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The two pneumogastric nerves are the right and left vagus nerves, the tenth cranial nerves: mixed sensory, branchial motor and parasympathetic pathways from the medulla oblongata to the neck, thorax and abdomen. A useful description separates their apparent origin at the surface of the brain from the origins and terminations of their component fibres.

Rootlets emerge in the groove behind the inferior olive, between the glossopharyngeal nerve above and the accessory rootlets below. Branchial motor fibres arise chiefly in the nucleus ambiguus; preganglionic parasympathetic fibres arise in the dorsal motor nucleus of the vagus and, particularly for cardiac control, the nucleus ambiguus. Visceral sensory fibres have their cell bodies chiefly in the inferior vagal ganglion and terminate centrally in the nucleus of the solitary tract; somatic sensory fibres associated with the superior vagal ganglion project to the spinal trigeminal nucleus. Consequently a sensory fibre is not accurately described as originating in a motor nucleus simply because its peripheral nerve emerges nearby.^[ref]

Each vagus nerve leaves the skull through the jugular foramen, with the glossopharyngeal nerve and accessory nerve. It bears the small superior vagal ganglion at the foramen and the larger inferior vagal ganglion below it. Connections include communications with adjacent cranial nerves and the cervical sympathetic nervous system. Traditional descriptions assign fibres joining the vagus nerve from the cranial part of the accessory nerve to the latter peripheral nerve; their modern classification is more nuanced and does not change the peripheral branches being described. In the neck the vagus nerve descends in the carotid sheath, behind and between the internal jugular vein and the internal, then common, carotid artery.

Its meningeal and auricular branches supply small sensory territories of the cranial covering and external ear. Pharyngeal branches contribute to the pharyngeal plexus, supplying much of the soft palate and pharynx; the stylopharyngeus muscle belongs to the glossopharyngeal nerve and the tensor veli palatini muscle to the mandibular division of the trigeminal nerve. The internal branch of the superior laryngeal nerve supplies sensation above the vocal folds; its external branch supplies the cricothyroid muscle. The recurrent laryngeal nerve supplies the other intrinsic laryngeal muscles and sensation below the vocal folds. The right recurrent laryngeal nerve loops beneath the right subclavian artery; the left loops under the aortic arch beside the ligamentum arteriosum. Both return towards the larynx near the groove between trachea and oesophagus.^[ref]

In the thorax, both vagus nerves pass behind the roots of the lungs, contrasting with the anterior course of the phrenic nerves. Cardiac branches join the cardiac plexus; pulmonary branches join the pulmonary plexus. The trunks break up into the oesophageal plexus, then collect principally as an anterior trunk derived from the left vagus nerve and a posterior trunk derived from the right. Through the oesophageal hiatus they reach the stomach; hepatic and coeliac branches distribute to abdominal viscera. Their parasympathetic territory includes foregut and midgut derivatives, extending into the proximal colon, rather than every abdominal and pelvic organ.^[ref] This extensive distribution explains why the level of experimental section is indispensable information.

The main consequences of section can be organized by the interrupted functions:

A discriminating historical experiment would record respiratory movements and heart rate before and after section, distinguish unilateral from bilateral section, and compare an intact airway with an airway bypass. A tracheal cannula can separate obstruction at the glottis from changes in the respiratory rhythm, while the central-versus-peripheral stimulation comparison separates incoming reflex traffic from outgoing motor effects. Later separate-lung recordings confirmed that a change following unilateral section could affect both lungs, supporting a central reflex interpretation rather than simple local paralysis.^[ref] The gastric distinction is also borne out by measurements of persistent acidity after surgical vagotomy, despite major reductions in stimulated gastric acid secretion.^[ref]

The liver is both a metabolic processing organ and the producer of bile. These functions must be distinguished: much of what the liver contributes to the body enters the blood, whereas bile is its secretion into the digestive system.

Portal venous blood brings absorbed materials from the alimentary organs to the liver, while the hepatic artery supplies oxygenated blood. Within the hepatic sinusoids, the incoming blood encounters hepatocytes and scavenging Kupffer cells. Hepatocytes take up, transform, store and release substances; their bile canaliculi conduct bile towards the bile ducts. The organ's position therefore makes it a useful regulator between absorption from a meal and supply to the rest of the body.

Its main non-biliary functions include the following:

This modern list extends beyond the knowledge and biochemical vocabulary of 1867. It is consistent with the organ's combined metabolic, storage and clearance roles, rather than treating bile production as the whole explanation.^[ref]

Bile contains water, electrolytes, bile salts, phospholipids, cholesterol and bilirubin conjugates. Hepatocytes form the primary secretion; ductal epithelium modifies it. The gallbladder stores and concentrates bile between meals and releases it into the duodenum. Production of bile must therefore be distinguished from its intermittent delivery to a meal.

Its two central functions are assistance with lipid digestion and nutrient absorption, and excretion of selected waste substances. Amphipathic bile salts help disperse dietary fat and form mixed micelles carrying products of lipid digestion to the absorptive surface of the small intestine. They thereby promote uptake of fatty acids, monoglycerides, cholesterol and fat-soluble vitamins. Bile is not itself a source of pancreatic lipase, nor does emulsification chemically hydrolyse triglycerides. Biliary bilirubin, produced through haem breakdown, provides an excretory route; cholesterol and selected other substances also leave in bile. Most secreted bile salts are recovered, especially in the terminal ileum, and return through the portal vein: the enterohepatic circulation conserves the useful detergent.^[ref]

Two comparisons reveal why both sorts of function matter. First, compare a fresh liver extract with an extract prepared after an appropriate controlled interval: testing for reducing sugar and isolating glycogen distinguishes a stored precursor from newly liberated glucose. A reliable interpretation needs prompt sampling and controls because post-mortem glycogenolysis can change the result after the animal has died; detecting sugar in an organ alone does not prove where all of it was made. Secondly, in classical biliary fistula observations, diverting bile away from the intestine while collecting it separately allowed its output to be measured and the loss of normal fat assimilation to be examined. Comparing faecal fat with and without delivery of bile distinguishes a digestive contribution from a merely excretory one. The modern explanation is that loss of intestinal bile salts impairs mixed micelle formation, while jaundice from retained biliary pigment is a separate consequence of failed pigment elimination.