¹ William A. Dembski, ‘Science and Design’, First Things, 86 (October 1998), p. 26.

² See Michael Denton, Evolution: A Theory in Crisis (Bethesda, MD: Adler & Adler, 1985), p. 323: “To get a cell by chance would require at least one hundred functional proteins to appear simultaneously in one place. That is one hundred simultaneous events each of an independent probability which could hardly be more than 10⁻²⁰ giving a maximum combined probability of 10⁻²⁰⁰⁰.”

³ I do not know myself how to make this calculation. I am assuming that the likelihood that the base pairs be sequenced in the correct order to produce such a protein corresponds fairly closely to the likelihood that the protein itself arise by chance, and that Richard Dawkins has correctly calculated the latter possibility. See Richard Dawkins, ‘Accumulating Small Change’ (excerpt from The Blind Watchmaker), in Ruse, Michael, ed., Philosophy of Biology (New York: Macmillan Publishing Company, 1989), p. 64Google Scholar.

⁴ See Aquinas, Quaestiones Disputatae de Potentia Dei in Quaestiones Disputatae, vol. 2, P. Bazzi et al., ed., (Turin: Marietti, 1965), q. 3, a. 17, ad 17: “that argument does not prove that motion always was, but that circular motion is able to be perpetual, for one cannot efficaciously conclude something about motion from mathematics.” (Hereafter cited as DP. All translations of Aquinas are my own.)

⁵ See Purves, William K., Orians, Gordon H., and Heller, H. Craig, Life: The Science of Biology (Sunderland, MA: Sinauer Associates, Inc., 1998), p. 382Google Scholar: “DNA sequencing has revealed that mutations occur most often at certain base pairs in human DNA. These ‘hot spots’ are often located where cytosine residues have been methylated to 5-methlcytosine (see Chapter 14). The explanation of this mutation phenomenon has to do with the natural instability of bases in DNA.” An internet search for “directed mutation” and “mutational bias” turns up many articles by mainstream scientists who argue that mutations do in some cases arise in a directed way in response to environmental stressors and that there are places in the DNA where mutations take place preferentially.

⁶ Dembski, The Design Revolution, p. 65.

⁷ Aquinas plainly thinks that the existence of God can be known by demonstration, and offers his five ways to this end (see Summa Theologiae, I, q. 2, a. 2–3. Hereafter ST).

⁸ The Design Revolution, p. 281.

⁹ Probability calculations were not initially part of Behe's argument, although they are prominent in his more recent book, The Edge of Evolution.

¹⁰ Behe, Michael, Darwin's Black Box (New York: The Free Press, 1996), p. 39Google Scholar: “By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning. An irreducibly complex system cannot be produced directly (that is, by continuously improving the initial function, which continues to work by the same mechanism) by slight, successive modifications of a precursor system…”

¹¹ See, for example, biologist Sean B. Carroll's critique of Behe's book, The Edge of Evolution: ‘God as Genetic Engineer’, Science 316 (8 June 2007), pp. 1427–28CrossRefGoogle Scholar.

¹² Kenneth Miller, ‘The Flagellum Unspun’, http://www.millerandlevine.com/km/evol/design2/article.html.

¹³ The unit is called the “type III secretory system”. It is found in gram negative bacteria. See ibid.

¹⁴ See Putz, Oliver, ‘Hormone-Receptors and Complexity: Putting to Rest Another God of the Gaps?’, Theology and Science 4:3 (2006), p. 211CrossRefGoogle Scholar. While I agree with Behe that Thorton's discovery concerning the hormone receptor MR and CR has to do with only one small part of a complex system, at the same time it is the case that this small part turned out to be producible by two small steps. Thorton et al's discovery opens the door to the possibility that other parts of complex systems can develop in gradual ways from a previous system that was simpler. The question does then remain as to how the simpler systems arose, for all known biological systems involve considerable complexity.

¹⁵ I can't help remark a certain disingenuousness as far as Behe's claims regarding biologists’ failure to explain irreducibly complex systems. The neo-Darwinian synthesis is of fairly recent date (1930s-1940s). Most biologists nowadays are not evolutionary biologists. And the majority of those that are do not spend their time researching pathways to putative irreducibly complex systems. Moreover, researching such pathways is very difficult to do. It is not as if one always had a lineage of living organisms, one descended from the other, whose physiology and genetics one could compare.

