"If the Designer is directly responsible for flagella then he is implicated as a cause of human diseases. Diarrhea is no joke; it is a leading cause of infant death in some parts of the world. To make matters worse, one can hardly give the Designer credit for flagella without also crediting him with TTSS's in general. This puts the Designer solidly behind Bubonic plague and many other diseases. Happily, science makes such beliefs unnecessary.
Diseases may be unpleasant in the natural world, but the Lord works in mysterious ways. He is not of this world, and His ways are not our ways. It is hubris to claim to know that a designer would not purposely create flaws.
This doesn't necessarily follow.
The natural world could have been damaged as a result of the Fall, or human nature could have been damaged by the Fall in such a way that it became newly vulnerable to various natural phenomena.
It's very difficult to argue that the natural world contains evils per se.
Metaphysical evil is the limitation by one another of various component parts of the natural world. Through this mutual limitation natural objects are for the most part prevented from attaining to their full or ideal perfection, whether by the constant pressure of physical condition, or by sudden catastrophes. Thus, animal and vegetable organisms are variously influenced by climate and other natural causes; predatory animals depend for their existence on the destruction of life; nature is subject to storms and convulsions, and its order depends on a system of perpetual decay and renewal due to the interaction of its constituent parts. If animals suffering is excluded, no pain of any kind is caused by the inevitable limitations of nature; and they can only be called evil by analogy, and in a sense quite different from that in which the term is applied to human experience. Clarke, moreover, has aptly remarked (Correspondence with Leibniz, letter ii) that the apparent disorder of nature is really no disorder, since it is part of a definite scheme, and precisely fulfills the intention of the Creator; it may therefore be counted as a relative perfection rather than an imperfection. It is, in fact, only by a transference to irrational objects of the subjective ideals and aspirations of human intelligence, that the "evil of nature" can be called evil in any sense but a merely analogous one. The nature and degree of pain in lower animals is very obscure, and in the necessary absence of data it is difficult to say weather it should rightly be classed with the merely formal evil which belongs to inanimate objects, or with the suffering of human beings. The latter view was generally held in ancient times, and may perhaps he referred to the anthropomorphic tendency of primitive minds which appears in the doctrine of metempsychosis. Thus it has often been supposed that animal suffering, together with many of the imperfections of inanimate nature, was due to the fall of man, with whose welfare, as the chief part of creation, were bound up the fortunes of the rest (see Theoph. Antioch., Ad Autolyc., II; cf. Gen. iii, and I Cor.ix). The opposite view is taken by St. Thomas (I, Q. xcvi, a. 1,2).
Whether in the state of innocence man would have been immortal?On the contrary, It is written (Rm. 5:12): "By sin death came into the world." Therefore man was immortal before sin.
I answer that, A thing may be incorruptible in three ways.
First, on the part of matter--that is to say... because it possesses no matter, like an angel...
Secondly, a thing is incorruptible in its form, inasmuch as being by nature corruptible, yet it has an inherent disposition which preserves it wholly from corruption; and this is called incorruptibility of glory; because as Augustine says (Ep. ad Dioscor.): "God made man's soul of such a powerful nature, that from its fulness of beatitude, there redounds to the body a fulness of health, with the vigor of incorruption."
Thirdly, a thing may be incorruptible on the part of its efficient cause; in this sense man was incorruptible and immortal in the state of innocence. For, as Augustine says (QQ. Vet. et Nov. Test. qu. 19 [Work of an anonymous author, among the supposititious works of St. Augustine): "God made man immortal as long as he did not sin; so that he might achieve for himself life or death." For man's body was indissoluble not by reason of any intrinsic vigor of immortality, but by reason of a supernatural force given by God to the soul, whereby it was enabled to preserve the body from all corruption so long as it remained itself subject to God. This entirely agrees with reason; for since the rational soul surpasses the capacity of corporeal matter, as above explained (76, 1), it was most properly endowed at the beginning with the power of preserving the body in a manner surpassing the capacity of corporeal matter.
Whether Adam in the state of innocence had mastership over the animals?
On the contrary, It is written (Gn. 1:26): "Let him have dominion over the fishes of the sea, and the birds of the air, and the beasts of the earth" [Vulg."and the whole earth"].
I answer that, As above stated (95, 1) for his disobedience to God, man was punished by the disobedience of those creatures which should be subject to him. Therefore in the state of innocence, before man had disobeyed, nothing disobeyed him that was naturally subject to him. Now all animals are naturally subject to man. This can be proved in three ways.
First, from the order observed by nature; for just as in the generation of things we perceive a certain order of procession of the perfect from the imperfect (thus matter is for the sake of form; and the imperfect form, for the sake of the perfect), so also is there order in the use of natural things; thus the imperfect are for the use of the perfect; as the plants make use of the earth for their nourishment, and animals make use of plants, and man makes use of both plants and animals. Therefore it is in keeping with the order of nature, that man should be master over animals. Hence the Philosopher [Aristotle] says (Polit. i, 5) that the hunting of wild animals is just and natural, because man thereby exercises a natural right.
Secondly, this is proved by the order of Divine Providence which always governs inferior things by the superior. Wherefore, as man, being made to the image of God, is above other animals, these are rightly subject to his government.
Thirdly, this is proved from a property of man and of other animals. For we see in the latter a certain participated prudence of natural instinct, in regard to certain particular acts; whereas man possesses a universal prudence as regards all practical matters. Now whatever is participated is subject to what is essential and universal. Therefore the subjection of other animals to man is proved to be natural...
Whether man had mastership over all other creatures?
On the contrary, It is written (Gn. 1:26): "That he may have dominion over . . . every creature."
I answer that, Man in a certain sense contains all things; and so according as he is master of what is within himself, in the same way he can have mastership over other things. Now we may consider four things in man: his "reason," which makes him like to the angels'; his "sensitive powers," whereby he is like the animals; his "natural forces," which liken him to the plants; and "the body itself," wherein he is like to inanimate things. Now in man reason has the position of a master and not of a subject. Wherefore man had no mastership over the angels in the primitive state; so when we read "all creatures," we must understand the creatures which are not made to God's image. Over the sensitive powers, as the irascible and concupiscible, which obey reason in some degree, the soul has mastership by commanding. So in the state of innocence man had mastership over the animals by commanding them. But of the natural powers and the body itself man is master not by commanding, but by using them. Thus also in the state of innocence man's mastership over plants and inanimate things consisted not in commanding or in changing them, but in making use of them without hindrance.