2. The structure and processes of autophagy:

Figure 1. The Cellular, Molecular, and Physiological Aspects of Autophagy

The cellular events during autophagy follow distinct stages: vesicle nucleation (formation of the isolation membrane/phagophore), vesicle elongation and completion (growth and closure), fusion of the double-membraned autophagosome with the lysosome to form an autolysosome, and lysis of the autophagosome inner membrane and breakdown of its contents inside the autolysosome. This process occurs at a basal level and is regulated by numerous different signaling pathways (see text for references). Shown here are only the regulatory pathways that have been targeted pharmacologically for experimental or clinical purposes. Inhibitors and activators of autophagy are shown in red and green, respectively. At the molecular level, Atg proteins form different complexes that function in distinct stages of autophagy. Shown here are the complexes that have been identified in mammalian cells, with the exception of Atg13 and Atg17 that have only been identified in yeast. The autophagy pathway has numerous proposed physiological functions; shown here are functions revealed by in vivo studies of mice that cannot undergo autophagy (see Table 1).[1]

Autophagy means self-eating.  Autophagy is the orderly removal of warn out parts and the subsequent shipment to lysosomes for utilization of some of its molecules, and thus by so doing autophagy makes room for new fully functional parts and cells.  It is a cellular service and replacement system.  Autophagy is similar to apoptosis (3:2,7) and the two overlap.  “Autophagy not only recycles intracellular components to compensate for nutrient deprivation but also selectively eliminates organelles to regulate their number and maintain quality control.” [2]  It is a major catabolic pathway in eukaryotes and fungi utilizing lysosomal degradation of cytoplasmic proteins and lipids.[3]   Replacement of defective cell parts is essential of cellular health, and this must be done in a controlled way so as to limiting the escaping of reactive chemicals through autophagy, apoptosis, and related repair systems.  The system promotes optional cell functions.[4]  “Autophagy principally serves an adaptive role to protect organisms against diverse pathologies, including infections, cancer, neurodegeneration, aging, and heart disease.” [5]   The downregulation of these processes is the major CC for CAWD; but how?

          AS will be developed in the subsequent chapters of this section, major contributors to CAWD are the delayed replacement of MTDD and collagen.  Other major downstream CCs includes a sensitivity to uric acid, the development of fatty liver, IR and its child LR.  Over 90% of the adult population has at least one of those just listed defects.  The norm on a blood test, such as for fasting glucose is pathogenically high because the standard should be that of LSPs.  Another sign is a malfunctioning WRS that results in a BMI above 25 or excess abdominal fat, a TOFI.  The comparison to the lean, health, and young is misleading.[6]  Under the umbrella of autophagy and apoptosis are the repair and replacement processes.  All of these require the optimal availability of ATP, which because of MTDD isn’t available.  Every cell in the body is operating at a substandard level.  Sub-optimal function of autophagy is the major CC for CAWD.  It is for these reasons that a survey of autophagy is in order.  There are six special structures and 9 processes described under the umbrella of autophagy:

          Organelle is a specialized membrane-bound subunit[7] within a cell that has a specific function, a cell compartment.  There are many types of organelles, there function.  One of them for vertebrates has DNA, the mitochondria.  They are bound to protect the reactions that occur within and to prevent the escape of reactive chemicals.  Major eukaryotic organelles include vacuole for storage and transportation; nucleus for DNA, mitochondrion for energy production, Golgi apparatus for sorting, processing and modification of proteins endoplasmic reticulum for translation and folding of new proteins.  There are at least 22 types[8] of organelle, for which 4 are described below because of relevance to autophagy. 

          Lysosome is a membrane-bound organelle found in most eukaryotic cell and most plant cells.  They contain hydrolytic enzymes that can break down many kinds of biomolecules.  Lysosomes are the repository for the items delivered to it for dismantling.  Besides the degradation of polymers, the lysosome is involved in various cell process including secretion, plasma membrane repair, cell signaling, and waste disposal—waste from both within the cell through autophagy and outside the cell through endocytosis.  “Structures targeted for destruction are sequestered into large double-membrane vesicles called autophagosomes and then delivered into the interior of the lysosome or vacuole, where they are consumed by resident hydrolases.  Autophagosome formation during selective autophagy is dependent upon the cargoes, and in all cases seems to involve expansion of the sequestering membrane.” [9]  The lysosome contains more than 60 different enzymes and 50 different membrane proteins.  Their enzymes are synthesized in the rough endoplasmic reticulum and imported therefrom by the Golgi apparatus in small vesicles.  Lysosomal enzymes can catabolize peptides, nucleic acids, carbohydrates, nucleic acids, lipids, and a number of their polymers found in larger structures such as organelles that have been transported to the lysosome.  Many components of animal cells are recycled by through the formation of protective vesicles.  Lysosomes are also part of the immune system in that pathogens are wrapped in vesicles and transported there for catabolism.          Lysosomes essential functions for autophagy consist of catabolism of wastes and providing molecules for the replacement process. 

