From Catholic to Naturalist
In this paper I will give an outline of some of the reasons that have led me to give up belief in God and the supernatural. After that I will give an outline of the reasons that led me to accept Metaphysical Naturalism. This paper is not meant to be either exhaustive, as in covering the totality of the reasons that have led me to give up belief in God and the supernatural, or technical, as in dwelling into deep theological issues and arguments. Rather, it is meant to be simple and easy to understand.
Part I. The road away from Catholicism
God and The Universe
God's activity in the world
When we open the Bible, we see affirmed across it's pages that a great number of events are the result of God's direct activity. Such things as the forming of the creature within the womb, forming the tree from the seed, good or bad health, victory or loss during war, rain leading to good or bad vegetation, pregnancy, etc. All these, we are told, are the direct result of God's activity--and in some cases, the direct consequence of being either obedient or disobedient to God.
Yet today, none of this events are said to be the result of God's direct activity, at least not in the same way as is claimed in the Bible. Why? Because back in that day, the full process by which such events occurred was unknown, there was a certain mystery to them, which men attributed to God. But these days, since we know the processes by which all of these events occur, we no longer attribute them to God. In fact, most Christians today would be shocked if you told them that God directly caused it to rain or directly caused any of those things which were once believed to be the direct result of God's activity.
When reading the Bible, we also see a trend when it comes to miracles and God's activity within the world. If we start from the book of Genesis and read all the way through the book of Revelation, one will notice a decrease in miracles and instances in which God intervenes in the world as one progresses from book to book. One goes from Moses, who turned his staff into a serpent, divided the sea, and spoke to God as if one spoke to a human being, to Paul, who performed few miracles, and who apart from having a vision did not speak to God like Moses did.
This trend continues as we move to more recent times. In spite of Jesus telling his disciples that they would be able to perform even greater miracles than he did, nowhere do we see Christians turning staffs into snakes, parting seas, calming storms, causing the shadow of a sun dial to move backwards, etc.
We seem to have moved from an era where miracles where commonplace, and where angels paid us regular visits to let us known what God wanted, into an era where it looks as if none of that actually takes place.
Of God and Gaps
Part of this may be attributed to the knowledge we have obtained about the universe. Most of the events that were credited to God have been explained in terms of natural processes which find no need to invoke God as an explanation. As a result, the instances in which God was believed to intervene in the universe have been dramatically reduced as the gaps in our knowledge have been filled by the natural sciences.
Contrary to the claims of fundamentalists, the issue is not that science is biased against invoking supernatural explanations when describing phenomena within the universe, rather the issue is that such explanations are sterile and simply do not offer any insight or useful information.
As an example, imagine that we describe how the the circulatory system functions. We outline all the processes that are involved in the workings of that system and we are able to account, with purely natural processes, for the workings of the entire system. Now, what room is there for a supernatural explanation? None. The supernatural explanation may be something like, "God created the circulatory system" or something along those lines, but that explanation tells us nothing about how that system works.
Supernatural explanations are also sterile in cases where the natural process is not yet fully known. Supernatural explanations shed no light on the available facts, attempting instead to fill a gap in our knowledge with a miracle that instead simply covers the gap with an unknown mystery. Yet, the testimony of history tells us that such gaps, instead of being filled by some unfathomable mystery, have been gaps in our knowledge which have been filled--not by appealing to supernatural explanations--but by further inquiry and investigation, and by appealing to purely natural explanations.
God, Science and Methodological Naturalism
As a result of these considerations, I came to believe that the failure of supernatural explanations to account for observed phenomena within the universe was simply because people who used the god-of-the-gaps argument were thinking of God as if he were a process within the universe alongside other natural processes. How could it be that if God created the universe that he could also be a process within that universe? He transcends the universe and sustains it, or at least that is what I believed. So, people who appealed to the god-of-the-gaps-argument were using the wrong tool for the job, so to speak.
