tireless thoughts for sleepless nights

The following is a recollection of a journal entry I made late one night when I couldn't sleep.  The thought process is similar that my generation however this particular thought seems to go overlooked.  Why that is I have no idea, I just know that it is indeed overlooked.  Atoms can be expressed quantitatively, in that they have an atomic mass, orbit, and energy levels.  In short, this building block of matter can be expressed through numbers and formulas.  This poses some interesting prospects.   If the building block of all that exists can be expressed through such simple means (albeit complicated formulas), then what does that say for the rest of existence?  Using these facts it seems as though these formulas should be the basis needed to explain everything in life, thus eliminating the need and purpose of a god.   However, this also creates a flaw in the fact that there are things that cannot be expressed quantitatively.  If all things are made of atoms, then all things should have the properties to be expressed quantitatively, no exceptions.  Therein lays the problem though, as this is not always true.  Exceptions to this law or occurrences commonly known as miracles have happened often throughout history and continue to happen up to this very day.  This creates a problem for the scientific outlook on life.  Exceptions to rule discredit these theories, and through that discredit atheistic beliefs.  How can anyone, scientists and atheists alike come up for a legitimate argument for things that cannot be quantitatively comprehended?  It’s just not plausible for one to think so. It is plausible to think that everything should have an explanation, whether that explanation comes through quantitative analysis or belief in an omniscient deity is strictly up to the eyes of the beholder, however it is my belief that there is line where one crosses over into the other and once there, explanations become concrete.  It is, impossible to quantify say a person who survives a bone crushing fall, or animals doing things that defy there basic instincts.  On a different tangent, energy is quantifiable too as explained by Einstein through E=mc² , where he states the particle level relationship between matter and energy.  If energy is quantifiable as well then this should seemingly cover all loose ends right?  Wrong, there are still miracles that defy this as well.  This thought process should prove the existence of some form of divine intervention, and is set out in the thought process of my generation.  However, for some reason, this has gone unlooked.