Why doesn't changing the spin state of a proton or electron impact the integrity of matter? I thought that spin was an intrinsic property to electrons and protons that related to characteristics of an atom, so I'm not clear as to how applying an electromagnetic field, such as in the case of an MRI, to change the alignment of protons does not have an impact on the atomic structure of the hydrogen making up the human body? To expand on that idea, if we assume that consciousness is in part based on the configuration of the atoms that make up the neurons in the brain, how would changing the characteristics of those atoms not alter who you are?
I guess what I'm asking is, if atoms of a particular element are essentially identical, what is the significance of spin from a practical standpoint?
 A: 
I guess what I'm asking is, if atoms of a particular element are essentially identical, what is the significance of spin from a practical standpoint?

There  is confusion in this statement:
Spin is a vector quantity, it has projections in spin space, and depending on the experiment the projection can be changed, if energy is supplied to change an energy  level in a lattice of atoms.
This is how an MRI works:

Certain atomic nuclei are able to absorb radio frequency energy when placed in an external magnetic field; the resultant evolving spin polarization can induce an RF signal in a radio frequency coil and thereby be detected. In clinical and research MRI, hydrogen atoms are most often used to generate a macroscopic polarization that is detected by antennas close to the subject being examined. Hydrogen atoms are naturally abundant in humans and other biological organisms, particularly in water and fat. For this reason, most MRI scans essentially map the location of water and fat in the body. Pulses of radio waves excite the nuclear spin energy transition, and magnetic field gradients localize the polarization in space. By varying the parameters of the pulse sequence, different contrasts may be generated between tissues based on the relaxation properties of the hydrogen atoms
therein.

Polarisation gives the direction of the spin but does not change the atomic and molecular composition of the atoms and molecules in the cells. There is no permanent impact because the energy levels are very low and nothing changes in the molecular composition except temporarily the spin orientation which will relax back to the lower energy level once the observation is finished.
A: 
I thought that spin was an intrinsic property to electrons and protons that related to characteristics of an atom,...

Subatomic particles have a magnetic moment and they have a charge (not for neutrons). The spin is correlated with the magnetic dipole moment and is more related to the deflection of moving particles in an external magnetic field, while the magnetic dipole moment is the more imaginable term for the interactions in atoms and molecules.
The Pauli exclusion principle as well as the Hund’s rules are best understandable if you use instead of the nebulous spin simply the magnetic dipole as the cause of the behavior.
Take it this way:

*

*The electric charges of the subatomic particles are the glue that holds the atoms together.


*The magnetic dipoles are the puppet threads with which atoms, molecules and materials interact as a whole.


*By applying an external magnetic field, one influences the subtle alignment of the magnetic dipoles of the particles within the atoms and between the molecules and the material as a whole
At very low temperatures, the photon exchange between the atoms and thus their chaotic motion is suppressed and some materials form a common magnetic behaviour known as Bose-Einstein condensate. If the magnetic dipole of a molecule or compound is stronger, then the temperature could be higher, for which we discover supercharacteristics.
The other way around, at very high temperatures the electric “glue* breaks and the ionized subatomic particles under some circumstances could form magnetic filaments.

...so I'm not clear as to how applying an electromagnetic field, such as in the case of an MRI, to change the alignment of protons does not have an impact on the atomic structure of the hydrogen making up the human body?

Even very high magnetic fields do not break up the inneratomare structure. When the external field is switched off, the magnetic orientations relax back to their original positions.

I guess what I'm asking is, if atoms of a particular element are essentially identical, what is the significance of spin from a practical standpoint?

Replace the term spin with the term magnetic moment and you will have an easily understandable idea of what is happening.