This led me to believe that, part of the design of the universe was it's intelligibility, I came to believe that we would be able to explain everything we observe within the universe by appealing only to natural causes. So, I came to hold the position known as Methodological Naturalism, which says that, when studying the universe, science appeals only to natural causes.
At this point, to me the evidence for God was not to be sought in the areas where we lacked an explanation. I was certain that we would eventually find explanations, thus invoking God for the unknown became unnecessary. To me the fact that science could explain by appealing to natural causes was actually evidence for God; the intelligibility of the universe and our ability to study and understand it was to me an indication that we were made in God's image and were able to understand how God worked.
With that came a shift that moved God from being active in some particular process, such as those attributed to him in the Bible, to God being the sustainer of all laws and processes within the universe, the ones we already had an explanation for and the ones we did not have an explanation for yet, the ones we knew and the ones we did not knew.
No process in the universe attests to God's activity within it
In short, God sustained everything in existence and was not responsible for only some particular process but for all processes within the universe. This all sounded good--for awhile. But when I sat down and thought about it, I noticed that this simply kicked God out of the universe. This approach simply made God's existence undetectable, there was no means for knowing what God does, no particular process by which I could say, "look this is God working in the universe!" Under that view, God's existence or nonexistence simply made no difference. All I could say to the skeptic was "well, something exists then that must mean God exists," or "the universe has X property so that must mean God exists." But none of that was convincing--not even to me. It was all really subjective and more a matter of interpretation than anything else.
That, coupled with the fact that no process attested to the supernatural activity in the world, led me to realize that there is not a single process or event in the universe that we can directly attribute to God. There is nothing in the universe that we can objectively and firmly say is the direct result of God's activity. We have, so far, found no evidence for God's activity in the universe. There is simply no evidence for any of these, rather there are just natural processes working in the universe with no indication of supernatural intervention. That is the only thing we find when we explore the universe. Yet, one is supposed to believe that God is active, guiding everything according to his divine will, answering prayers, performing miracles, etc.
Sure, one can say that God works through secondary causes which are natural causes and processes, but that does nothing to remedy the problem because it still makes it impossible to know whether or not God is active in the world.
The Bible and Science
The Bible as a source of truth
I now turn to the Bible, which is said to be divinely inspired by God and which claims a number of things that God has done, such as how he created the universe, and also claims what sort of things we can now and in the future expect to see God do within the universe.
Catholics hold the Bible to be divinely inspired and without error, this because God who inspired it cannot ever assert anything that is in error. Thus, we would be led to believe that the Bible would contain an accurate description of the universe, how it works and how it was created. Granted that the Bible need not be a scientific textbook, but whatever it presents, then, must be in accord with what we find in the universe. After all, since it is the same God who created the universe and who reveals himself in the Bible, and since God can neither err nor deceive, then we can expect that both the creation and revelation will agree and be in complete harmony, without any need for additional rationalizations.
Science forces Christians to reinterpret the Bible
But this is not what we see in the world today or what has happened during the entire history of the Church. The early Christians such as Paul, Peter, John, and others, were all limited to the scientific knowledge of their day, and their writings clearly reflect that. Augustine, for example, believed in a young earth that during his day had not yet reached an age of 6,000 years. Thomas believed that the earth was fixed and that the moon and sun orbited around the earth. All this was based on the scientific knowledge of their day and is reflected in their writings and in the Bible itself. Pope Leo XIII in his encyclical Providentissimus Deus admits this, both for the apostles and for the fathers of the Church.
This realization led to the metaphorical interpretation of several parts of the Bible. According to Augustine, the literal sense is to be held unless it is not possible to sustain it on rational or evidential grounds, in which case a metaphorical sense is allowed. Now, why would there be need for that when it comes to the Bible, which is supposedly inspired by the same God who created the universe?
