Secondary Causation is the philosophical proposition that all material and corporeal objects, having been created by God with their own intrinsic potentialities, are subsequently empowered to evolve independently in accordance with natural law. Traditional Christians would slightly modify this injunction to allow for the occasional miracle as well as the exercise of free will. Deists who deny any divine interference past the creation event would only accept free will exceptions. That the physical universe is consequentially well-ordered, consistent, and knowable subject to human observation and reason, was a primary theme of Scholasticism and further molded into the philosophy of the Western Tradition by Augustine and later by Aquinas.
Secondary causation has been suggested as a necessary precursor for scientific inquiry into an established order of natural laws which are not entirely predicated on the changeable whims of a supernatural Being. Nor does this create a conflict between science and religion for, given a Creator, it is not inconsistent with the paradigm of a clockwork universe. It does however remove logical contradictions concerning the unfettered expression of man’s free will which would otherwise require not just God’s acquiescence but rather His direct intervention to implement.
Opposing Philosophies of Volunteerism and Occasionalism against Secondary Causation
According to the Jewish Torah which brought down the original idea in Genesis, the phrase "free will" is a mistranslation from the Torah, rather what humans are given is "freedom to choose". Freedom to choose to do God's Will at all times even though God gave us a good inclination and a not-good inclination to use in choosing, we are told "Therefore choose life".
Occasionalism itself was derived from the earlier school of thought of “volunteerism” emanating from Al-Ash'ari who held that every particle in the universe must be constantly recreated each instant by God’s direct intervention.
According to the Kabbalah and brought down in Chasidic philosophy in the book "Tania, the Book of Intermediates" composed by Rabbi Shneur Zalman of Liadi (Russia) at the beginning of the 19th century, the will and desire to create the universe is integral to the Creator's very essence & thought this being the source for all the physical and spiritual worlds.
Once the Creator has created the universe and God knows & wants the Creation as the One who created it in His very essence, God then enlivens and vivifies all parts of the universe at every moment or the physical universe & the many spiritual worlds would revert instantly to their source in the Creator from where they came. At the same time as molecules move, human cells divide the Creator must know the Creation as it was a moment ago and makes allowance for the finite Creations to grow and later slowly wither, and by the evaporation of water, the wearing down of rocks and soil, the birth, growth and weakening of the flesh of fish, animals and humans all Creations as they are built from the 4 main spiritual worlds which also break down, they have a mirror on earth of air, fire, water, dust and slowly all created beings wear down by God's constant enlivening of them until each of the 4 elements return to their spiritual source which mirror the 4 elements. This is not an independent of God activity, rather it is all controlled by God's Will.
Torah explains that before Creation there was only God and nothing else as is seen in the highest Name the letter "Yud". When it came time for Creation the want and will of God to Create a universe which meant expansion of the Holy Name the Holy Name Yud-Hey-Vav-Hey how this Creation came about by G-D's use of the 10 Sefirot would be too great a task to explain here but basically we find "And God said let there be..."
The Creation made no change in the Creator God was, is and always will be but the Creation is available to those Created as an order always vivified by God since God must know the Creation in order to keep it as it is, yet allow for His change according to his will. The body sees a Creation while the soul sees only The Infinite One God.
Having the gift from God, "the Freedom to choose" to serve God and always do God's Will here on earth makes us partners in creation. Being that God's Will was revealed to the People of Israel on Mount Sinai and spread to the world in the Torah we have Freedom to choose to do so. If a human does the opposite of God's Will it is in God's realm to alter the cosmic plan of Creation that He Himself devised, that He Himself wants but since nothing exists but God, including the universe and this "nothing" is not above the knowledge that "nothing is too hard for God" and "Our wisdom is not His Wisdom", it is a fundamental theme in Torah that we must do God's will yet we have Freedom to serve or not and if we go against God's will, it is still a lack on our part as partners with God here on earth but this itself is God's Will and will not upset the cosmic original plan.
We see this when Shimi cursed King David and threw stones at him that King David did not get angry since he realized that Shimi was an agent from God himself or Shimi could not possibly use his physical God given talents to speak or throw stones if God did not want. Even though Shimi was not told by God, Shimi used his Freedom to Serve in the wrong way, but if Shimi had not cursed David at God's Will, "God has many messengers to do His will"
In fact, with Adam and Eve there in, the Tree of the Knowledge of Good and Evil was created before Adam himself by God and this is all part of His plan, to turn away from evil.