          Phagosome is a vesicle is formed around a particle engulfed by a phagocyte.  Professional phagocytes include macrophages, neutrophils, and immature dendrite cells (but not mature dendrites).  When the phagosomes attaches to the lysosome it is called a phagolysosome.  Its contents can have included a microorganism, a senescent cell, or an apoptotic cell.  The membrane has proteins which enable fusion with lysosomes.  The lysosome can also destroy and digest a pathogen with its ROS, RNS, and hydrolytic enzymes.  The products of digestion if useful are moved into the cytoplasm, and the waste is removed by exocytosis.  In addition to professional phagocytes, there are non-professional phagocytes that have only some degree of phagocyte activity, such as thyroid, bladder, and epithelial; they lack the specific phagocytic receptors.  Phagosomes also play additional important immune functions through inflammation.  Erythrocytes are by numbers the most of all cell that undergo apoptosis by the macrophages, which occurs in the liver and spleen at their lysosomes.

Endomembrane system, details of and its components

Golgi apparatus (Golgi complex, Golgi body, and Golgi): is an organelle found in eukaryotic cells.  It is part of the endomembrane system in the cytoplasm.  Golgi apparatus packages proteins into membrane-bound vesicles for transport to destinations.  It either proceeds to the lysosome or return to the Golgi apparatus.  The Golgi apparatus resides at the intersection of the secretory lysosomal and endocytic pathways.  Of particular interest is the proteins that are transported into the MTD, in that system which supplies over 90% of the MTD proteins.[10]  And there are other uses, for example, the endosomes seek out LDL that has entered the cell through LDL receptor.  The endosome is a receptor for the contents of LDL and then the endosome proceeds to the area in need of cholesterol and fatty acids.  

Autophagosome are organelles which during autophagy function as transport vehicles that deliver cytoplasmic contents to the lysosomes.  The outer membrane fuses with a lysosome to deliver the autophagosome’s contents[11] for dismantling that results in re-usage and excretion.  “The formation of autophagosomes is regulated by genes that are well-conserved from yeast to higher eukaryotes.” [12]  Despite its simplicity, recent progress has demonstrated that autophagy plays a wide variety of physiological and pathophysiological roles.  “Autophagy consists of several sequential steps—sequestration, transport to lysosomes, degradation, and utilization of degradation products—and each step may exert different function.” [13] Among autophagosome’s functions is the regulation of fat metabolism, thereby they are part of the WRS and involved in its dysfunction; just how, as far as I know, has not been adequately determined.  And there are other functions:  “This degradative pathway allows cells to eliminate large portions of the cytoplasm, from aberrant protein aggregates to superfluous or damaged organelles and even entire organisms such as invading bacteria.” [14]  However, it is mainly the phagosomes that digest bacterial, and autophagosomes are used mainly to selectively degrade damaged cytosolic organelles such as MTD (mitophagy).  The complex of the autophagosomes which often varying according to tissue type, is illustrative of the advancements made that promote survival in vertebrates.

Macroautophagy, which is the main pathway used to dismantle damage organelles for recycling of and disposal of the molecular constituents, in a process that occurs in the lysosomes.  An autophagosome membrane is formed around the organelle for transport into the lysosome for degrading via acid lysosomal hydrolase.   

Microautophagy occurs with the engulfment of cytoplasmic material and transport into the lysosome and vacuole in plants, fungi and some Protista (one of the 4 types of eukaryote).  Macroautophagy and microautophagy perform nutrient recycling, which promotes survival during starvation by recycling amino acids. membrane proteins, and other membrane components which would otherwise be in short supply and cause the dismantling of proteins as a source for building materials.  Microautophagy as with macro is part of the cellular/tissue tune up process, removing the old beyond repair to make room for the new functional replacement, and there is a net conservation of energy (ATP). 