In many instances where science makes some new discovery that seems to contradict the Bible, Christians either change their interpretation of the text to twist things so that the new evidence does not contradict the Bible, or they simply appeal to the fact that the Bible was not meant to teach science but only how to obtain salvation. But there is a serious problem underlying this sort of thinking: if the Bible is not meant to be taken literally, then the logical consequence is that there are no means to determine what the Bible really says. Also, if the facts of science contradict what the Bible clearly says and the Bible can only be rescued from falsification by appeals to metaphorical interpretations, then this places the biblical creation story on the same level as other creation stories that Christians brush off as mere superstition.
Reconciling evolution and the Bible
Perhaps the most controversial issue dividing Christians today concerns the theory of evolution. There is good reason for that, of course: if there is anything that evolution has done, it is to debunk every single creation story that has ever been written. There is simply no creation story I am aware of that describes anything like evolution. What this means is that, if evolution is fact, then all creation stories that have been written are false.
This issue is also a good example of a scientific theory contradicting a literal reading of the Bible. As a result, Christians are divided between those who reject evolution and take the Bible literally, and those who accept evolution and take the Bible metaphorically.
Now which side is right? First there are those who adhere to a literal interpretation of the Bible, who believe in a young earth and deny evolution. While it is not the purpose of this paper to present the evidence for evolution, it is safe to say that Christian "creationists" are contradicted by the evidence in favor of evolution, which has accumulated for about the past two hundred years from different scientific fields, all of which points to an old universe and to the fact that evolution, both micro and macro, has occurred.
Then there are those who accept evolution and an old earth but who hold that Genesis can be interpreted as a metaphor, or that it can be considered mythological, only meaning to convey religious truths. But these believers fall into the same trap I described above: that they reduce the Bible to the same level as any other religious text, lacking scientific evidence to support it and elevate it beyond the others. Of course, any religious text can convey religious and moral "truths," but what religious or moral truths one gets from such texts is determined more by how the reader interprets the text than by anything the text actually says, especially when a metaphorical interpretation is used.
The Bible does not tells us how God created the universe
Where does all of this lead? A literal interpretation of the Bible is also refuted by the evidence. A metaphorical interpretation makes what the Bible says of no consequence. Either way, the Bible simply does not tells us how God created the universe.
Since Christians are forced by science to not take the Bible literally, there is no way to use the Bible as evidence that the God of the Bible created this universe. The evidence from the universe clearly contradicts the description the Bible gives about the universe. The God who created this universe--if there is one--is not the God of the Bible.
The Religious Experience
Living as a religious person
One of the many charges made against people who are critical of religion is that they rely too much on logic and reasoning and want to find God by reading or resorting only to arguments. They say that, instead, God must be found through religious experience, that one must not just know about religious things, but one must also lead a religious life. As a Catholic one must pray, go to Mass, say the rosary, go to confession, receive communion, be baptized, confirmed, etc. These things are said to give one the grace necessary to obtain salvation, to put one in communion with God.
To put things in perspective, under Catholicism one must do these things in order to avoid Hell, the everlasting punishment of those who die in a state of mortal sin or original sin. That being the case, it would be fair to expect some tangible evidence of God or the supernatural.
My experience as a Roman Catholic
During my time as a Catholic, I simply found no evidence for there being a difference between a state of original or mortal sin and a state of grace. Certainly one might believe that one state leads to hell while the other leads to heaven, but if I were to stand two people in front of me, one representing each state, I would never be able to tell the difference between them--and when it came to their health and physical state, neither could they. The only means by which they and I could know the difference would be by their telling me if they had recently committed a mortal sin, and this, of course, could be forgotten. While forgetting to confess a mortal sin does not leads to condemnation, it serves to point out the fact that there is nothing objective affecting the individual who is in a state of original sin or mortal sin; everything is a subjective feeling of guilt, of having offended God--something that almost any believer feels in one way or another.
If I were to take the person in a state of mortal sin to confession, and this person had the willingness to confess and be forgiven, when this person came out of the confessional after having been absolved from her sins, you would notice no difference in the person. If the person had a cold or fever, for example, the person would come out of the confessional with the same cold or fever. The only difference would likely be a subjective feeling of having done "right," of being absolved of sin. But that again is something that nearly every believer feels in one way or another, and it is not exclusive to confessing your sins at the confessional.
