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In the movie, they said that they were able to wipe off "five to six years" worth of protein from the experiment. I'm not sure how long, even if they are running the experiment for days or even months from what I have heard from the movie, how could they get 5-6 years worth of protein?

The timeline is well, quite a blur even before the bigger time machine plot started. Can anyone explain this to me? Does this mean that they are running the smaller time machine nonstop for 2.5 years or more in the movie?

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The way the time machine in Primer worked, once activated, they formed a closed "loop" between the starting and ending points. An object in the timeline was continually moving forward and backward within that closed loop. In essence, the object would get to one end of the loop -- where the device transitions from "on" to "off" -- and if it didn't exit the box, it would just bounce backwards and travel to the other end.

Each time the object reached one of the endpoints, there was a probability that the loop would collapse on itself, and the object would exit the device. This probability appears to increase the longer the object is inside. From the outside, of course, the object always exits the device, because eventually the probability will reach one, but the object may have made many trips back and forth.

Aaron and Abe calculate that one minute of "outside time" spent in the device, on average, results in ~1340 minutes spent inside, but it could be much higher (probably as many as 10,000 minutes.) That means that, if the fungus secreted protein at a constant rate, in order to accumulate 5 years worth of protein would only take, on average, about a day and a half, and could take as little as 4 hours, in the machine. In the movie, it actually takes about 5 days to secret 5-6 years of protein -- more than enough time.

The breakthrough in using the box was figuring out how to force the channel to collapse on demand from inside; this is how the humans were able to use the device without aging decades at a time. They could compute exactly when they were about to reach the appropriate endpoint and exit at will.

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    Actually, the reason Abe and Aaron didn't spend years in the box was simply that they had the power to leave when they wanted. They didn't have to force the collapse of anything. They simply timed it out so they would exit at the proper external time. So Abe and Aaron exit halfway through the loop, which puts them at the moment the boxes were activated, which is also when the fields involved are weakest, making it the least dangerous time to exit, as well. The toy, however, just sits there until it gets pushed out by probability, as you said, which is generally after many complete trips. – John Sensebe Aug 15 '16 at 1:39
  • Thanks for the answer. Can you elaborate more on the probability thing? I'm not really good at math. On your last paragraph, how were they able to "force" the channel? I can't remember all they talked about but what part of the movie they discussed on that? – Chronos Aug 15 '16 at 2:03
  • Also, I understand from your first unedited answer that you said the smaller device has many 'iterations', so it is a faster time machine than the coffin sized one, is that correct? Because, from my understanding of the movie the object would need 2.5 years in coffin sized time machine to get 5 years worth of protein, time forwards 2.5 years + time backwards 2.5 years. So I was confused in the smaller device it just took days. – Chronos Aug 15 '16 at 2:10
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    @Chronos no. all of the devices worked the same. if they had put an inanimate object in a bigger time machine it would have worked the same way. it would have only needed a day or so, on average, to age 5 years. The only reason the bigger boxes don't do this in the movie is because there's a live person inside who has more control over it than an inanimate object. – KutuluMike Aug 15 '16 at 2:45
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    @KutuluMike - That's not supported by the film. Abe: "Aaron, the WeebIe's stupid. It can't move. Even if we ere to put the Weeble in at point B, it's still going to bounce back and forth until it's kicked out at the B end. But if it were smart, it could enter at the B end and exit at the A end before it flips back." Then they discuss how to make a box big enough to contain a person. – John Sensebe Aug 15 '16 at 13:45
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The actual line from the film was

There's another way to secrete that much protein. Do it naturally.

To get the same amount of protein that we have, the amount that I was wiping off every five days...and five days later it would accumulate... he says it would take about five to six years.

So the machine was only running for about five days in total, during which time the contents of the box aged 5 years.

Interestingly, this shows that the progression of time was both linear (time literally sped up for the contents of the box) and recursive (time inside the box would move forward and backward relative to the outside world).

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