Evolution Theory
The evolution theory, especially in its purely materialistic interpretation, seems to be incomplete and in itself insufficient to explain the development of the various species (particularly that of the human race) in its entirety. Before taking a (brief) look at the problems around this theory, first it should be noted, that, of course, those parts of this theory, which describe the relations between the different species, are well founded and proved with scientific accuracy, and a dualist evolutionary theory can accept this side of the materialistic interpretation (i.e. the fact that the species were formed from each other during billions of years) without any reluctance. (Actually, fighting this aspect of the theory from an idealistic point of view does not make much sense, since in reality it could be used to stress even more the importance and singularity of the human race, as it is on the top of a billion years long evolutionary process now (instead of only a 6-day creation), furthermore it is now scientifically confirmed the only species which has liberated itself from the effects of the evolutionary mechanisms (see below in more detail), thus in its "divinity" qualitatively separated from the animal world, contrary to the only quantitative difference in the old, traditional "theory", where the animals were also god-made creatures.)
The problems around the theory begin with the purely materialistic interpretation of the facts discovered by the evolutionary scientists, and with the intention to use this in itself very logical and nice theory to discredit the dualist world view, to define the humans as mere physical beings without any soul and spiritual nature, and to try to expel the providence and any divine principle from the world. To invalidate this "theophobic" translation of the evolutionary theory it is basically enough to recognize, that even the most materialistic interpretation of the theory (i.e. if all species, including the human race, were developed and formed solely by physical and biological mechanisms without any supernatural force) could not disprove completely the existence of spiritual beings or gods in the human history, as it would remain possible, that these beings started to influence the humanity after it has already evolved into its current biological constitution (i.e. around some ten thousand years ago), and since then they continously affect our fate. (Actually, it is much more probable to observe divine effects in the history of the mankind after the beginning of the civilization than before it, since a civilized community obviously needs a much higher degree of care and protection, than a subhuman horde at the level of half-animals.)
Another problem with the evolutionary theory is the fact that it could not find any automated mechanism in the really creative, the mutational part of the process, exclusively in the selectional part. E.g. if we have two "twin" bacteria with the exact same duplicates of the genome, and we start to breed two populations from them in the same environment (temperature, light, etc.), then at the end (after many generations) we will get two almost completely different populations with divergent genomes as a result; moreover, we have absolutely no clue before the process, which population will develop in which direction, at what phase and in which gene a mutation will appear, but these mutations seem to come literally "out of the blue", without presenting any possibility to predict them. The evolutionary theory is apparently not able to make any prognosis about the exact type of mutations during the breeding process, even in such an uncomplicated scenario (with fully controlled environmental factors and very simple organisms), and can provide at most a statistical type of expectation in a rather uncertain manner (e.g. in 50 generations there will be roughly 1000 mutations observable). It seems probable (at least at the level of the science today) that there are no physically or biologically describable mechanisms behind the mutational process, and that these changes in the genes appear completely randomly (from a purely biological or materialistic aspect). But, since this is the actually creative part of the process, while the selectional part serves only the purpose of throwing the defective individuals away, the (well proven) existence of the selectional automatism in itself could easily be reconciled with a hypothesis about the divine source of the mutations, because we could suppose that these mutations do originate from spiritual beings (e.g. through the medium of the quantum uncertainty), and the selectional part is only there to relieve these from the burden of checking each new mutation "by hand". In fact, it would be much less godlike, if these beings did not have enough intelligence to recognize that this selectional part of the process could be automated, and instead they performed the selections over and over again "manually". Let's notice too, that we humans also tend to automatize the selectional part of the creative processes, and exactly this section of the development procedure is the one, where even the most ingenious and thoughtful creators behave passively (e.g. Edison only stared at the newest version of his light bulb to see, how long it lasts, or, during the development of a car, the engineers only watch without any interventions, as the prototype rounds on the test circuit). Hence, for a complete materialistic evolutionary theory evidently a purely biological mechanism should be found in the mutational, the truly creative procedure (i.e. it should be proved that the nature tries out every gene combination in some systematic way), and until such a discovery, the fact itself, that the selectional part is automated, could support at least as much the dualistic as the solely materialistic interpretation.