Central to the function is the autophagosome, a spherical structure with double layer membrane, used mainly for the degradation for cytoplasmic contents and also for invading microorganisms.  Eventually the autophagosome will attach to a lysosome and deliver its contents. 

          Barbieri’s 382-day fast:  A person can go for quite some time without metabolizing muscle during starvation, depending on percentage of stored fat to lean weight.   Angus Barbieri, a 456 lbs. Scotsman, starting in June 1965, went on a medically supervised water fast lasting 382 days and lost 276 lbs.  He consumed only vitamins, electrolytes, and zero-calorie beverages.[15]   The case study published 7 years later found that his average blood glucose was 30 mg/dL (1.7 mmol/L),[16] which confirmed that he wasn’t eating—as too the weight loss.  That he didn’t need an operation to remove the folds of skin is an example of his body’s efficient use of autophagy to recycle amino acids from the skin and adipose tissue.[17] Only when fat stores become low, does the body start metabolizing muscle. Not all are so fortunate, and a friend of mine, a geriatric physician, had to undergo surgery to remove the folds.  He lost nearly 200 pounds eating 1 meal a day and without medical supervision.  Note: after a half hour I gave up on trying to find Agnus’s cause of death at the age of 50 and weight at that age.  However, on an examination at after 7 year, he had gained only 16 pounds—much better than the contestants on the Biggest Looser show[18] 5:1.     EXPAND

A top view of the GroES/GroEL bacterial chaperone complex model

Chaperone-mediated autophagy (CMA) targets proteins with hsc70 complex, which allows the binding of the protein to the chaperone.[19]  “CMA is significantly different from other types of autophagy because it translocates protein material in a one by one manner, and it is extremely selective about what material crosses the lysosomal barrier.” [20]  There in for example the endoplasmic reticulum 4 types of chaperones. There are many different families of chaperones; each family acts to aid protein folding in a different way. Look up at the photo of a chaperone and the hundreds of amino acid placed in exact positions.  To paraphrase Darwin, there is grandeur in the complexity of chaperone system.

Mitophagy is the selective degradation of MTD by autophagy.  It thereby prevents the accumulation of dysfunctional MTD, which can lead to stress from the release of ROS, and from the diminished production of the fuel ATP, both of which are CC for cell degeneration.  Moreover, when there are sufficient MTDD or the cellular functions are downregulated are sufficient, the MTD will start the signalling pathway for apoptosis.  Mitophagy is essential for normal cell functions.      EXPAND

          Lipophagy is the degradation of lipids by autophagy, a process that also occurs in animals and fungi.  Lipid droplets store triglycerides and then supply them as needed for metabolism.  “The triglycerides are taken up by autophagosomes and delivered to lysosomes for degradation by acidic hydrolases.  . . . by the lysosomal degradative pathway.  . . .  to supply free fatty acids.  . . . Lipophagy regulates intracellular lipid content.”[21]

          Xenophagy as part of the immune system the degradation of infectious particles there are a long list of pathogens are destroyed including tuberculosis. A subset of pathogens has evolved to evade that process and promote their own replication, while others have been able to block the maturation of phagosomes. 

Peroxisome is an organelle known as a microbody[22] found in the cytoplasm of eukaryotic cell.  It is a digestive organelle, involved in catabolism of every long-chain fatty acid and branched chain fatty acids (through beta oxidation), D-amino acids, polyamines, and reduction of ROS, and also the biosynthesis of phospholipids, which are used to from myelin that is used for the myelination of nerve cells.   Peroxisomes also play a role in the synthesis of digestive biles.  Humans lack the oxidative enzyme uric acid oxidase found in most other mammals in the peroxisome, and because of this specie-wide elision some human develop gout.  Peroxisomes are found in addition to vertebrates in plants and yeast.     