On a similar vein, one would not likely be able to tell the difference between a person right before baptism, with the stain of original sin--something for which she is worthy of hell--and her state of grace after baptism. She would have the same abilities she had before baptism, the same knowledge, the same sickness (if any), the same bodily functions and compositions; in short, there would be no difference other than, again, a subjective feeling of having done right, of feeling relieved from sin and having entered the Church. But again, this is something that nearly every believer feels in one way or another, and it is not exclusive to being baptized.
Given the consequences everlasting torture and damnation that not doing these things is supposed to have, the lack of tangible evidence even after one decides to do these things is quite perplexing.
Miracles, visions and other supernatural events
Miracles, if they happen at all, are very strange occurrences. They do not occur regularly. If they did, we would have plenty of documented cases. Given the means we have to document them, such as surveillance cameras, the fact that we do not have a single documented and convincing case of a miracle should tells us something about the reality of said miracles.
There is a factor that plays a huge role when it comes to miracles, and it is a cultural one: all miracles are interpreted in light of the religion or culture in which they are said to occur. Not once will one find a miracle of Jesus appearing in a country that has never heard of him and has never had contact with Christianity.
Not only do people from different cultures interpret miracles differently and associate them with their particular religion, but also people from the same culture come to disagree about really happened. Thus, one is left with a series of confusing and contradictory opinions. If there were a single God revealing himself, then he would prevent cultural influences to give the miracle he performs in a particular place a different and contradictory interpretation than another miracle he performs in some other place. But this is not what we see; what we see is a claim that miracles occur and these are associated, as expected, with the particular deity of the culture in which the miracle occurs.
There is another issue: none of the miracles that are said to occur are useful in anyway. A person getting stigmas is not useful, a statue with tears of blood is not useful, a burning host is not useful, a face of Jesus on a wall or in the clouds is not useful, etc. None of these alleged miracles offers anything that we can use in the world; they offer no new insight about the world or what we should do. Yet, this is assumed to be an all-good, wise and powerful God revealing himself to us.
To think that God, when he does reveals himself, simply makes a statue shed tears of blood, or some similarly useless thing, is quite hard to understand.
Religion does not provides a means for knowing the supernatural
From my experience, religion provides no clear and objective way by which one can know whether or not God or the supernatural is real. All one can experience is a subjective feeling of having done something, which is more the product of the framework that your worldview provides than it is something objective by which one can experience the supernatural. These feelings are also not unique to any particular religion, or even to religion, per se, but can be obtained in many different ways outside of religion. Also, these feelings are not identical even amongst all believers in the same religion. There is no specific religion that objectively provides some particular experience better than the others; it all depends on the individual.
I believe that this lack of objectivity is quite problematic. Even if we overlook the fact that we do not see anything tangible occur that we could consider supernatural, and we rely only on feelings, we still can't get anything tangible and objective that would allow us to determine whether or not an individual is interacting with the supernatural in one religion and not in another.
The Catholic Church
Obeying the Church
I have no problem with the concept of obeying some authority in religious matters. If it were to turn out that I have to obey the Church in matters of faith and morals, then I would have no problem with doing that. However, I believe that some evidence must be given that justifies the demand to obey the Church in matters of faith and morals, and I also believe that this evidence is lacking.
Obeying the Church forces an individual to mold and change his life in accordance with Church teaching: changing his beliefs, giving up certain things he used to do, doing other things that he did not do, and so forth. Again, I would have no problem with something like that, but I believe that some evidence must be given that justifies the demands on the individual.
To provide this evidence, an appeal is often made to the Church's continuity over the ages and her apparent immutability: how she has remained teaching the same things across history, without being swayed by the spirit of the different times in which she has found herself in. This is said to be a testimony of her divine origin and the protection that God provides to his Church. While it is true that the Church has been fairly consistent across history, there are some happenings that undermine the Church's claim to infallibility, immutability, and a divine origin.
