Matter the physical is contrasted with spirit - the non-material or non-physical.  Spirit is what is real but is not physical.  It is not just an idea.

What is a matter? The obvious answer is that something that has mass and is detectable if there is a person or machine there to detect it is material.

Yet this is challenged. Matter is thought to be ultimately comprised or composed of photons which are like spirits - beings without mass or materiality.

The fact is that massless is not the same at all as being spirit and/or non-material. Reality is not composed of non-material particles!

Spirit is without material component and cannot be measured. Spirit is massless but it does not follow that the particles that make all things which are massless are spirits!

If we were able to get small enough we would sense those massless entities so they are capable of being measured in some way. The particles are material in some way for they can affect each other. We are talking about interactivity. This is the main sign that something is of a material non-spirit nature. If protons and nuclei were spirits they would not need electrical forces to help them connect with each other

If spirit is real why cannot microscopes observe it like they can protons?

Particles have spin and mass - two things that make them material. It would seem that any particle that does have only one of these is the nearest to spirit we can imagine.

Protons like electrons and neutrons can spin. A photon is a particle with spin but no mass. Higgs boson is a particle that has mass but no spin. Yet it is not a spirit or anything like it either.

The entities are strange and ghostly but they are still real. There is no need for the spirit idea. Saying some spirit made all things from nothing is strange for why not say that massless particles are the ultimate reason why anything exists?

Nature tells us that you can have what to all intents and purpose seems to be spirit but is not. Spirit as a hypothesis is totally an accessory. It is not needed. Nature teaches us about the "substitute" - that is massless particles so we can assume that spirit is only in our heads!

Science finds consciousness is a mystery.  There is a problem understanding how the brain can do this.  There is even the sensation that you are living in the brain.  It is like you are observing from inside yourself.  Consciousness is an observer but that does not mean we know how it does it. None of what we have written means we should regard consciousness as ultimately non-physical. 

First of all, once we start talking about non-physical spirit we are talking about what cannot be detected or understood.  If it cannot be detected then it could be a different kind of physical we do not detect.  Using spirit to get out of the problems of materialistic views of reality does not work and shifts from one problem to a worse one.  Ethically it is just cheating. 

Secondly, nature at its most basic level is strange anyway so we cannot presume that consciousness is some kind of magic or miracle.  What looks like it is supernatural is not necessarily supernatural.

Thirdly, we have a reason for regarding consciousness as a mystery - it lies to us and science can be helpless in the face of lies.  It pretends that you are not your body and your body is your house. It is a degrading illusion. 

Fourthly, it can be argued that spirit and massless particles have no important difference.  Massless particles cannot have a memory, understanding, will or consciousness or even any one of these powers of the human soul which we are told is real by the Catholic Church.  For the same reason, white cheese has the same uses as light yellow cheese and we learn about one in the absence of the other, we can be sure that massless particles are the only "spirits" you are going to get.  You learn from a non-material soul about a massless particle and vice versa.  If a massless particle cannot have soul abilities then there is no need for the non-material soul idea and it cannot have the abilities either.  A soul if it existed is only invested with memory and understanding for believers don't want to believe the will is without rhyme or reason.  Memory and understanding are not mysteries as our physical brain structures show.  A massless particle shows that the spirit idea is unnecessary.  If the concept of spirit was needed by metaphysics and any thinker in the past it is not today.