Lysosomes are acid-containing vesicles that enable cells to digest unwanted material. They are characterised by specific hydrolases which are most active at low pH. Sometimes called "suicide bags," lysosomes are organelles used for the digestion of macromolecules from phagocytosis (ingestion). They form the cell's recycling process, where old components such as worn out mitochondria are destroyed and replaced by new ones, and receptor proteins are recycled. Other functions include digesting foreign bacteria that invade a cell and helping repair damage to the plasma membrane by serving as a membrane patch to heal the wound in the cell membrane. Protein processing in the lysosome system is modulated heat-shock proteins (HSP).

The nervous system, with its long-lived neurons, is vitally dependent on an effective lysosomal waste disposal system. Unlike other cell types, neurons cannot divide to replace cells that have died through the accumulation of indigestible material. Lysosomes are responsible for this catabolism of damaged cells and are particularly prominent in nerve cells, as an efficient way of turning over proteins and dealing with any abnormal proteins.

The products of metabolic breakdown are acidic, and this acid breaks the membranes of lysosomes spilling hydrolytic enzymes into the area to digest the damaged cyctoplasm. The release of hydrolytic enzymes from lysosomes may be a primary cause of neuronal damage. Aged neurons have more difficulty processing proteins and the reduced efficiency of the lysosome-related system may be implicated in ageing and many diseases including Alzheimers.
 
Lysosomes also are also responsible for cell-self-digestion during autophagic cell death, a form of programmed self-destruction, or autolysis. As well as the clean cellular recycling that occurs through apoptosis, there is obviously some occasional messy autolysis that occurs during metamorphosis. As I mentioned before occasionally the sweating of blood happens during peak kundalini intensity of some saints such as Jesus, St. Lutgard and Blessed Christina. This is probably brought about when the body’s capacity for programmed cell death is overwhelmed and a more necrotic form of cell death takes over. Due perhaps to a simultaneous activation of the HPA axis from an acute shock, during a normal die-off immune activation. Such as when Jesus bled through his pores in the Garden of Gethsemani, before being carted off for cruxification. At this time free radical oxidation damage to the lysosomal sacs in his cells was so great they punctured, releasing enzymes into the cell. Whereupon they proceed to eat through that cell, and neighboring cells producing more free radicals as they go. Lysosomal activity is responsible for the accelerated rate of muscle protein breakdown during and after exercise.

A successfully adapted metamorphosis results in a more subtle, efficient body and youthful appearance. If increased free radicals means that the collagen of the body will invariably be attacked and cross-linked then why is it that kundalini leads to a relaxing of the connective fibers of the body? The answer may come from cancer research: “An increase of free radicals could break down the barriers that hem cancer cells in. In most areas of the body, cells and tissues are held together by collagen—a fibrous material made of protein. The University of California’s Bruce Ames theorizes that free radicals and ROS could activate latent collagenases—enzymes that break down collagen. As these enzymes dissolve the collagen glue, local cells and tissues would separate. Cancer cells could escape and move easily to other areas of the body.” 91 Hari Sharma, M.D., Freedom From Disease. Both high free radical and high acid conditions would tend to break the membranes of lysosomes spilling their catabolic enzymes into the surrounding tissue. This could be what Bruce Ames is observing.
Note that in the above quote by Hari Sharma the body becomes “unglued” under the influence of increased free radicals and collagenases. This undoubtedly would make the blood-brain-barrier more porous, plus increase diffusion of chemicals between the central nervous system, cerebrospinal fluid and the blood.

After the initial fight-flight response of the HPA axis backs off the immune system comes on with avengence. The immune cells spew free radicals into the surrounding tissue as well as using them internally in their job as janitor. The immune cells engulf and digest the inferior cells that cannot cope with this increased free radical load. This removal of the weak and old makes way for the new cells to be constructed at a higher energy level, using the building blocks of the old cells. The butterfly is thus metamorphosizes from the gestating pupae.

The release of free radicals and collagenases (collagen digesting enzymes) from macrophages and neutrophils can result in widespread cell damage, amounting to widespread cellular inflammation. Also while fighting the macrophages release interleukin-1 which travels to the hypothalamus and increases the body temperature, this mechanism for creating fever disables bacterial reproduction. The increased heat helps to eliminate the body’s microbe population to free up the immune system for the work of reconstruction.

Eric Van Winkle (Toxic Mind Theory) says that these lysosome enzymes degrade proteins, nucleic acids, mucoplysaccharides, fats and glycogen, but they do not degrade catecholamines, serotonin, GABA and amino acids, and that during the detoxification crisis these substances flood the synapses.

 (See more on how the body catabolically dissolves and recycles itself in Autolysis—Self Digestion)