¹⁶ See Behe, Darwin's Black Box, pp. 203–4: “Throughout this book, however, I have shown why many biochemical systems cannot be built up by natural selection working on mutations: no direct, gradual route exists to these irreducibly complex systems… Alternatives to gradualism that work through unintelligent causes, such as symbiosis and complexity theory, cannot (and do not even try to) explain the fundamental biochemical machines of life… Might there be an as-yet-undiscovered natural process that would explain biochemical complexity? No one would be foolish enough to categorically deny the possibility. Nonetheless, we can say that if there is such a process, no one has a clue how it would. Further, it would go against all human experience, like postulating that a natural process might explain computers… In the face of the massive evidence we do have for biochemical design, ignoring the evidence in the name of a phantom process would be to play the role of the detective who ignores the elephant.” His more recent book also gives as reason for positing deliberate design the insufficiency of natural causes for the production of complex molecular machinery (see The Edge of Evolution, [New York: Free Press, 2007], pp. 165–66Google Scholar).

¹⁷ ST I, q. 22, a. 3.

¹⁸ See Scriptum super Sententiis (Paris: Lethielleux, 1956)Google Scholar, Bk. 2 dist. 10, q. 1, a. 3 ad 1: “There is found in regard to artificial things an artisan who only works with his hands, executing the orders of another and commanding no one, as the one who prepares the material; another who commands the one preparing the material, and himself works to introduce the form; another who does not work at all but commands, possessing the plan (rationes) of the work taken from the end of which he is the director, and such a one is called an architect…”

¹⁹ Behe has since modified his position to allow for natural causes to be the immediate causes of biological complexity. His position, however, is incoherent. His reason for concluding to the existence of a deliberate designer is that known natural causes are unable to change DNA in ways that produce new complex parts and new life forms, and that hypothetical natural causes fare no better, but then he turns around and says that the same hypothetical causes he just dismissed can be adequate immediate causes of evolution when ordered by a deliberate designer. See Behe, The Edge of Evolution, pp. 165–66.

²⁰ In a number of passages, Aquinas shows that he is open to the possibility that the substantial forms of certain created things do not exist in act in the beginning, e.g., ST I, q. 65, a. 4, ST I, q. 69, a. 2, ST I, q. 73, a. 1, ad 3, and Scriptum super Sententiis, Bk. II, dist. 12, q. 1, a. 2. The latter passage reads: “Thus, therefore, something concerning the beginning of the world pertains to the substance of the faith, namely that the created world began, and this all the saints say in one accord. In what manner and in what order it is made, does not pertain to the faith except accidentally, insofar as it is narrated by Scripture, whose truth the saints preserve by diverse exposition, handing on diverse [views]. For Augustine is of the opinion that in the beginning itself of creation certain things existed distinct in their proper nature, such as the elements, heavenly bodies, and spiritual substances; others only in seminal reasons (rationibus seminalibus), such as animals, plants, and human beings, all of which were produced afterwards in their proper natures by that work in which God, after the six days [of creation], governs previously established nature.” And ST I, q. 65, a. 4, ad 2 Aquinas adds concerning these seminal reasons that they can be traced back to the divine intellect: “from which the seeds of the forms are put in created things, so that through motion they may be educed in act” (emphasis added).

²¹ ST I, q. 103, a. 6.

²² Summa Contra Gentiles, Pera, C. O.P. et al., ed., (Turin: Marietti, 1961), III, 70Google Scholar. (Hereafter cited as SCG).

²³ See also SCG III, 69: “to detract from the perfection of creatures is to detract from the perfection of divine power.”

²⁴ Though I am not sure that Thomas would make this case, as he viewed angels as being responsible for many seemingly natural events on earth (see ST I, q. 110, a. 1, ad 2), one might argue that it would not befit a wise, omnipotent, and most good maker that he create a universe of beings in which he or his angels must periodically intervene to make new non-rational species appear. If a human being can design a dishwater to go through a variety of different cycles without needing someone to step in and nudge it along, and this pertains to his perfection as engineer, it seems unfitting that God would choose not to design a universe in which new kinds of beings can develop as a result of natural causes within that universe. This view does not entail the endorsement of deism, as is sometimes claimed, but rather is rather a rejection of occasionalism, i.e., of the view that affirms God's causality in regard to every becoming and motion at the expense of denying that creatures can do things; see SCG III, 69 and 70, “On the opinion of those who subtract from natural things their proper actions’, and “In what manner the same effect is from God and from a natural agent.”