Confusion within God's house
What we see today, especially since the Second Vatican Council, is a situation that undermines the claim of immutability. Not only do we see bishops and priests speaking things contrary to what the Church had taught before, but we also see Popes doing the same.
There is also another issue: corrupt men within the Church. It is well known that there have been numerous cases of child-molesting priests. While it may be true that this has been overblown by the media, it is nevertheless true that plenty of people, including the Pope himself, arranged to have deviant priests hidden and protected. And what is the result? The moral voice of the Church has lost credibility. People tend to not take the Church seriously, and it is common for skeptics to use the scandals as an objection to anything the Church says about moral issues.
We also see that Popes and churchmen are unwilling to speak and teach the whole of Catholicism. They do not like speaking about Hell, for example, or the necessity of the sacraments for salvation. None of that seems to be important anymore. Mostly, we see them speaking about moral and political issues: abortion is wrong, divorce is wrong, homosexuality is wrong, etc. There has been a curious shift from a theological emphasis to a moral and political emphasis. This is strange given the fact that there are very specific things that the Church teaches on theology which one must believe in order to be saved.
We also see the implementation of the Novus Ordo Missal published by Pope Paul VI, which has led to several changes: the altar has been removed, the priest instead of facing the altar now faces the people, the prayers of the mass have been greatly reduced or removed entirely, the missal instead of presenting a single reading to the priest now presents a set of different readings that he can choose freely making each mass completely different than the other, etc. There are many more changes and abuses occurring from parish to parish, but these are the most common. It could be said that the Second Vatican Council teaches against this, but after the publication of Pope Paul VI's missal, what the council said has been overturned and a new era of reformation and experimentation with the Mass has been set in motion.
This has led to confusion and division within the Church. Because the sacraments are made in such a way that the wording must be very precise, if the priest changes the wording or the manner in which he performs the sacrament, it may become invalid. Thus, a Catholic can no longer be certain that the priest is giving him a valid sacrament.
How could God allow something like this to happen? If God wants everyone to be saved, then how can he allow this sort of confusion within his Church? If eternal damnation is the consequence of not obeying the Church and following what it teaches, then I believe it is fair to expect some clear indication of what it is that one must do in order to be saved. But this is not what we see.
Traditional, conservative and liberal Catholics
This result of this confusion has led to division within the Church made up of traditional, conservative and liberal Catholics. Which is right?
First, Traditional Catholics reject the council on the grounds that it was not infallible, and that it contradicted previous Church teaching. In the Traditionalist view, everything becomes a matter of whether or not the Pope was teaching ex cathedra, or whether or not a council pronounced some new dogma. This leaves individual Catholics, not the Church, as the final authority, thus opening everything up to individual interpretation.
But when has it been said that the Church must only be obeyed when it pronounces some new dogma? Nowhere. In fact, the teaching of Papal Infallibility while implicitly held before the First Vatican Council, was not formally defined until that Council, less than 150 years ago. Before that, what had always been taught is that all Catholics were bound to be subject to the Pope in order to obtain salvation.
In the Conservative view, reconciliation is ought between previous Church teaching and the teachings of the Second Vatican Council. But it is clear that this council made some pronouncements that seem to contradict previous teachings, (e.g., liberty of conscience, freedom of religion, salvation outside the Church, etc.). While it may be possible to reconcile both sides, once cannot do so without sacrificing something either from the previous Church teachings or the teachings of the council. This is why conservative Catholics are in disagreement with traditional Catholics. To conservative Catholics, the past is no longer important and what was said "back then" cannot be said to apply today. Thus, conservative Catholics downplay the importance of previous Church teachings in order to accommodate the newer and most-recent teachings.
The Liberal view picks and chooses what to believe, downplays the necessity of the Church for salvation, says nothing about the need for the sacraments or about the reality of Hell, etc. Liberal Catholics spend more time finding excuses by which non-Catholics can be saved instead of telling them why they should join the Church. They would consider any Catholic that preaches about Hell, or that teaches that other religions are false, to be an intolerant bigot.
