Algodoo

i like it
your words "It was originally going to be a single, simple machine that simply were to convert a given binary number into a decimal number. " remember me of startrek video, called v'ger,
http://memory-alpha.wikia.com/wiki/V%27ger
which is a vessel original planned to collect information and bring it back to its creator, but on its way it gained much more power and abilities and in the end even gained a life of itself

This is quite interesting and is rather fun to watch it operate!

Now the bad news. It has a lot of problems. For starters, the plungers that you made for resetting the total and for starting the calculations are so touchy and unstable that they fall apart if not extremely careful when pushing them. And generally, the "instruction manual" for operating this device needs a lot more detail in how to work it. I destroyed the machine a number of times while trying to figure out how to make it work. It is not at all intuitive.

The plunger (button) that resets the numeric total should also reset the input values to all zeros. That way, the users won't need to manually reset the input switches.

Also, (and this is true for any scenes that people make) if you know that your creation has a flaw or a problem, rather than explain to people how to work around those flaws (such as, "grab the purple box directly"), you really should FIX the poor design issues so that they work correctly, rather than to put the burden on users to have to work around your problems by manually grabbing or moving things.

Disable those darn Algodoo CLOUDS in scenes where it doesn't make sense to have clouds constantly floating by! Sure, any user can do that themselves, but they should not have to since the scene creator can do that only once and it's done for everyone!

Suggestion: Decide who you want your users to be. What I mean by that is, for a technical or esoteric subject like this type of scene is used for, you will limit the people who can figure it out and know how to use it, to only a handful of educated users. But if you want a wider range of users, including young folk, and users with a limited education, then you must dramatically improve your instructions, and also make the device a lot more "user friendly" and intuitive to operate.

I hope that you take these suggestions as being helpful and constructive. They were not meant to be insulting or criticizing in any manner.

nice work