          Endosome is an organelle in eukaryotic cells that are part of the transport from the Golgi membrane to the lysosome and back.  They have been shown to be involved in iron metabolism and regulation[23] as a hub for contents from lysosomes,[24] and they are involved in neural development[25] and neurodegenerative diseases.[26] 

3. Apoptosis:  There isn’t a clear separation between the 3 types of cell death, in that there often is a shift during the dismantling process between one type to another type of cell death.  “Cell death has been subdivided into the categories apoptosis (Type I), autophagic cell death (Type II), and necrosis (Type III). The boundary between Type I and II has never been completely clear and perhaps does not exist due to intrinsic factors among different cell types and the crosstalk among organelles within each type.  Apoptosis can begin with autophagy, autophagy can end with apoptosis, and blockage of caspase activity can cause a cell to default to Type II cell death from Type I. Furthermore, autophagy is a normal physiological process active in both homeostasis (organelle turnover) and atrophy.   ‘Autophagic cell death’ may be interpreted as the process of autophagy that, unlike other situations, does not terminate before the cell collapses.” [27]  The type of dismantling is highly dependent on conditions in which it occurs, needs for amino acids, cell parts, availability of ATP, and therefore on inter and intra cellular signaling.  When types I & II systems functioning at optimal level there is better tissue functions, and thus health.  The role of ATP and thus MTD is at the core of these processes.    

4.  Necroptosis in response to pathogens, cell death turned on in response to pathogens.  “Unlike in apoptosis, necrosis and necroptosis do not involve caspase activation. Necrotic cell death culminates in leakage of cell contents into the extracellular space, in contrast to the organized disposal of cellular contents into apoptotic bodies.  [The release of reactive chemicals could be destructive to the pathogen.]  Unlike in necrosis, permeabilization of the cell membrane during necroptosis is tightly regulated.  . . . The necrosome inhibits the adenine nucleotide translocase in mitochondria to decrease cellular ATP levels.   Uncoupling of the mitochondrial electron transport chain leads to additional mitochondrial damage and opening of the mitochondrial permeability transition pore, which releases mitochondrial proteins into the cytosol. The necrosome also causes leakage of lysosomal digestive enzymes into the cytoplasm by induction of reactive oxygen species by JNK, sphingosine production, and calpain activation by calcium release.”[28]   

5. Autophagy’s role in cancer suppression:  while I wish not be sidetracked by this topic, given the fundamental flaw in the model for cancer, and this flawed model is used to explain autophagy’s role, I shall briefly go over the topic.  Simply put, a precancerous cell is normally marked by MTD for apoptosis (3:2,7); however, when certain mutations occur, the precancerous cell deforms the MTD sufficiently to turn off the MTD directed apoptosis therefor permitting the that cell line to grow vegetatively.  At this stage it might be able to invade adjacent tissues.  To become a fatal (thus metastatic cell line) certain genes are turned on which make that new cell line immortal and others to make it line invisible to the immune system.  These are the genes which make macrophages invisible permitting the macrophage to travel to distant tissues.   A seminal article argues that this occurs through a gene swap with a macrophage[29]—the validity of this swap claim I cannot now comment upon.  This event of activated genes converts a stage I, II & III cancer into a stage IV cancer.  Autophagy is essential for preventing cancer through apoptosis of the precancerous tumor, and also of the non-metastatic cancers. “In this review, we discussed the relationship between autophagy and carcinogenesis. Based on multiple studies, it has been concluded that autophagy plays an anti-neoplastic role in cells.” [30]  There are many reports that autophagy may act as a censer suppressor.” [31]Again we have pharma muddling the science to promote profits and using association to blame the bystander. 

5.  Necroptosis in response to pathogens,

Necroptosis is programmed cell death, that has been turned on in response to pathogens.  It is a form of necrosis with the release of reactive chemicals within the cell that often disable the pathogenic-infective contents.  It is grouped by many under the label of autophagy.  This is a major role in the war against pathogens which is outside of what is labeled as the immune system.

Although necroptosis may have evolved as a line of defense against intracellular infection,^6,7 recent studies implicate it in a variety of disease states. Necroptosis is of central pathophysiological relevance in myocardial infarction and stroke,^8,9 atherosclerosis,¹⁰ ischemia–reperfusion injury,^11,12 pancreatitis,^2,4,13 inflammatory bowel diseases,^14,15 and a number of other common clinical disorders. At the molecular level, intracellular assembly of a highly regulated complex, the necrosome, can be triggered by death receptors (e.g., tumor necrosis factor [TNF] receptor 1 [TNFR1]),^16-18 by cell-surface toll-like receptors,^19-21 by DAI (which may act as a cytoplasmic viral RNA sensor),^22,23 and probably by other signals.[1]

          The list above places necroptosis as to importance well above the normal conception of immune system functions.

