Cells are not factories. Nor do their parts in any way resemble gears. And despite the benefits of using a concept like cells-as-factories and similar analogies as mnemonic learning aids, failing to describe the limitations of those same analogies is likely to result in significant misunderstandings.
Perhaps the most profound difference between a factory and a cell is the way the latter came to be. Cellular life evolved through billions of long years and countless generations of creatures facing natural selection pressures. The end products only hint at that long evolution of fits, starts, niche fills, and failures.
Humans can build factories in just a few years or months. And new factories don’t spring from the wreckage of old ones. We clear the land to make them.
The tendency to mechanize biology feeds teleological arguments as well, which can be corrosive to science education. As the theologian William Paley reasoned in 1802, if we find an object that has a complex design, doesn’t this indicate the actions of an intelligent designer?
Yet, to have a complex structure is not equivalent to, and does not require, having a designer.