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Amoebae have a very complex 3D structure; check out some SEM images, like http://www.sciencephoto.com/search?subtype=keywords&searchst... or http://www.photomacrography.net/forum/viewtopic.php?t=21719 . Moreover, most of their molecular machines require third dimension to work.

Sure, but if we're assuming there's life in two dimensions, the amoeba's digestive system is much simpler than zipper organs.

It seems so on a first glance, but if you think about how this 2D phagocyte can be formed (especially on a macroscopic scale) and how would it interact with other structures it becomes much less obvious.

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