Here is the scene where Godwin Baxter make bubbles while eating:
Why does Godwin Baxter make bubbles while eating ?
God's father was an experimenter and used his own son as his test subject. One of his experiments resulted in the disablement of Baxter's digestive system. The machine seems to create stomach acid, but at the cost of also creating other unwanted byproducts, presumably including waste hydrogen since the bubbles are lighter-than-air.
Per the script
The three of them sit at the table. A machine, bubbling away in the corner of the room, is making a foul smelling liquid.
MAX: What is that?
BAXTER: My father took out my oxyntic and pyloric glands, so I must make my own gastric juices.