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I have taken measurements and by the time the slim side of the salmon hits 60c, the middle is barely scratching 30c. With that gap how can you make sure the inside is cooked without overcooking the surface?

  • How are you cooking it? Are you fine with just totally changing cooking method? – Cascabel Feb 28 '16 at 10:47
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Laws of physics dictate that if you roast / bake a side of salmon (or other fish or meat) with different thicknesses using traditional methods, you will reach different levels of doneness.
This can actually be a good thing, e.g. I have a group of guests who prefer their beef anywhere from rare to well-done and I serve whatever each one prefers.

But of course there are methods to minimize or even completely avoid this, namely those where the fish / meat is exposed only to the target temperature or slightly above, thus eliminating the danger of overcooking.

  1. Sous-vide
    Using a carefully tempered water bath to bring your food to the desired temperature over a rather long time. As the water bath is exactly at the target temperature, you can't over cook.
    This method alone won't give your any "roast" flavours (no maillard reaction), if those are desired, a quick sear or some torching must follow the sous-vide process prior to serving. The disadvantages are a quite long "cooking" time (sometimes hours) and the need for special equipment like special bags, a vacuum sealer and the heating pump. Home equipment is available for around 200$, pro tools can quickly exceed 1k.

  2. Low temperature cooking in an oven
    Either first searing the piece of meat and then slowly bringing it to the desired core temperature in an oven slightly warmer that the desired core temperature or heating first and then searing to finish it off (reverse low-temp).
    Needs no special equipment, is a bit faster than sous-vide but there is the risk of the fish / meat drying out a bit in the oven. Not all ovens run low enough, forcing you to use a slightly hotter than ideal process.

  3. Forgoing the "one big showy piece"
    You can of course cut the fillet into portions and adjust cooking time for each piece individually, either by putting the thick pieces into the oven or pan first and the thinner ones later or by removing the thin ones earlier.
    This of course means that you need to judge the doneness for each piece individually.

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You can also sear skin side down and when you flip it tuck under the thinner side to match the thickness of the rest of the fish. At this point, the skin shouldn't burn as you have reduced the pan temp or finished baking in the oven.

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