To understand the shortcomings of modern medicine, you first need to understand the shortcomings of tools that are used every day.

For example, most clinicians will order X-rays or CTs because they think it provides some window to the truth.

What they don't appreciate is that these are simply projections, with several layers of data processing.

In the case of x-ray/CT, we use high-energy beams to communicate with atoms.

This communication consists of interactions with orbital electrons, which have characteristic absorption/emission spectra.

This spectrum is then translated into density, which is normalized to the density of pure water at standard temperature and pressure. This standard value is 0 (zero) Houndsfield Units (HU).

Everything else in the body is displayed in relation to this density, above zero (soft-tissue, bone, metal) and below zero (fat, air).

This density metric is then transformed onto a digital monitor, and adjusted to be perceived by the human eye; which has a non-linear perception of light density/grayscale.

And we haven't even yet discussed the fact that living systems are dynamic, and almost all imaging is static. 

Momentary snapshots in time.

As you can see, there are far more to this than simply "looking into the body."

And at every level, there are limits.