Unlike in apoptosis, necrosis and necroptosis do not involve caspase activation. Necrotic cell death culminates in leakage of cell contents into the extracellular space, in contrast to the organized disposal of cellular contents into apoptotic bodies.  [The release of reactive chemicals could be destructive to the pathogens.]  Unlike in necrosis, permeabilization of the cell membrane during necroptosis is tightly regulated.  . . . The necrosome inhibits the adenine nucleotide translocase in mitochondria to decrease cellular ATP levels.   Uncoupling of the mitochondrial electron transport chain leads to additional mitochondrial damage and opening of the mitochondrial permeability transition pore, which releases mitochondrial proteins into the cytosol [and ROS]. The necrosome also causes leakage of lysosomal digestive enzymes into the cytoplasm by induction of reactive oxygen species by JNK, sphingosine production, and calpain activation by calcium release.”[2]   

This ties in with statement of the functions of ROS, one of which is as an immune function.

6. Autophagy’s role in cancer suppression:  while I wish not be sidetracked by this topic, given the fundamental flaw in the model for cancer, and that this flawed model conflicts with the role of autophagy, I shall briefly go over the topic.  Simply put, a precancerous cell is normally marked by their MTD for apoptosis (3:2 & 3:4).  When certain mutations occur that cause major dysfunctions of the cell, the MTD within the cell cause signaling markers on the cell surface that cause apoptosis (a similar process (#5) initiated by the MTD when their cell is infected; markers are transported to the cell walls which turns on necroptosis.  Apoptosis is the body’s mechanism for dismantling precancerous cells.  For a cancer to become life threatening, it turns off the MTD though mutations; thereby turning of the apoptosis signaling system.  To obtain the essential ATP the tumor cell switches to t he  anerobic fermentation system, which produces about 1/15^th the ATP it would through the Krebs cycle.  Nobel Laurette Otto Warburg around 1923 observed that cancer cells have defective mitochondria.  That process of turning off the MTD is known as the Warburg hypothesis; the implication of which pharma opposes.[3].  thereby bypassing the MTD.  This process is underperforming for those on the western diet, which is why among the elderly, for example the prostate, there are about half whom upon autopsy are found to have clumps of local cancerous cells.  Undoubted, if a similar study was performed among LSPs that finding would not occur. 

What turns a local cancer growing vegetatively or having reached it limit, into a metastatic cancer is not a series of six mutation.  IR is the turning on of certain genes that make the cell line immortal and others to make it line invisible to the immune system.  These are the genes are found in every cell, and are those which make macrophages invisible permitting the macrophage to travel to distant tissues.   A seminal article argues that this occurs through a gene swap with a macrophage[4]—the validity of this swap claim I cannot now comment upon, it could be just turning those genes on.  This event of activated genes converts a stage I, II & III cancer into a stage IV cancer. 

Autophagy is essential for preventing cancer through apoptosis of the precancerous tumor, and also of the non-metastatic cancers. “In this review, we discussed the relationship between autophagy and carcinogenesis. Based on multiple studies, it has been concluded that autophagy plays an anti-neoplastic role in cells.” [5]  There are many reports that autophagy may act as a cancer suppressor.” [6] 

Again, we have pharma muddling the science to promote profits and using association to blame the bystander.  Pharma in articles claims that autophagy works to restore the functions of cancerous cells though the healing process of autophagy, and thus diet and drugs that hinder autophagy would increase the effectiveness of their chemo cocktail.  Like Otto Warburg, I am limited to publishing the scientific analysis of cancer, and watch Pharma control the behavior of oncologists and public. 

