We cannot actually see what things are. In a sense, we can only see what they are not. This is the nature of sight.
You see, we see photons that impact the photoreceptors of our retina. When the photon is absorbed the energy is sensed and then information set to the visual cortex and it’s auxillary neural regions to form a perception. This process of sight means we are understanding the photons that came from something, not that something itself. We can infer qualities of the source of the photons, but never can we “see” it in any other way than the disembodied photons. This leaves an inherent mystery to the nature of things that are not visible; i.e. that are not photons. It also leaves us with a sort of indirect version of reality. The underlying matter that photons fly from is not our view of the world. Rather, our reality with respect to matter is just radiation relevant to that matter.
When scientists use machines to image atoms and molecular structures they are still bound to this indirect reality. For instance, an atom is smaller than the wavelengths of light we can see with our photoreceptors. The visible spectrum ranges from 380 to 700 nanometers; violet to red, respectively. An atom is around 0.1 to 0.2 nanometers. Essentially, scientists use photons or electrons of much smaller wavelengths than what’s visible to us – such as x-rays with a range of 0.01 to 10 nanometers – to interact with these small scales, then use machines and analysis to convert that to the visible light scale and display it on a computer monitor.
Ultimately, we will never see matter itself because we can only perceive a small range of matter’s radiation.
To add another aspect to this perspective, everything we see has two layers of lag. The first, which is negligible, is that light is not instant. It interacts with electrons and travels through spacetime at no more than 670,616,629 mph. On Earth, that’s rounded off to instant, though. The serious lag is biophysical. When visible light interacts with a photoreceptor it takes time for the neuron to send the first signal down it’s axon, then for the resulting cascade of neural actions to bring that light into sense then into perception. This duration can be on the order of 50 to 150 milliseconds or more, depending on the stimulus and conditions.
So not only do we indirectly see the universe via radiation, but our processing of that speed-limited radiation is delayed. By the time we make an assumption about matter based on it’s photons, it’s mysterious nature is already doing something different than what those photons are telling us.