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In my opinion, this article is more informative. I can see how he incorporates the Scientific Method, asking questions and experimenting, etc. I like the box idea, but I personally understand better when the example is something real. Like at the end when he uses the example about cream in coffee or perfume fillig the air, because when I think of diffusion I don't think of dots in a box per say, but (like in the book) dye in water dispersing itself over time.
The statement the author makes is logical because we can understand and explain how objects are what they are. In other words, when we know microscopically what objects are made up of we can understand them better.