7.  Apoptosis turning it up with natural supplements.      There are complex signal systems for broad set of biological processes.  Several natural to the body supplement turn up autophagy.  Among them is the salicylates, widely distribute (like our vitamins) in plants as part of their growth and immune systems, “a critical plant hormone.” [7]  It is also synthesized in humans from benzoic acid.[8]  Not surprisingly many mammalian biological processes are enhanced by plant sources of salicylates—similar to vitamins, but not essential for life, thus, not a vitamin for the same reason as B-5[9]  Aspirin which upregulate genes that turns up the apoptosis process has been shown to reduce with long-term daily usage (over 5 years) cancer risk by over 50%.  Those figures are imperfectly gathered since most studies don’t exclude low-dose aspirin which are ineffective because of tolerance and enteric coated aspirin which doesn’t dissolve for 5 to 8 hours and thus is poorly absorbed—more pharma protecting profits from illness.  Test for aspirin resistance of the low dose show that over 90% are resistant to the blocking of platelet production after one year.  The average patient after an MI will consume over $70,000 of drugs a year.  I assume that tolerance effect other functions of aspirin.  Recent studies support that conclusion.[10]  There are other bio-mechanisms by which aspirin reduces cancer risk.  For more on those process based mostly on research in the orient, go to http://healthfully.org/rc/id18.html.  Aspirin’s ability to prevent illnesses is why pharma and the FDA stress its potential to cause ulcers and Reyes condition,[11] and to promote other NSAIDs, all of which increase the risk for myocardial infarctions and strokes.  For this and more on aspirin go to http://healthfully.org/rc/id3.html.   As Goodman and Gilman pharmacology text book state “many clinicians favor the use of other NSAIDs perceived to have better gastrointestinal tolerability, even though this perception remains unproven by convincing clinical trials”[12]  

Certain substances significantly turn up genes that promote the autophagic processes and thereby lower the risk for the progress to stage I for abnormal cells, and also the progression from stage I, II, & III into stage IV.  By stimulating autophagy there are an assortment of other health benefits including the apoptosis of abnormal cells.  My research as of 5/19 has found 3 more  substance (progesterone, estradiol, and  testosterone) and there are likely more.  The sex hormones estradiol (rc/id2)and testosterone (/rc/id7) reduces the incident of cancer and fatal cancers and have many other health benefits.  Sex hormones[13] and aspirin turn up the apoptosis-autophagic system[14] and thereby increase survival of those with local cancers (stages I, II, and III) but not stage IV for which the cancer is invisible to the immune cells and to apoptotic systems.  Since there are receptors in the MTD, it is likely that through the benefits for MTD and thus through increased ATP and thus the upregulation of autophagy, these hormones, and other ways, promotes health.  For example “Estradiol rescued osteoblast apoptosis via promotion of autophagy through the ER–ERK–mTOR pathway.” [15]  “In many cases, E2 plays a role in promoting autophagy [8-16].” [16]   As expected, there are similar finding for testosterone and progesterone.  Nature works to improve our health.

“Non-toxic compounds endowed with the capacity to reduce the overall levels of protein acetylation and to induce autophagy have been categorized as caloric restriction mimetics (CRMs). Here, we show that aspirin or its active metabolite salicylate induce autophagy by virtue of their capacity to inhibit the acetyltransferase activity of EP300.” [17]   

For the sex hormones chapter 2 has a review of their effects upon cancers. Like aspirin through upregulating autophagy it very significantly reduces the risk of non-metastatic cancers becoming fatal.  The mutation theory of cancer which promotes chemo sales for the various types of “essential mutations” has been questioned by a small group of researchers, and I find their evidence compelling.  Thomas Seyfried (book Cancer as a metabolic disease and his lectures on YouTube is a excellent source.  Thus, pharma is against aspirin and sex hormones, as too its lap dogs the national regulatory agencies.  I have gone over the evidence on cancer including how tumors become invisible to the immune system; it is at http://healthfully.org/rl/id4.html   Because of having the wrong model, this explains the very limited progress made since under President Nixon administration and the Republican Party started what they termed The War on Cancer.  Need I say more about the role of pharma and the government dole?

Like all simple models on complex processes, there are exceptions. Indolent cancer[18], for example, some are able to enter adjacent tissues because they are not marked as foreign by the surface proteins, or because they have been able to obtain a degree of invisibility to the immune system, but not total invisibility comparable to the macrophage.   Leukemia and lymphomas are a much different type of cancer.  It is autophagy which makes cancer rare among LSPs and wild vertebrates.

8. Long-term water fasting and apoptosis, Barbieri’s 382-day fast::

His first meal in 392 days in 1966[19]

            A person can go for quite some time without metabolizing muscle during starvation, depending on percentage of stored fat to lean weight.  A lean person with about 13% body fat can go without food for about 65 days.  Angus Barbieri, age 27, a 456 lbs. Scotsman, starting in June 1965, went on a medically supervised water fast lasting 382 days and lost 276 lbs.  He consumed only vitamins, electrolytes, and zero-calorie beverages.[20]   Weekly blood work confirmed his fast.  The case study published 7 years later found that his average blood glucose was 30 mg/dL (1.7 mmol/L),[21] which confirmed that he wasn’t eating—as too the weight loss.  After his weight loss he moved to Warwick and had 2 sons.  Barbieri die in September of 1990.  Causes of death I couldn’t find after 2-hours of search. 