²⁵ Quaestiones Disputatae de Veritate, in Quaestiones Disputatae, vol. 1, Spiazzi, Raymundi M. O.P., ed., (Turin: Marietti, 1964)Google Scholar, q.3, a.1. (Hereafter cited as DV.)

²⁶ In Octo Libros de Physico Auditu Commentaria, Pirotta, Angeli M. O.P., ed., (Naples: M. D'Auria Pontificius Editor, 1953), 519Google Scholar. (Hereafter In Phys.)

²⁷ See Paley, William, Natural Theology, (1802) (Houston: St. Thomas Press, 1972), pp. 1–2Google Scholar: “[W]hen we come to inspect the watch, we perceive (what we could not discover in the stone) that its several parts are framed and put together for a purpose, e.g. that they are so formed and adjusted as to produce motion, and that motion so regulated as to point out the hour of the day.”

²⁸ See Paley, Natural Theology, p. 9: “Arrangement, disposition of parts, subserviency of means to end, relation of instruments to an [sic] use, imply the presence of intelligence and mind.”

²⁹ ST I, q. 2, a. 3.

³⁰ In Phys., 491.

³¹ Aquinas also reasons to an intelligent being starting from finality in the parts of organisms, rather than in the actions of the inanimate natural things in DP q. 2, a. 3, ad 5, and in In Duodecim Libros Metaphysicorum Aristotelis Expositio, Spiazzi, Raymundi M. O.P., ed., (Rome: Marietti, 1950), 98Google Scholar. Hereafter cited as In Meta.

³² Throughout this paper I lump together chance occurrences with random ones. A full understanding of the relation of design arguments to evolutionary accounts would require distinguishing the two. It would also require distinguishing randomness in nature from purely mathematical randomness.

³³ Quaestio Disputata de Anima in Quaestiones Disputatae, vol. 2, Bazzi, P. et al., ed., (Turin: Marietti, 1965)Google Scholar, a. 8: “And through this very mode [looking to finality] the reason for the disposition of the human body is to be assigned as to each single part which is proper to man. But nevertheless one needs to consider in those things that are from matter that there are certain dispositions in the matter itself for the sake of which this sort of matter is selected for this form, and other dispositions which follow from the necessity of the matter, and not from the choice of the agent.” See also Quaestiones Disputatae de Malo q. 5, a. 5 and ST I, q. 91, a. 3.

³⁴ Although the production of new species through evolution rather than by directly forming them means that there will be more defects in them, still from a Thomistic point of view this is outweighed by the following goods: first, God imparts the dignity of causality more extensively to things; secondly, God renders things in the world more interactive (what evolutionary biologist would prefer the comparably static world of pre-Darwinian biology?); thirdly, evolution bears better tribute to God's infinite wisdom insofar as the project of getting from unicellular organisms to complex organisms like ourselves through an unbroken series of intermediary living species requires far more intelligence than simply creating each living species from scratch.

³⁵ One could maintain that novelty arises in an entirely determinate way, rather than at least in part by chance, but this fits poorly with a number of facts. For example, there is reason to think that mutations in some cases do not occur in response to environmental pressure, but arise randomly before a given environmental pressure appears (see ‘The Lederberg Experiment’, http://evolution.berkeley.edu/evosite/evo101/IIIC1bLederberg.shtml). Also, if transitions to new species are automatic, then one would not expect different patterns in evolution; yet parent species sometimes giving rise to a single daughter species, and sometimes to more than one.

³⁶ SCG III, 74.

³⁷ See SCG III, 72.

³⁸ See SCG III, 69 concerning the goodness of interactivity: “[T]o subtract the order from created things is to subtract from them what they have that is best… If, however, one takes things’ actions away from them, one takes away the order of things to each other. For there is no assembling of things which are diverse according to their natures in a unity of order, except through this that certain of them act and certain of them are acted upon.”