A further problem concerning the evolutionary theory seems to be the importance, which it attributes to the sexual type of selection. It turned out really soon in the 19th century, that the natural selection in itself is not enough to explain many, seemingly completely irrational, phenomena in the animal world, and to resolve these objections the sexual selection was introduced, which derives the often observable irrationality in the appearance of the various species from the irrationality of the female thinking (in accordance with the views of the Victorian age about the characteristics of the women). For instance, the "official" answer to the question, why the male lions have a mane and the male tigers not, is, that the female lions are attracted by a mane and the female tigers not. But, honestly, to what degree is this explanation better scientifically, than e.g. referring to some gods' intentions, and supposing, that they wanted to have a lion with mane and a tiger without one, or, that the creator spirit of the lion had an affection for the manes, whereas the god creating and managing the tiger species has a dislike for it? Of course, it is better in the aspect that we do know a mechanism between the female affection and the success of the male individual (i.e. the probability of this feature to get inherited), but we have absolutely no chance to explain materialistically, exactly why a female has this type of affection and not another one, why are these differences observable between the females of the various species, and why not between the females of the same species (which latter is naturally also needed to help a new male feature succeed, an individual female affection is not enough at the level of the species). In fact, a dualistic evolutionary interpretation could deduce, that the sexual selection (and the entire sexual reproduction) was invented by the gods exactly for the purpose, so that the brutality of the natural selection could have been tempered, and that they would get back the opportunity to support (through the medium of the female irrationality determined by them) seemingly irrational features, which do not increase the life chance in the short term (or actually decrease it), but in the long term could evolve into something more complex designed and favored by these spirits. If the materialistic interpretation would like to disprove such a hypothesis, then it should at least try to construct a theory about the female affections and dislikes, which could be able to explain the nature of these without any superficial element and completely on a materialistic basis. But until that, the sexual selection seems to support more a dualistic interpretation, as it renders this part of the selectional process too (additionally to the mutational process) materialistically unpredictable, and, while at the very last step (between the female affection already manifested and the chance of the male winning this female over) is indeed a mechanism provided, the entire development and maintaining procedure of the affections and dislikes itself is completely obscure and mysterious from a materialistic point of view.
Similarly, the fight between the male individuals could also be seen as a medium for the gods to support a favored feature despite its current unfinished state, since obviously in a short fight (only some minutes long) the individual luck plays a much greater role, as in the everyday struggle for life, and so these fights could give a chance to the individuals possessing favored features to eliminate quickly (with the help of their protecting spirits) the other individuals, without the need of coming through all the difficulties of the usual struggle (as e.g. in the middle ages an individual could make rapidly his fortune by taking part in a campaign or a tournament without having to succeed in the everyday work).
Another problem with the evolutionary theory seems to be its tendency to use the statistical approach even at a low number of individuals. Obviously, at the level of a single individual, a new feature, even if it is very advantageous, simply cannot modify this one animal's chance to succeed in the struggle for life to a determinative extent, and this trait must already have some frequence in the population, before its advantage can have a statistical effect on the individuals' life expectancy and success chance. The question is, what really happens in the time frame between the appearance of this new feature in one individual and the point, where it is widespread enough to have a determinative impact on the survival chance of the individuals possessing it, as in this time only the pure luck (in the materialistic interpretation) or the protection of its managing spirit (in the dualistic one) can help this precious single individual survive and succeed in transmitting the new trait to the next generation. We obviously do not have the methods computing the probabilities for the two interpretations exactly (or even approximately), but it is certainly hardly justifiable scientifically to use the statistical approach already for this time frame (with low number of individuals having the new feature) and to make this pure luck appear as a materialistically determined necessity.