What we have is confusion and contradiction running rampant, the result of the confusion that came after the Second Vatican Council, the poor catechesis, and the deviant Popes and churchmen who have been teaching confusing and contradictory things.
The Gates of Hell prevailed
If The Catholic Church were really God's divine institution and under his protection, then I believe that things would be less subject to confusion and corruption. If we put things in context and believe that it is necessary for salvation to obey the Church in all matters of faith and morals, then I believe that we can expect no less from a benevolent God who desires all to be saved, that his Church would be holy and perfect. I see no reason why this should not be the case. Yet, the Church does not provides us with an objective means by which to know what God wants us to do in order to obtain salvation.
Conclusion, Part I
Having explored these four areas, and after having seen the lack of evidence in each area, as well as the lack of an objective means by which one could know God or the supernatural, I simply find no rational or justifiable reason to hold to the belief in God or the supernatural. I also believe that the demands that a religion such as Catholicism makes on the individual are unjustified in light of the lack of evidence provided for belief.
Part II. The road to Naturalism
Science and Methodological Naturalism
What we see in the universe
What events take place in an ordinary day of our lives? What sort of processes are in place at all hours of the day whether we find ourselves at work, at home, or in any other place? Everywhere we go, everywhere we look and no matter what we do, all we see around us, and all we do, is nothing more than natural processes working in accord with natural laws.
When you are at work, where is God? Does he step in to help you when things get rough? When you are at home taking care of your children, where is God? Does God help you in anyway to raise them? When firemen are trying to rescue people from a fire and they die trying--and so do the people they are trying to save--where is God?
I could go on, of course, with many more examples. But the important question is, "Where is God?" In none of the events I mentioned, and in none that I could mention, do we find God doing anything discernible. God offers no help when we most need it, nor does he gives us any useful knowledge that would help us solve a problem. These events take place just as if no benevolent and all-powerful God existed. All we see are natural processes working in accord with natural laws. No instance of supernatural intervention or God-activity is evident in any area of our lives. Yet, the God professed by Christians is a God who is said to care for humans, answer prayers, and intervene in our lives. But why is none of this evident?
Absence of evidence is evidence of the absence
The only valid answer seems to be that there is simply nothing supernatural interacting with the universe. But even it were, the fact that we have no means of knowing anything about it or detecting it makes it irrelevant to our lives. And more likely than not, a supernatural being, if it exists, is not really concerned with our lives either.
Some Christians would say that God is everywhere, that he sustains everything in existence, but that and "nothing" are the same thing. If God is everywhere, yet he is invisible and can't be seen or experienced in any way, then how is that different from God being nowhere? If God sustains everything in existence, then how is that different from God sustaining nothing at all? How would we know the difference? We can't. We have no means of comparing a universe where God is nowhere against one where he is everywhere.
All of this leads one to conclude that there is an absence of evidence within the universe when it comes to God or the supernatural operating within it. What we observe is an absence of evidence when it comes to an all-loving and all-powerful God that interacts with the universe and desires all humans to be saved. The universe gives us nothing to support such a notion and much evidence to assume nonexistence of a God with those qualities.
The success of science in explaining the universe
If there is anything that has given us accurate and useful knowledge about the universe it is science. Science has been extremely successful in explaining the universe in terms of processes and laws that operate within it. Science has had an incredible success in gaining knowledge about how things work in the universe, and also in our bodies and minds. Science is by far the most successful human endeavor in history.
Why is science so successful? What is it about science that has allowed it to gain so much knowledge about the universe and apply that knowledge in order to provide solutions for our needs?
Science and Methodological Naturalism
What makes science so successful is it's methodology. The combination of rationalism, empiricism and skepticism is at the root of what is called the Scientific Method. This method is also known as Methodological Naturalism, and since science employs this method, it operates with the assumption that the only things at work within the universe are natural processes operating under natural laws, without supernatural intervention.
