After doing some scanning and research you should have unlocked the Observation: Alchemy field. Once you have done this, go to your Thaumonomicon and complete the first step of the Discovering Alchemy stage.
The next step will require you to make a Crucible. This is done by right-clicking Salis Mundus on a Cauldron:
If your Crucible is close enough to your research table you will get another icon on the table giving you more bonus research:
The Crucible will allow you to insert items, break them down to their aspects and will allow you to combine them to make new items. This is a very crude way to making items because any extra aspects will be released into the air causing FLUX. The more flux you have in the air, the higher chance you have of causing Taint, and Taint is not good.
In order for the Crucible to work it will need to be filled with water and have a heat source below it. You can use fire, lava, magma, or later nitor. To insert items into the crucible you can either drop them in or right-click them onto the Crucible while in hand. Later, using Goggles of Revealing will give you the ability to tell which aspects are currently in the crucible. Be careful not to right click the water with an item as you will lose it.
PLEASE ENSURE THE CRUCIBLE IS IN A SAFE AREA. ACCIDENTS DO HAPPEN AND ITEMS WILL BE LOST IN THE CRUCIBLE.
Once water is placed into the Crucible, the water will take a few seconds to boil and then you know it is ready for items to be inserted.
Complete the next step of the Discovering Alchemy stage in your Thaumonomicon. Once completed, you will be given more information about Alchemy and how to create Yellow Nitor.
To create Yellow Nitor you will first need to fill the Crucible, then you will need to add in the following aspects:
Once these are in the crucible we will need to add in 1 Glowstone Dust. The best way to create this is with:
Once these have been put into the Crucible, you will notice different coloured bubbles appearing. This means that there are Aspects in the Crucible (always check your Crucible).
Next, you can right click with your Glowstone Dust. A big puff of smoke will appear and you will be given one Yellow Nitor.
In the beginning of Alchemy it is difficult to add in the exact amount of Aspects needed per item. In the above case we added in extras:
These extra aspects will still be left in the Crucible even after crafting the Yellow Nitor. You can see this by looking into the Crucible and seeing colourful clouds. This will slowly in time dissolve into the world and cause small amounts of flux. You can also sneak-right-click the Crucible to remove this manually but it will release all the flux into the air at once.
You can see how much flux was let loose by using your Thaumometer and look at the top left of the screen:
This small dark sliver is flux entering into the local area.
You can also extract some of the remaining Essences by right-clicking the Cauldron with Quartz Slivers (Nether Quartz in a crafting grid).
These will turn into Vis Crystals of whatever essences are in the Crucible:
Nether Quartz Slivers can be used to soak up most leftover aspects. For each sliver, 2 Essentia will be removed from the crucible in return for one Vis Crystal of that aspect. As it takes 2 Essentia, this is best done with even numbers of Essentia and is safer than letting it turn into flux.
If you do have a build up of flux, you might have to move your base, depending on how much has built up. Flux will dissipate into surrounding chunks so be careful how much is around. Scanning this flux will also unlock the Flux Section.
You can complete this section, however, this guide will cover more on Flux later.
Yellow Nitor can be placed in the world as a cool light source, and when put under your Crucible it will heat up the water. It is also used in a few crafting recipes.
Once you have completed the last stage of Discovering Alchemy, a new tab will open up for you on the first page of your Thaumonomicon called Alchemy:
Looking in this section and clicking “Basic Alchemy” will unlock more options about Alchemy and a lot more in this section of the Thaumonomicon:
Since we now have access to the Alchemy tab, it’s a good idea to start some very basic Alchemy so we can advance the first section of the Thaumonomicon.