That he didn’t need an operation to remove the folds of skin is an example of his body’s efficient use of autophagy to recycle amino acids from the skin and adipose tissue that were dismantled by apoptosis.[22]  Only when fat stores become low, does the body start metabolizing muscle. Not all are so fortunate, and a friend of mine, a geriatric physician, Bill had to undergo surgery to remove the folds.  He was 20 years older than Angus.  Bill lost nearly 200 pounds eating 1-low-carb meal a day done without medical supervision.  Note: after two attempts, separated by 2 years, I gave up on trying to find Agnus’s cause of death at the age of 50 and his weight.  Thus, I don’t know if there was weight gain; however, on an examination at 7 years, he had gained only 16 pounds—much better than the contestants on the Biggest Looser show (5:1).[23]  The 1966 photo of his first meal at 180 lbs. shows him too thin. 

9. AMPK (5-AMP-actived protein kinase, 5’ adenosine monophosphate-activated protein kinase)

Some of the systems modulating the autophagic processes

There is a flurry of research on the switches that turn on and off autophagy; what follows is 3 of those switches that have drawn research dollars.  Again, I must caution that messing with a complex system often has significant side effects and is a net negative, but for pharma.  The big exception is those system which have been downregulated to lower the burden of the elderly; restoration is healthful. 

AMPK is an energy sensing protein enzyme that plays a role in cellular-energy homeostasis mainly through the uptake of glucose and fatty acids and their oxidation as needed.  As an energy sensor it functions to turn on autophagy, and is inhibited by mTOR.[24]  “Under glucose starvation, AMPK promotes autophagy by directly activating Ulk1 through phosphorylation of Ser 317 and Ser 777. Under nutrient sufficiency, high mTOR activity prevents Ulk1 activation by phosphorylating Ulk1 Ser 757 and disrupting the interaction between Ulk1 and AMPK” supra.   AMPK activation stimulates hepatic and myocyte fatty acid oxidation (ketogenesis), inhibition of cholesterol synthesis, lipogenesis, and promotes FFA conversion to triglycerides, as well as inhibition of adipocyte lipogenesis and activation of adipocyte lipolysis.[25]  “Due to isoforms, there are 12 versions of AMPK in mammals, each of which have different tissue localizations and different functions under different conditions. . ..  AMPK is inhibited by insulin, leptin, and diacylglycerol. AMPK may be inhibited or activated by various tissue-specific ubiquitinations.” [26]   AMPK is highly conserved in eukaryotic protein family and its orthologues in yeast and plants.  AMPK can be induced by caloric restriction, exercise, and ketogenic diet.  AMPK functions as a switch.  m-TOR through insulin, leptin and diacylglycerol turn off the switch for autophagy.[27]  “One of the central regulators of cellular and organismal metabolism in eukaryotes is AMP-activated protein kinase (AMPK), which is activated when intracellular ATP production decreases. AMPK has critical roles in regulating growth and reprogramming metabolism, and has recently been connected to cellular processes such as autophagy and cell polarity.” [28] And there are other mechanism regulating the functions of AMPK, such as the inhibition of protein synthesis.

“Taken together, these results suggest that AMPK association with ULK1 plays an important role in autophagy induction, at least in part, by phosphorylation of raptor to lift the inhibitory effect of mTOR on the ULK1 autophagic complex.” [29]  That is the simple answer, as the diagrams below show, it is much, much more complex.  And which switch or combination should be thrown and how much because given our tools hopelessly beyond science today:  “due to isoforms, there are 12 versions of AMPK in mammals.” [30] 