³⁹ See DV q. 5, a. 9, ad 9: “It is necessary to reduce the diversity of the sexes to the celestial powers. For every agent, to the extent it can, tends to assimilate the patient to itself; whence the active power which is in the seed of the male tends to always lead the conceptus to the male sex, which is more perfect; whence the female sex happens outside the tendency of the nature of the particular agent. Therefore, unless there was some power which tended to the female sex, the generation of the female would be entirely by chance, as even is the generation of other monsters; and therefore it is said that although it [i.e., the generation of females] is contrary to the tendency of the particular nature, by reason of which the female is called a ruined male, nevertheless is it of the tendency of universal nature, which is the power of the heavenly body, as Avicenna says.”

⁴⁰ DV q. 5, a. 2.

⁴¹ Aquinas was inclined to think that spontaneous generation could occur since this is what he understands Genesis to indicate: “Let the waters produce creeping things having a living soul” (Gen. 1:20); see ST I, q. 118, a. 1, sed contra. Aquinas did not think that every living thing that is spontaneously generated belongs to a new species, but certain imperfect animals can be generated both by spontaneous generation and by seed; see In Meta., 1454. While the mule could be added to the list of species that Aquinas thought have newly arisen, Aquinas regards the mule's characteristics as intermediary between those of its parents, rather than being entirely new; see DP q. 3, a. 8, obj. 16 and ad 16, and In Meta., 1432–33.

⁴² See SCG II, 16: “every agent whatsoever produces something like itself; for it acts according as it is in act.”

⁴³ In Meta., 1403.

⁴⁴ In the passage quoted in footnote 38 “universal nature” is identified with power of the heavenly bodies, and elsewhere as well Aquinas refers to the heavenly bodies as a universal agent, responsible, among other things, for spontaneous generation (see SCG III, 102 and DP q. 6, a. 1, ad 1). While there is reason to attribute change in the living realm primarily to the heavenly bodies, and especially to the sun whose heat and light are crucial for the actualization of various life forms on earth, still they alone do not seem to be what Aquinas is referring to when he says that “the corruption of seeds and every defect are contrary to the particular nature of this [individual] thing determined by a form, although it is according to nature at a universal level, by whose virtue matter is brought to the act of every form to which it is in potency, and when one thing is generated it is necessary that another is corrupted” (Quaestiones Disputatae de Malo, q. 5, a. 5). There seems no need for an additional cause within nature to bring about that the right number of acorns is eaten by squirrels, etc., so that squirrels, etc. are kept alive and the area is not overrun with oaks, while enough acorns remain to continue the species. The question of universal agent causality in nature needs to be examined at greater length, and then applied to the case of evolution.

⁴⁵ Whereas a habitat is the environment in which an organism lives (including both the living and the non-living things found there), a niche is the role an organism plays in a given habitat. A niche is sometimes described as how an organism makes its living.

⁴⁶ See Menno Schilthuizen, Frogs flies & dandelions (Oxford: Oxford University Press, 2001), pp. 191–2: “As should now be apparent, speciation likes nothing better than a good empty niche. Given half a chance, it will rapidly fill it. And that is exactly what happened. Almost immediately after the great dying [Cretaceous/Tertiary], new species started to appear, splitting off from the few species that had survived the cataclysm. Things happened slowly at first, but, as ecosystems began to reassemble, new niches opened up and a great profusion of speciation a few million years later brought species richness back to pre-catastrophe levels… whichever map scale you look at, speciation is prompted by vacating niches at any scale between apple orchard and asteroid impact.”

⁴⁷ Aquinas himself seems to go along with Aristotle's view that new species have frequently arisen by spontaneous generation; see Scriptum super Sententiis, Bk. II, dist. 15, q. 3, a. 1, arg. 7, and ST I, q. 73, a. 1, obj. 3.

⁴⁸ It seems then that Aquinas would have to revise his critique of Empedocles, namely, “[Empedocles reckoned that] it came about by chance that through friendship the parts of animals were brought together so that the animal could live, and that this happened many times. This, however, cannot be, for those things that happen by chance happen in the fewer number of cases; however, we see that suitability and usefulness occur in the works of nature either always or for the most part…” (DV q. 5, a. 2). There is no reason for chance events not to always or frequently be involved in the regular achievement of a goal, namely, the filling of vacant niches, any more than there is a reason to deny that the bad luck of the sperm must frequently occur to maintain the desirable and regularly occurring sex ratio.