This leads us to the problem concerning the nature of the (objective) randomness and the scientific value of referring to the unpredictability as explanation factor. Obviously, from the randomness everything can be derived and also the opposite of everything; therefore, it hardly provides any real quality scientifically to attribute the development of the species (or any other occurrences) to the work of the objective randomness. And although it seemingly does possess the advantage that with this explanation the assumption about the potential existence of mental, spiritual factors behind the material realm could be made apparently invalid or superfluous, but this would only mean (as we have already seen) "casting out devils by Beelzebub", since the objective randomness is much worse from a rationalist point of view, than any gods or spiritual principles could ever be. E.g., the materialist interpretation of the evolutionary theory could not have made any predictions, let's say, 1 million years ago, about the emerge of the human race (or any other evolutionary event after that point), because the nature of the randomness is absolutely unpredictable (from a materialist aspect), and anytime could happen a mutation, which turns the process into a previously unsuspected direction; however, a dualistic interpretation actually could have provided such a prognosis at that time (1 million years ago), if the intelligent principles behind the mutational process (potentially determining it through the medium of the quantum uncertainty) had then already decided to let the human race appear and emerge (or any other development process happen). Evidently, a dualistic interpretation of the randomness can supply (theoretically) scientifically much valuable predictions than a materialistic one (which latter virtually cannot supply any), and only the fact that in the evolutionary theory there is no real need for predictions about the future developments of the various species, makes the materialistic interpretation look as if it were scientifically exhaustive and complete. Furthermore, since there is only one nature that we can observe, and the evolution progress is extremely slow and practically irreproducible, we simply cannot compute the probability of receiving such an organized biological world exclusively from the source of the the mutational process' randomness as a result, and, consequently, we also do not possess any methods to determine a scientifically justifiable relation between the possibility of a materialistic and a dualistic explanation.
Finally, the materialistic interpretation seems not to recognize that by forcing itself also in the case of the human race it actually weakens or even contradicts itself, and would be better off leaving the human race out of this interpretation (and accepting its possible god-made nature). First, it is already problematical to explain the quick development of the human race biologically at the beginning of the civilization in itself, but it is even more difficult to justify, why the other species (especially the great apes) could not take this hurdle, and why they did not develop further in that direction. It is also hard to understand, why should a species possess intelligence and reasoning for the pure survival, since all the other species can solve this simple task using their inborn instincts only. Moreover, it is obvious that the human race does not accommodate to the environment changes with the genetical method (i.e. by mutating its genes), but with the help of tools and by modifying intelligently its environment, and so makes itself liberated from the evolutionary mechanisms and procedures, eventually emerging to the ruler of the entire animal kingdom without the need of any genetical variation or mutation. This fact shows evidently that the evolutionary process is too slow to be really effective, and that the genetical accommodation is a very undeveloped and primitive way for assuring the survival of a group, which works only so long as all the other species are on this path, but if only one comes through somehow to the intelligent method of adaptation, then the chance of the survival for the other species drops immediately significantly. So, if we accept the materialistic interpretation about the development of the human race, then we must also accept that the intelligence can be developed exclusively biologically, and, since it is a much more effective way of the survival than the genetical one, it is only a question of time that other species also will take this hurdle, and after some millions of years, the evolutionary (i.e. the biological) method will be completely eliminated from the development, since all species will be intelligent (or already extinct) at this point. Actually, a bit paradoxically, for the materialistic interpretation it would be more advantageous, if the human race turned out to have been created by some supernatural forces (e.g. by improving the genomes of evolutionary developed apes in the laboratories of extra-terrestrials in ancient times), because then the evolutionary process could remain in its place even for billions of years, but in the other case, if the human race is a pure natural product of the biological evolution, it would be clearly proved that the evolution is able to generate an intelligent species on its own, and then of course it could repeat this stunt at any time, eliminating itself completely in the end.