The first and most serious is that any type of modification will produce a certain type of outcome. While it is true in the most general sense that helpful modifications are more likely to be retained, it is imperative to keep in mind that significant mutations to an organism are typically fatal, and that most genetic mutations that yield living organisms either cannot produce viable offspring or have an insignificant or slightly negative effect. Hence, pure quantity of variance within a species is meaningless, and the big decisions fall to fate: is species X capable of adapting to cataclysmic event Y? While the ability to adapt to diverse conditions is helpful, no significant change will occur in a species without...
Significant alterations, as previously noted, are typically fatal or incidental. Even if they are beneficial, they may not be beneficial at the time, as of a wolf that develops gills. This may be the reason for punctuated equilibrium; the tendency of evolution to progress very quickly in short periods of time, and then slow down incredibly. Cataclysm Y has the capability of isolating a very small group of organisms that are capable of adapting to resulting conditions, thus modifying the entire population without the necessity of waiting on natural selection to perform its slow miracles.
