The disorder in the temporal order is due to Original Sin. Adam and Eve started the whole problem of evil in the natural order. We cannot deny this. The world was created in a perfection which was lost by sin and the consequences of sin.
God permits evil for many reasons.
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Evil is threefold, viz., "malum naturæ" (metaphysical evil), "culpæ" (moral), and "paenæ" (physical, the retributive consequence of "malum culpæ") (I, Q. xlviii, a. 5, 6; Q. lxiii, a. 9; De Malo, I, 4). Its existence subserves the perfection of the whole; the universe would be less perfect if it contained no evil. Thus fire could not exist without the corruption of what it consumes; the lion must slay the ass in order to live, and if there were no wrong doing, there would be no sphere for patience and justice (I, Q. xlviii, a. 2). God is said (as in Isaiah 45) to be the author of evil in the sense that the corruption of material objects in nature is ordained by Him, as a means for carrying out the design of the universe; and on the other hand, the evil which exists as a consequence of the breach of Divine laws is in the same sense due to Divine appointment; the universe would be less perfect if its laws could be broken with impunity. Thus evil, in one aspect, i.e. as counter-balancing the deordination of sin, has the nature of good (II, Q. ii, a. 19). But the evil of sin (culpæ), though permitted by God, is in no sense due to him (I, Q. xlix, a. 2).; its cause is the abuse of free will by angels and men (I-II, Q. lxxiii, a. 6; II-II, Q. x, a. 2; I-II, Q. ix, a. 3). It should be observed that the universal perfection to which evil in some form is necessary, is the perfection of this universe, not of any universe: metaphysical evil, that is to say, and indirectly, moral evil as well, is included in the design of the universe which is partially known to us; but we cannot say without denying the Divine omnipotence, that another equally perfect universe could not be created in which evil would have no place.
St. Thomas also provides explanations of what are now generally considered to be the two main difficulties of the subject, viz., the Divine permission of foreseen moral evil, and the question finally arriving thence, why God choose to create anything at all. First, it is asked why God, foreseeing that his creatures would use the gift of free will for their own injury, did not either abstain from creating them, or in some way safeguard their free will from misuse, or else deny them the gift altogether? St. Thomasreplies (C. G., II, xxviii) that God cannot change His mind, since the Divine will is free from the defect of weakness or mutability. Such mutability would, it should be remarked, be a defect in the Divine nature(and therefore impossible), because if God's purpose were made dependent on the foreseen free act of any creature, God would thereby sacrifice His own freedom, and would submit Himself to His creatures, thus abdicating His essential supremacy--a thing which is, of course, utterly inconceivable. Secondly, to the question why God should have chosen to create, when creation was in no way needful for His ownperfection, St. Thomas answers that God's object in creating is Himself; He creates in order to manifest his own goodness, power, and wisdom, and is pleased with that reflection or similitude of Himself in which the goodness of creation consists. God's pleasure is the one supremely perfect motive for action, alike in God Himself and in His creatures; not because of any need, or inherent necessity, in the Divinenature (C. G., I, xxviii; II, xxiii), but because God is the source, centre, and object, of all existence. (I, Q. 65:a. 2; cf. Proverbs 26 and Conc. Vat., can. 1:v; Const. Dogm., 1.) This is accordingly the sufficient reason for the existence of the universe, and even for the suffering which moral evil has introduced into it. God has not made the world primarily for man's good, but for His own pleasure; goodfor man lies in conforming himself to the supreme purpose of creation, and evil in departing from it (C.G., III, xvii, cxliv). It may further be understood from St. Thomas, that in the diversity of metaphysical evil, in which the perfection of the universe as a whole is embodied, God may see a certain similitude of His own threefold unity (cf. I, Q. xii); and again, that by permitting moral evil to exist He has provided a sphere for the manifestation of one aspect of His essential justice (cf. I, Q. lxv, a. 2; and I, Q. xxi, a. 1, 3).