"Science has taught us to assume a natural explanation for every event based upon methodological naturalism.” (p. 61)
What Loftus overlooks is that God can operate through secondary causes. A primary cause is when God directly intervenes in the natural order to part the sea or turn wine into water. A secondary cause is when God is not the proximate cause of change. We don’t directly control the temperature in the room but, we do so through a medium like a thermostat. We are ultimately in control but, we aren’t the proximate cause of change. We control the thermostat. The thermostat in turn directs the devices that change the temperature. God can work this way and, to us, this would look natural although suspicious at times. An example of this might be a circumstance or string of circumstances occurring against great odds like a person getting cured of a fatal disease for no readily apparent reason. This is what many people would consider a modern day miracle. Since there isn’t a direct, proximate intervention by God, all empirical events could just look like normal, everyday operations of the physical universe not guided by any divine process. Science can certainly provide empirical explanations for many aspects of our existence but, science will never be able to guarantee that there isn’t a supernatural being behind it all pushing the buttons and twisting the dials.
Non-theists clamor for God to work in primary causes since we now have more sophisticated noetic sensibilities and empirical equipment. We would be much more astute in assessing God's activity than our predecessors. To not do so means that God is unfairly concealing Himself from us or just doesn’t exist. This problem is referred to as the "divine shyness" problem. The Christian case is that biblical style miracles are not necessary after the completed work of Christ’s ministry. Unfortunately, the non-Christian who is asking for God to work as a primary cause does not accept the authority of the Bible or the divinity of Jesus. Therefore, their request stands as an enabler to belief. Without God’s role as proximate cause, they do not accept the biblical injunction. However, the dynamic expressed in the Bible means that God works more as a secondary cause now whereas in the past, He worked as a primary cause. He is much more subtle today.
God's work as a primary cause is inversely proportionate to our scientific knowledge [qualitatively, not quantitatively]. Obviously, the non-theist will object that there is no empirical proof of this and that this explanation is either ad hoc or an excuse for God’s lack of presence in our lives. The flaw in this objection is that as God's direct intervention in natural affairs increases, His activity becomes more compelling which leads to less freedom. This means that God was much more coercive in the past than today. While this prima facie seems like a violation of freedom of our ancestors, Loftus has adamantly pointed out that ancient people were more superstitious and less scientific than we are today. This means that God had more room to operate in the past without being coercive because to them, there were many events that seemed incredible to our ancestors that to us, seem mundane and standard operating procedure of causality. Even though people had a cursory understanding of causality, our ancestors did not have prior scientific endeavors to draw from as we do. They did not have the tools to seek scientifically empirical explanations for events like we do today as a result of the Scientific Revolution. Consequently, God was not contradicting their thought processes in the same way as He would be today. Granted, people had a general sense that seas don’t part on their own without some extraordinary force acting on them but, they didn’t have the scientific experience to know it is as certainly as we do today. If God were to perform proportionately miraculous actions in the modern/postmodern age, He would violate physical laws of causality in a way only He could which would in turn dramatically diminish, or extinguish altogether, our freedom. Keeping in mind that God’s quantitative activity has probably not changed over time, we have a condition in our lives that ancient people did not have; that of scientific advancement. This is a dynamic that is rarely, if ever, allowed for by critics of Christianity. Concordantly, non-theists are not able to justify why God’s modus operandi should remain the same throughout time despite changes in human epistemology. Non-theists want to criticize ancient people for being gullible and not seeking scientific causality for events but, don’t want to acknowledge that moderns would be enraged at the devastating effect God would produce if He did violate the laws that our present epistemology is based on thus mortally wounding our freedom. Essentially, atheists want to be coerced yet free which is logically absurd.
Another perspective on this issue is basically a rephrasing of the previous point of inverse proportionality. It comes from the testimony of many people who say that the less they have tried to manipulate their circumstances, the less they have tried to figure out truth on their own, the more God has revealed Himself to them. The more we lean on our own understanding, the more we occlude our ability to perceive God. This is an incredibly powerful point in regards to non-theism because of the irony that the more non-theists try to discover truth, the more they are not able to grasp it. Keep in mind that this has nothing to do with the intelligence of a person. There are smart people who are Christian and non-Christian alike. It’s about the motivation of a person, genius or not. The sacrifice of Isaac in Genesis 22 made no sense to Abraham but, he did not rely on his own rationality and the divine presence was revealed to him. Moses recognized his limitations that he wasn’t worthy of being God’s ambassador and Exodus 3 records Moses in direct contact with YHWH. Job fought off the temptations of his friends and family and was granted an audience with God. The Psalms are replete with examples of God’s presence being revealed to the penitent. In Matthew 19, Jesus illustrates this truth to the rich young man when Jesus tells him to relieve himself of his worldly accoutrement insinuating that such solipsistic attachments prevent us from having fellowship with the Almighty.
In the Pensees (577), Blaise Pascal points out that “There is sufficient clearness to enlighten the elect, and sufficient obscurity to humble them. There is sufficient obscurity to blind the reprobate, and sufficient clearness to condemn them, and make them inexcusable…If God had permitted only one religion, it had been too easily known; but when we look at it closely, we clearly discern the truth amidst this confusion.”
What we see from Pascal’s “thoughts” is a truth that has been well known for a long time. The issue isn’t one of evidence as atheists claim. That is obfuscation. It’s a matter of the heart; the motivation of the individual. Atheists need to ask themselves in regards to the perception of God’s presence, why their standards are so much less reasonable than that of theists.
In the final analysis, Loftus’ statement should at least be amended to say “Science has taught us to assume a natural explanation for every natural event based upon methodological naturalism.”