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What gaping holes?  If you are referring to the fossil record, there are several reasons for this.  First, the relevative geologic time scale is not complete because the Earth is a dynamics system.  Rocks erode, or else don't leave a complete record.  Secondly, the fossil record is incomplete for the same reasons in addition to the fact that fossil preservation is the exception rather than the rule.  If yo are referring to the "no transition fossils" argument, that is a false argument, since transitional species hae been found, and and since all species are transitional.