⁴⁹ P. B. Moyle, biologist at UC Davis, contends that: “Some of the myriad confusions surrounding the niche concept result from the idea of “empty” or “vacant” niches. Some ecologists have suggested that niches actually exist out in the environment and that organisms evolve to ‘fill’ or ‘occupy’ them. Most ecologists consider this to be nonsense. Hutchinson's niche concept very clearly expressed the idea that a species’ niche is the sum total of adaptations to the environment possessed by the species in question. The niche is just as much an attribute of a species as its color, size, shape, or physiology” (‘Essays on Wildlife Conservation’ http://marinebio.org/Oceans/Conservation/Moyle/ch7.asp). However, while it is true that being a college professor is an attribute of me, still it could not be an attribute of me, if there had been no job opening in a college for me to fill. In a similar way, dung beetles could not live off dung before animals that produced dung arrived on the scene, nor could the specialized bacteria that live in the termite gut do so before there were termites. And if one considers how the evolution of trees was followed by the apparition of new species of moss that grew upon them, it is plain that trees created new “job openings” which the mosses went on to fill.

⁵⁰ I agree that available niches have a quasi infinite character about them, which makes it seem that one could never determine whether or not there was a tendency for them to be filled. For example, the microorganism Symbion pandora lives part of its life cycle attached by an adhesive disc to the lips of the lobster. Many other sea creatures plainly have lips, yet most of them do not have microorganisms making their living there. This would seem to show that there is no tendency for living things to evolve to fill niches. However, the situation is similar to human job market. The possibility of creating jobs that piggyback on other jobs is endless. Yet this does not prevent us from distinguishing a society which is stagnant from the point of entrepreneurship and one that is not. Parasitologists tell us: “Beginning students are often surprised to discover how many different kinds of parasites can infect a single host species; parasitologists considering the rich opportunities provided by vertebrate bodies, however, might wonder why they are so few” (Gerald D. Schmidt and Larry S. Roberts, Foundations of Parasitology, 6^th edition [New York: McGraw Hill, 2000], p. 9). At the same time, they also inform us that “there are far more kinds of parasitic than nonparasitic organisms in the world” (ibid., p. 1) So despite unoccupied sea animal mouths and non-parasitized vertebrate organs, it is possible to ascertain that evolution displays spectacular fecundity when it comes to filling niches, rather than being stagnant. Certainly nowadays, there are fewer niches than there were millions of years ago, so any such tendency would not be so readily observable. However, even now there is evidence that some species in our day are headed in the direction of becoming two species. See Schilthuizen, Frogs flies & dandelions, chap. 6, ‘A Chronic Case of Rhagoletis’.

⁵¹ DP q. 2, a. 3, ad 5. In another place, Aquinas, instead of arguing against the notion that natural necessity removes the need to posit an external governor, simply asserts the contrary as if it were evident: “The natural necessity inhering in things that are determined to one is a certain impression of God directing them to an end; just as the necessity by which an arrow is driven so that it tends to a certain target is the impression of the archer and not of the arrow. But it differs in this, that what creatures receive from God is their nature; what, however, is impressed on natural things by man outside their nature pertains to violence. Whence just as the violent necessity in the motion of the arrow demonstrates the direction of the archer, so the natural necessity of creatures demonstrates the governance of divine providence” (ST I, q. 103, a. 1, ad 3).

⁵² One might ask how is this argument different from Behe's? Again, Aquinas is not arguing that natural causes are unable to produce the effect (e.g., natural causes could not produce the first flagellum), but rather that they are not responsible for the ordering to an end in the effect (e.g., natural causes cannot account for a thing being so adjusted that it serves to propel an organism). In the words of Aquinas: “For material and agent causes, as such, are a cause of the being of the effect; they, however, do not suffice for causing goodness in the effect, as it is both suitable in itself, so that it can continue in existence, and in regard to other things, that it might help them” (DV q. 5, a. 2). The blind material and agent causes of evolution produce the features that allow organisms to survive, e.g., a flagellum, but they themselves do not account for why the feature (e.g., the flagellum) has an arrangement such that it is beneficial to the organism in question (e.g., the bacterium).