Opposing Philosophy of ”Dual Truth” against Secondary Causation
The concept of there being two distinct truths, even concerning the same object or phenomena, was most notably developed by Averroes (1126-1198 from Spain). By thus separating the sanctity of religious revelation from the practical world of physical observation, it was an attempt to circumvent proscriptions on the discredited rationalist heresy of Muʿtazila, which had heretofore not gained traction in any venue.
Following Augustine and many others, this concept of double truth was soundly rejected by Aquinas in his Summa Theologiae which reiterated the long established view in the West that there can be only one truth. The original quote from Augustine was
"In matters that are obscure and far beyond our vision, even in such as we may find treated in Holy Scripture, different Interpretations are sometimes possible without prejudice to the faith we have received. In such a case, we should not rush in headlong and so firmly take our stand on one side that, if further progress in the search of truth justly undermines this position, we too fall with it. That would be to battle not for the teaching of Holy Scripture but for our own, wishing its teaching to conform to ours, whereas we ought to wish ours to conform to that of Sacred Scripture."
Development of Philosophy in Support of Secondary Causation
The assignment of intrinsic qualities to objects which can mutate and evolve of their own accord without divine intervention was a crucial step in the transformation of the rational logic of the Greeks into the scientific method in the Western Tradition of the late Middle Ages. Because man could thus observe and characterize the natural flow of events without impugning the prerogatives of supernatural forces, burgeoning philosopher-scientists became free to experiment and especially to question and debate the results.
In Western Europe this rationale was further strengthened by the motivation that science was uniquely able not only to efficiently manage the world as charged to do so in Genesis but also to be able to distinguish miracles from natural occurrences.
One of the first to take advantage of this opportunity was Albertus Magnus of Cologne (1193-1206), who wrote
"In studying nature we have not to inquire how God the Creator may, as He freely wills, use His creatures to work miracles and thereby show forth His power; we have rather to inquire what Nature with its immanent causes can naturally bring to pass." 
This sentiment was echoed in various European forums of the day notably by the secular Professor of Theology at the University of Paris, John Buridan (1300-1361) who liberally commented on the works of Aristotle.
“It should also be noted that [when we ask whether metaphysics is the same as wisdom,] we are not comparing metaphysics to theology, which proceeds from beliefs that are not known, because although these beliefs are not known per se and most evident, we hold without doubt that theology is the more principal discipline and that it is wisdom most properly speaking. In this question, however, we are merely asking about intellectual habits based on human reason, [i.e.,] those discovered by the process of reasoning, which are deduced from what is evident to us. For it is in this sense that Aristotle calls metaphysics ‘theology’ and ‘the divine science’. Accordingly, metaphysics differs from theology in the fact that although each considers God and those things that pertain to divinity, metaphysics only considers them as regards what can be proved and implied, or inductively inferred, by demonstrative reason.”
- “Causality Primary and Secondary”, Mariano Artigas, Encyclopedia of Science and Religion, ©2003 Gale Cengage; online at http://www.enotes.com/causality-primary-secondary-reference/causality-primary-secondary
- “Kant’s Theory of Divine and Secondary Causation”, Des Hogan, University of California at San Diego; online at http://philosophy.ucsd.edu/_files/facultysites/watkins-conference/hogan.pdf;
- “Causation as a Secondary Quality”, Peter Menzies and Huw Price, Brit. J. Phil. Sci., 44 (1993), 187-203.
- Huff, Toby E. The Rise of Early Modem Science: Islam, China and the West, Cambridge University Press, (2003).
- “St. Augustine, the Literal Meaning of Genesis”. vol. 1, Ancient Christian Writers., vol. 41. Translated and annotated by John Hammond Taylor, S.J. New York: Paulist Press, 1982.
- “The Origin of Science”, by Stanley L. Jaki.
- “De vegetabilibus etplantis”, by Albertus Magnus(1193-1206)
- Compendium of Dialectic [Summulae de dialectica]. by Buridan (<1300-1361)
- Stanford Encyclopedia of Philosophy, John Buridan online at http://plato.stanford.edu/entries/buridan/