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I don't believe he "ate" them.
He just breathed the dust in.
"He explained that he contracted the illness when, in one of his wild ideas, he was grinding moon rocks together in the name of science in order to form a new type of substance called the 'Conversion Gel', most likely named due to its ability to serve as a portal conductor and allow portals to be placed on any surface. As the symptoms of his terminal illness became more severe however, he decided to re-purpose the 'conversion gel' to create new portals that would hopefully leech the poison out of his system."
How does one breathe in a gel.
He breathed in the dust when he was grinding the rocks up.
They don't really clarify and it is Cave Johnson, so it's perfectly possible he could've done both, it's just up to speculation really.
Chell didn't had the same problem because of that stuff she has on her legs [which probably absorbed all the shock]
Just saying.
They left GLaDOS with the infinite ability to test, however there are a few things that mean it's not Impossible.
#1 What happens to Chell?
Being in such a crazy world as that of Half-Life surly means Chell won't just find a husband and settle down. That's a massive cliff hanger!
#2 If Chell could do, couldn't someone else?
With the thousands of now in GLaDOS' control test subjects, one of them would be bound to start their own rebellion like Chell did. Who knows, maybe you have to go into aperture and save GLaDOS.
#3 Other cores and versions of GLaDOS.
In co-op it was revealed that prototypes of GLaDOS existed, and in Portal 2 we see that there's an almost endless sea of cores to use. It wouldn't be surprizing if there were some civil war going on in Aperture.
These are just some suggestions that it's possible.
Well, personally, Valve kinda ruined Portal 2's story with the PTI. They not only wrecked the prat where Chell ever existed, they also revived Cave Johnson and made craploads of alternate worlds in the Multiverse. So if there ever would be a Portal 3, I'd count on it continuing from one of those test chambers. Maybe in some years, Valve's gonna have a contest with who made the best tests the last 3 years, and put them all together in a compilation, and make it's own story for it. OR they'd go ego on our asses and make their own levels and continue off the Perpertual Testing Initiiative's "story". That's also one of the possible starts of a sequel...wait, and it also PERFECTLY connects with Thinking with Time Machine, since maybe (I haven't actually finished it, I'm still on the first levels) Greg (Who could very well be Chell's father, since he worked at/was a test subject at Aperture Science), went back in time to save Johnson from dying, and instead told him about the Multiverse? GLaDOS' statement of her parents not loving her could be right, and Greg could've very well thought she was a mistake, and also made an abort in the past, AND since Cave never died, GLaDOS was never made either, which could also mean that Caroline WAS Chell's mother anyway. But the chance of that part being true is very small...anyway, Thinking with Time Machine could just as well connect with the main story. AND Half-Life 2: Episode Three.
...illuminati confirmed?