Clara notices things about the Doctor. She observes him when he's too preoccupied with the TARDIS or babbling on about some spacey-wacey stuff that she can hardly wrap her head around; the mere thought that there were millions upon millions of solar systems out there with hundreds and thousands of planets and billions of people makes her head throb. However, all of this information seems to excite the Doctor and he never seems to stop babbling on and on about the planets and all of the alien species out there. It makes her lips quirk at the corners. When the Doctor's talking about all of these things his eyes are alight with wonder and he seems younger.
She also notices how quick he is with his hands; how they dance across the TARDIS's control panel and seem to know every knob and lever and button, and how they move animatedly when he's running on and on about space. He seems so deft with his hands even though he carries himself like a giraffe that's unsure how to use its limbs.
Clara knows she shouldn't be surprised at what she's seeing now. Even though the Doctor was able to pilot the TARDIS with such dexterity, she had a hunch that his hands weren't very clever in the kitchen. He almost dropped the eggs needed to make the soufflé and he could barely crack them without Clara's assistant. It seems like he couldn't make a soufflé, let alone do anything that involved cooking, without Clara's help. He stands back and watches with slight amazement as she cracks the eggs in a bowl and stirs them, like it was a form of witchcraft. She smiles to herself. The Doctor may know so much, but he was just beginning to scratch the surface of the universe.