⁵³ One might object: how could it be self-evident that intelligence must be invoked to explain the ordering to an end of non-intelligent beings (e.g., why the bacterium's flagellum is organized in a way that allows the bacterium to propel itself through liquid) when so many people, including educated ones, deny it? It is the work of another paper to examine the reasons why people in general deny the obvious, and why they are prone to do so in this particular instance. One of the most widespread reasons is failure to grasp the distinction made in the preceding footnote. One might also object: it cannot be self-evident that intelligence is requisite in order to fully explain the ordering to an end of non-intelligent beings because one can give an argument to establish this proposition, namely, only an intelligent being is able to direct something to an end because it takes intelligence to know the end and the notion of the end, and the proportion between means and the end; indeed Aquinas says as much in SCG II, 23 and DP q. 5, a. 1. It seems to me, however, that this is simply to make explicit a proper accident of intelligence, and therefore the proposition would still be self-evident, granted perhaps only self-evident to the wise (for the latter distinction, see ST I-II, q. 94, a. 2).

⁵⁴ See ST I, q. 103, a. 5, ad 1: “The very fact that something chance is found in things of this sort [i.e., “things under the sun”] shows them to be subject to some governance. For unless corruptible things of this sort were governed by something higher, they would tend towards nothing, most of all those which lack knowledge; and thus in those things nothing could happen [that falls] outside of tendency which is what chance means.”

⁵⁵ Chance events do not escape God's providence: “Divine providence imposes necessity on certain things, but not on all, as certain people believed. For it belongs to providence to order things to an end. However, after divine goodness, which is an end separate from things, the principal good existing in things is the perfection of the universe; which certainly would not exist if all the grades of being were not found in things. Whence, it pertains to divine providence to produce all grades of beings. And therefore for certain effects it prepares necessary causes, so that they happen necessarily; for others contingent causes, so that they happen contingently according to the condition of the proximate causes” (ST I, q. 22, a. 4).

⁵⁶ See Mayr, Ernst, Towards a New Philosophy of Biology (Cambridge, MA: Harvard University Press, 1988), p. 319Google Scholar: “The question is sometimes asked, Why are there species? Why do we not find in nature simply an unbroken continuum of similar or more and more widely diverging individuals? It is now clear that the isolating mechanisms of a species are a protective device for well-integrated genotypes. Any interbreeding between different species would lead to a breakdown of well-balanced, harmonious genotypes, and would quickly be counteracted by natural selection. Such counterselection against hybridization has been demonstrated in nature in literally thousands of cases, even though cases of successful hybridization, particularly in plants, have also been demonstrated.”

⁵⁷ See In Decem Libros Ethicorum Aristotelis ad Nicomachum Expositio, 255, and DV q. 5, a. 1, ad 9.

⁵⁸ I do not mean to imply that I think that chance causes alone are a sufficient source of evolutionary novelty and that other non-chance causes are not operative. This is a matter for biologists to determine. A certain number of biologists see a need to look for natural causes other than chance causes in order to explain evolutionary novelty. For one view on this issue, see M. Parter, N. Kashtan, U. Alon, ‘Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments’, PLoS Computational Biology 4:11 (2008): “The origin of the ability to generate novelty is one of the main mysteries in evolution. … Recent decades saw breakthroughs in the depth of understanding of molecular and developmental biology. Many of these findings were unified in the theory of facilitated variation, presented by Kirschner and Gerhart, that addresses the following question: how can small, random genetic changes be converted into complex useful innovations? In order to understand novelty in evolution, Kirschner and Gerhart integrated observations on molecular mechanisms to show how the current design of an organism helps to determine the nature and the degree of future variation. The key observation is that the organism, by its intrinsic construction, biases both the type and the amount of its phenotypic variation in response to random genetic mutation. In other words, the organism seems to be built in such a way that small genetic mutations have a high chance of yielding a large phenotypic payoff.”

⁵⁹ See In Aristotelis Librum De Anima Commentarium, 851: “Nature makes members for the sake of certain operations. But from this that members are of such a disposition, it follows that they may have some accidents, such having a certain hairiness or colors or corruptions, which are not for the sake of an end, but arise rather from the necessity of the matter.”

⁶⁰ SCG III, 64.

⁶¹ SCG III, 94.