This method is what has driven science to explain and penetrate into areas that were once considered the result of God's activity within the universe. Science has dispelled such mysteries and instead of finding any evidence for the supernatural, it comes back--every time--with a set of natural processes that are responsible for what was previously attributed to divine causality.
The demonstrated success in explaining the universe in terms of natural processes and laws is what justifies the assumption that science makes: that only natural processes and laws are operating within the universe. And as I explained in the first part, this assumption is not an arbitrary, but rather it is one that follows from the success that using this assumption has in giving accurate and useful explanations about the workings of the universe.
An additional justification for this assumption is that, so far, there is no viable method to detect and study the supernatural. Given this fact, science simply ignores the supernatural. Until some evidence that can be accessed using Methodological Naturalism proves that the supernatural exists, or until some method by which the supernatural can be known is discovered, science will necessarily continue to ignore the supernatural.
Methodological Naturalism and Metaphysical Naturalism
Methodological Naturalism vs Methodological Supernaturalism
Some theists charge that science is atheistic and that it unfairly rules out supernatural explanations in favor of natural ones. But this accusation is without merit.
First, it would be enough to point out that the history of science has had a tendency of moving from what is called Methodological Supernaturalism, which is the use of supernatural explanations within scientific investigation, to Methodological Naturalism, which is the use of only natural explanations within scientific investigation.
What caused this change? The fact that supernatural explanations are sterile and do not provide us with any valuable information about how the universe and the things within it work.
Whenever we find something we want to explain, we would have three possible answers to investigate. Let's assume, for example, that we want to explain how the digestive system works. What are the three possible answers?
Which of the three explanations is the best and most accurate answer? The first one gives us no insight about how the digestive system works; it is sterile and blocks any further inquiry; it merely covers the gap in our knowledge about how the digestive system works with a greater mystery. If some food gets stuck in your throat, for example, are we to assume that God suddenly interfered with the functioning of the system?
The second explanation, while giving us a description of how the digestive system works, adds God into the equation, but doing so provides no additional insight.
The third explanation gives us something of a description of how the digestive system works and of what happens when one eats food. It does not uses God in the explanation and it avoids adding something that is simply superfluous to the equation.
If adding God to our explanation of the digestive systems results in no useful or additional knowledge about that system, then the simplest explanation, the one that doesn't add God, is to be preferred. In this sense i the purely naturalistic explanation is preferred to the supernatural one or to a mixture between both. We can use this same process for anything that we might want to explain about the universe; if we do, we will come up with the same answer over and over again.
Thus, as can be seen, a naturalistic explanation is superior even if we do allow supernatural explanations on the table. This is why science makes the assumption that only natural processes and laws are operating within the universe. It is because all things being equal, naturalistic explanations have a long track record of proving themselves to be superior to supernatural explanations.
Many theists acknowledge this fact, and consequently they subscribe to what is called Ontological Supernaturalism. This view entails that while the theist believes in God, she admits that the universe is to be studied by science using Methodological Naturalism, that is, by assuming that only natural processes and laws take place within the universe and that no supernatural entity operates to change those laws and processes.
The inconsistency of Ontological Supernaturalism
But how is such a view consistent with the belief in a God that answers prayers, performs miracles, and interacts with the universe? It isn't.
In fact, most Christians--even those that hold to Methodological Supernaturalism--live as if Methodological Naturalism is true. If you want to test this, tell a Christian that his money has mysteriously disappeared from his bank account, leaving no transaction that could be tracked. What would be his response? Either he wouldn't believe you, or perhaps he would propose that someone stole it or that there had been a bank error. If you told the Christian that it a demon had done this in order to ruin his life, he would not believe it or even consider that a possibility.
We can do the same with any other event. For example, if you tell a Christian that the files of his computer mysteriously disappeared, he would not believe it or even consider the possibility of something supernatural being responsible for it, rather he would demand a natural explanation. Christians live as if Methodological Naturalism were true. When they accept Methodological Naturalism as the only valid scientific method, they are simply being consistent with how they normally live. When they reject it they are being inconsistent with how they normally live.
