such; still, no change is going to be simple, merely on account of how interconnected it is.

Who's TIW?

#16
Steelcan

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DeinonSlayer wrote...

It's not necessarily the kind of thing one thinks to grab in the course of fleeing for their lives. We're already making significant strides in that area with our own genome, though. A species several hundred years more advanced than us would probably have that mapped out to a greater extent for diagnosis of genetic diseases and such; still, no change is going to be simple, merely on account of how interconnected it is.

Who's TIW?

Quarians did seem more interested in engineering and mechanics over biology.  I'm sure the Salarians would have collected samples and stored them.  They are those "little grey men".

(The Illusive Woman, kind of an unofficial title that the Miranda group has come up with)

#17
DeinonSlayer

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Steelcan wrote...

DeinonSlayer wrote...

It's not necessarily the kind of thing one thinks to grab in the course of fleeing for their lives. We're already making significant strides in that area with our own genome, though. A species several hundred years more advanced than us would probably have that mapped out to a greater extent for diagnosis of genetic diseases and such; still, no change is going to be simple, merely on account of how interconnected it is.

Who's TIW?

Quarians did seem more interested in engineering and mechanics over biology.  I'm sure the Salarians would have collected samples and stored them.  They are those "little grey men".

(The Illusive Woman, kind of an unofficial title that the Miranda group has come up with)

Which brings in the political aspect to all of this... whoever held the last copies of those gene records (Geth, Salarians, whoever) would literally be holding the entire Quarian species by its throat.

Modifié par DeinonSlayer, 15 juin 2013 - 03:29 .


#18
Steelcan

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DeinonSlayer wrote...

Steelcan wrote...

DeinonSlayer wrote...

It's not necessarily the kind of thing one thinks to grab in the course of fleeing for their lives. We're already making significant strides in that area with our own genome, though. A species several hundred years more advanced than us would probably have that mapped out to a greater extent for diagnosis of genetic diseases and such; still, no change is going to be simple, merely on account of how interconnected it is.

Who's TIW?

Quarians did seem more interested in engineering and mechanics over biology.  I'm sure the Salarians would have collected samples and stored them.  They are those "little grey men".

(The Illusive Woman, kind of an unofficial title that the Miranda group has come up with)

Which brings in the political aspect to all of this... whoever held the last copies of those gene records would literally be holding the entire Quarian species by its throat.

The Salarians would not be an ideal choice to be holding those.   They'd probably part with them, for a cost, but they are tricksy....

#19
Steelcan

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If there is a template that the quarians use as a basis, they should use as many as possible. Several thousand ideally. Otherwise they run the risk of intermingling those genes. A population of 17 million that has been isolated for only 300 years should still be genetically diverse, but they should not take risks with this. Population bottlenecks only make genetic problems more pronounced.

#20
DeinonSlayer

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Steelcan wrote...

If there is a template that the quarians use as a basis, they should use as many as possible. Several thousand ideally. Otherwise they run the risk of intermingling those genes. A population of 17 million that has been isolated for only 300 years should still be genetically diverse, but they should not take risks with this. Population bottlenecks only make genetic problems more pronounced.

Absolutely. That's a "must." Although, there is the question of how extensive the degenerative changes are within the genome. It could be the combination of hundreds of epigenetic changes, or there might only be a handful of settings to correct.

Any changes, though, would require a retrovirus tailored to the DNA of its specific recipient.

#21
Steelcan

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DeinonSlayer wrote...

Steelcan wrote...

If there is a template that the quarians use as a basis, they should use as many as possible. Several thousand ideally. Otherwise they run the risk of intermingling those genes. A population of 17 million that has been isolated for only 300 years should still be genetically diverse, but they should not take risks with this. Population bottlenecks only make genetic problems more pronounced.

Absolutely. That's a "must." Although, there is the question of how extensive the degenerative changes are within the genome. It could be the combination of hundreds of epigenetic changes, or there might only be a handful of settings to correct.

Any changes, though, would require a retrovirus tailored to the DNA of its specific recipient.

.  I doubt the quarians will have the technology or money to get this done on a wide scale without VI assistance. 

I guess that means that the quarians will need to rebuild the geth.


the cycle continues
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#22
Phatose

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Wait, so we're back to actually *thinking* about things?

You should not be allowed to make such a change on a Friday night. That's my drinking time.

Anyway, there's one issue I have here.

"No baseline exists".

We're told that Quarians are symbiotic with the native flora of Rannoch.

Thing is, symbiotic relationship work both way. If the Quarians are breaking after 300 years away from the native flora, the native flora should be equally breaking after 300 years away from the Quarians. Either the plant life will have necessarily changed since their pollinators have vanished - in which case, they may now be hostile to Quarian life - or they haven't adapted, in which case they're dead. That would explain all the lifeless deserts on Rannoch, but would also mean the Quarians are going to be dead real soon too.

The third - and I think infinitely more likely scenario - is that Quarians were one of many species who evolved symbiotically, and their loss simply lead to their non-robot-building Quarian equivalent of chimpanzees to take over their ecological niche. Quarians were clearly a planet wide species, so it's extraordinarily unlikely that they were the single species filling that niche. They'll have closely related species the same way humans have the great apes, and on a large scale all of kingdom Mammalia.

So realistically, even if a Quarian genetic baseline doesn't exist, an awful lot of it should be inferred from their close relatives on the Rannoch. Humans and chimps share 99% of our DNA. It can be inferred that Quarians have genetic relatives as similar to them as chimps are to us, simply because if there weren't, the Rannoch ecosystem would've collapsed and they'd have been doomed. And we know from the endings, they aren't.


So, anyway, that brings us to the question of why the Geth can simulate infections and thus allow the Quarians to be suitless on Rannoch for a generation. The answer - at least as I see it - is that they've had to learn how to do that to actually prepare Rannoch for the Quarian return. Which, they claim to be doing.

It's not going to be a simple matter of just cleaning up the chemical weapons from the morning war - that's like thinking you could clear the air and rubble after Alvarez's meteor and the dinosaurs would've been OK. To return Rannoch to livable requires an understanding of the interrelationships between the flora and fauna there.

Which means that the Geth have likely been studying the ecology of Rannoch, it's interrelationships, and in particular the roles the Quarian's close genetic relatives play in the ecosystem for 300 years. They don't actually require pre-exile quarian DNA - they'll have necessarily built an understanding of the entire ecosystem to repair it, and given their claimed goal - in all likelihood theoretically considered what would be needed to re-incorporate the Quarians into that ecosystem. After all, it's not a lot of good to preserve a planet for 300 years for their return, if they're going to show up, take off their masks and kill everything like in War of the Worlds.

Also, please do not ever do this on a Friday again. I should be drunk now.

#23
Steelcan

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

#24
LieutenantSarcasm

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Steelcan wrote...

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


It's a matter of resources, it always is. Assuming that the proper genome maps could be sourced (Geth, STG, Council archives, etc.) , It shouldn't take more than a couple months to rework existing gene therapy production to suit the needs of the Quarians. Both the Humans and Turians have large companies involved in this market, and the STG also have efforts here.

#25
Phatose

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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.

Modifié par Phatose, 15 juin 2013 - 06:42 .