In Asylum of the Daleks, the Doctor knows
Clara is not alive,
because she is making soufflés. The Doctor asks her where she got the milk from.
Here is my problem. In the future (I assume it is far into the future), there is technology to convert any species into a Dalek, technology to beam on to planets. Even humans travel in space in luxury cruisers, which means they are quite advanced.
Which means, in this future, technology to store milk long term should be possible. Even now, we can store milk for 6-9 months. If humans travel long distances in space, they must have created a way to store milk for even longer. Surely they don't carry a cow with them?
So why would the Doctor assume Clara is dead, rather than assume the more simple, "She must have really high quality, long life milk powder, and I must try some with my tea"?