While Methodological Naturalism is not inherently incompatible with Ontological Supernaturalism, it puts the theist that holds both positions into the realm of inconsistency, something like being an atheist by day and a theist by night. Given the fact that the theist has no sure way of knowing what God does and what he does not do--or what demons do and what they do not do--the theist's rejection of supernatural explanations in favor of natural ones in everyday events is completely arbitrary.
The success of Methodological Naturalism as the truth of Metaphysical Naturalism
Where does this leave us? Every process we see occurring within the universe is a natural process operating under natural laws. Every useful and productive explanation we can give about the universe and the things that are at work within it is a natural explanation.
Science has been successful in explaining the universe by assuming that natural processes and laws operate within the universe without any sort of supernatural influence. We have not found an objective method by which to study and know anything about the supernatural, thus there is a lack of any objective evidence for the existence of the supernatural.
If there is any one worldview that is supported by the best evidence available, it is Metaphysical Naturalism. It is the only worldview that is fully consistent with, and that logically follows from, the evidence that we have. So, with Dr. Barbara Forrest I am led to say:
I conclude that the relationship between methodological and philosophical naturalism, while not one of logical entailment, is the only reasonable metaphysical conclusion given (1) the demonstrated success of methodological naturalism, combined with (2) the massive amount of knowledge gained by it, (3) the lack of a method or epistemology for knowing the supernatural, and (4) the subsequent lack of evidence for the supernatural. The above factors together provide solid grounding for philosophical naturalism, while supernaturalism remains little more than a logical possibility.
Metaphysical Naturalism as the only rational conclusion
And that to me, makes Metaphysical Naturalism the only rational and empirically justifiable world view. All we know about our universe is that it is a natural one, made up of natural laws and processes, and laws that operate uniformly.
All we know about our lives is that they are natural. And everything we do is natural; our works, virtues and achievements are all natural and the product of natural processes. Our consciousness is natural and depends on our natural brain. That we know of, there is nothing supernatural about the universe. What we don't know is reduced, day by day, as our knowledge of the universe increases. And that which increases our knowledge about the universe consists of natural explanations--leaving no room for the supernatural and making it superfluous when invoked.
Metaphysical Naturalism, far from being an a priori assumption, is an a posteriori conclusion which is grounded in the massive amount of evidence that science has gathered over the centuries, and the success that science has had by using Methodological Naturalism as it's method. Metaphysical Naturalism is essentially a conclusion made after looking at the evidence. This is what sets Metaphysical Naturalism apart from other worldviews that use by asserting metaphysics before science and then seeking to fit the discoveries of science into their a priori metaphysical assumptions.
Because of this, Metaphysical Naturalism does not accept other forms of obtaining knowledge, such as revelation, as do theistic positions. The epistemology of Metaphysical Naturalism is the scientific method, the same method by which it's validity and truth is established.
That being the case, if one would like to falsify Metaphysical Naturalism one would need to provide some evidence for the supernatural that is accessible to Methodological Naturalism, or provide a method by which the supernatural can be objectively known. So far, this has not been done. Thus, Metaphysical Naturalism remains the conclusion to which the evidence points, and any new scientific discovery and explanation that is given in terms of natural processes and laws only fortifies the foundation on which Metaphysical Naturalism is grounded.
Conclusion, Part II
My original ambition of being a faithful Catholic, of obeying the Church and having faith, are simply not supported by the available evidence or my daily experience. As I said at the end of the first part, I do not have enough faith to overlook this fact. I have never experienced anything that could be considered supernatural. So, I simply have no reason for believing in God or the supernatural. All of what I have seen, all of what I do, and all of what I have experienced in my life, is exactly what one would expect to experience if Metaphysical Naturalism were true. Because of that, and given the reasons I have provided in this paper, I have concluded that it is more likely than not that Metaphysical Naturalism is true whereas theism or supernaturalism, while a logical possibility, lacks the support that Metaphysical Naturalism enjoys.
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