Cells vs. Animals: Is Cellular Machinery an Artifact of Experimental Methodology?

In high school, I was fascinated by the living cell: this building block of life appears as a tiny, finely tuned factory consuming and producing various substances, all of that being orchestrated by a clear, rather mathematical system of pathways. Take, for instance, one of the most amazing things that happen to a cell: division. Division is a very complex process consisting of apparently clearly defined phases, separated by checkpoints verifying that the previous phase has was concluded properly before transitioning into the next one (see, for example, [0]).

Human and animal physiology didn't attract nearly as much, however (I didn't really know plants had a physiology too at that time). Indeed, where the cell is mechanistically precise, macroscopic living organisms seem pretty much approximate and shaky: in the cell, everything is organised by proteins, synthesised according to the cellular program, the DNA.  The regulation of our bodies seems to be quite less centralised and uniform.  From a high-school student's point of view, the cell clearly wins in what concerns clear regulation of processes.  And then, take a look at the brain : this horrible soup of neurons, axons, and various supporting cells, which appears to only have some superficial, rather macroscopic structures, and looks quite messy at smaller scales.

Clearly, the presence of various intertwining signalling mechanisms in higher vertebrates and the very complex structure of their brains allows them to be very adaptable.  Later on, I learned that a lot of the fabulously clear organisation of the cell is actually just a slice of the whole picture of the immensely complex processes happening inside it.  Still, the terminology around the living cell is way more mechanistic than that concerning macroscopic organisms.

Is it because macroscopic organisms, being extremely large and complex instances of cooperation between the already very complex cells, just cannot (structurally) be so well organised as the cell, which is a clockwork of biomolecules?

Or rather, is it that, due to the lack of direct, naked eye, unintrusive observations of the microscopic parts of the cell, we are tempted to invent the missing details to fit the mechanistic explanation, so very natural to us?

(The question about whether the cell is a machine or not was originally posed by Nicolas Glade.)

[0] Paul Nurse. A Long Twentieth Century of the Cell Cycle and Beyond. Cell , Volume 100, Issue 1, pp. 71-78. http://dx.doi.org/10.1016/S0092-8674(00)81684-0