[SABR42]

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why aren't there tens of thousands of species that are at varying stages between, say, lizards and birds?

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This question shows you really don't understand evolution.

Evolution is constantly branching. The reason you don't see intermediates between lizards and birds is because their ancestors diverged more than 150 million years ago. In short, all "intermediate" forms have all died out and no longer exist. What you are left with are "end-points" that have seperated long ago, but were connected in the past.

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But if the animals were being created on a 'day' (i.e. from the creation account in Genesis, with 'day' being a period of time of millions of years) and species were going extinct with God then creating more.

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There is simply no way you can "excuse" Genesis using the "day = millions of years" idea because the events are still out of order.

Genesis actually states that there were plants, before the SUN. Next...