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I like this and bookmarked it, but I have to say that the extended "atom" metaphor is kind of confusing.

"Atoms" are already called elements. "Molecules" are called many things (components, widgets, templates, etc.). And most baffling of all, you're calling apps "organisms"?

I totally get the end-to-end branding thing, and I even like it when it's done simply (e.g. "Droplets" on Digital Ocean).

But in principle, all it's doing is forcing us to learn a new language that isn't adding anything to our understanding or simplifying anything -- all it's doing is maybe, slightly strengthening your brand.