10.  Switches, mTOR, & insulin, pericytes, mesenchymal stem cells:  Like any switch for turning on a key process, there are feedback mechanism and switches for turning down and off the system;  mTOR is an off switch.  “Nutrient starvation induces autophagy in eukaryotic cells through inhibition of TOR (target of rapamycin), an evolutionarily‐conserved protein kinase.  TOR, as a central regulator of cell growth, plays a key role at the interface of the pathways that coordinately regulate the balance between cell growth and autophagy in response to nutritional status, growth factor and stress signals.” [31]  mTOR is a member of the phosphatidylinositol 3-Kinase-related kinase family of protein kinases.  mTOR links with proteins to form mTOR complex 2 or complex 2, both of which regulate cellular processes.  It does this though its enzymatic phosphorylation of proteins, in particular the amino acids serine and or threonine which ultimately regulates cell growth, proliferation, motility, insulin receptors, insulin like growth factor 1 receptor, survival, protein synthesis, autophagy, and transcription.  Given its various function there is an association with a long number of conditions.

The evolutionarily conserved checkpoint protein kinase, TOR (target of rapamycin), has emerged as a major effector of cell growth and proliferation via the regulation of protein synthesis. Work in the last decade clearly demonstrates that TOR controls protein synthesis through a stunning number of downstream targets. Some of the targets are phosphorylated directly by TOR, but many are phosphorylated indirectly.[32]

Complexity, there are the isoforms for mTOR, how much of them?  It’s time to back away from mTOR and AMPK, and retain the fact that as a team they and their isoforms are essential for heath, which is why autophagy is one of the B-5, and the first for healing.  The long list of actions and regulation demonstrates the ability of evolution to fine tune processes. 

          Insulin is an indirect switch to which others such as the AMPK are responsive to the level of serum glucose.  Elevate glucose causes the switching off of autophagy, and thus IR reduces the duration of autophagy.  “Our results show that autophagy was suppressed in the livers of mice with insulin resistance and hyperinsulinemia. . . . Transcript levels of some key autophagy genes were also suppressed in the presence of insulin resistance and hyperinsulinemia.” [33]  The elevated insulin affect upon autophagy is one more way insulin contributes to CAWD.  At 3:6, 5 is a summary of the various effects of insulin, 16 of them.

Anti-aging

Aging

Physiological regulation of AMPK. A schematic summarizing the mechanisms underlying the regulation of AMPK activity under diverse physiological and pathological conditions. Arrow indicates activation, and bar-headed line indicates inhibition (see text for details).[1]

Many types of cells function to promote the health of tissues, helper cells, among them are the glia cells in the brain and the pericytes for the endothelia cells.  We have a system on a grand scale for the maintenances of tissue functions. 

Pericytes (previously known as Rouget cells)^[1] are multi-functional mural cells of the microcirculation that wrap around the endothelial cells that line the capillaries and venules throughout the body.^[2] Pericytes are embedded in basement membrane, where they communicate with endothelial cells of the body's smallest blood vessels by means of both direct physical contact and paracrine signaling.^[3]  Pericytes help to maintain homeostatic and hemostatic functions in the brain and also sustain the blood–brain barrier.^[4] These cells are also a key component of the neurovascular unit, which includes endothelial cells, astrocytes, and neurons.^[5][6] Pericytes regulate capillary blood flow, the clearance and phagocytosis of cellular debris, and the permeability of the blood–brain barrier. Pericytes stabilize and monitor the maturation of endothelial cells by means of direct communication between the cell membrane as well as through paracrine signaling.^[7] A deficiency of pericytes in the central nervous system can cause the blood–brain barrier to break down.^[4]    the emerging evidence (as of 2019) suggests that neural microvascular pericytes, under instruction from resident glial cells, are reprogrammed into interneurons and enrich local neuronal microcircuits^[42].

This response is amplified by concomitant angiogenesis, the creation of new blood vessels as needed.

Given the importance for survival of endothelial cells, they too have helper cells.  “Mesenchymal stem cells:  are multipotent stromal cells that can differentiate into a variety of cell types, including osteoblasts (bone cells), chondrocytes (cartilage cells), myocytes (muscle cells) and adipocytes (fat cells which give rise to marrow adipose tissue).^[  Mesenchyme is embryonic connective tissue that is derived from the mesoderm and that differentiates into hematopoietic and connective tissue, whereas MSCs do not differentiate into hematopoietic cells.” [2]  It takes all this and much more for complex life to survive.  The list of helpers goes on and so do I, to other topics.

11.  DRUG FIXES?  The role of mTOR, AMPK, and autophagy are highly regulated so as to promote survival, and we are decades away from producing road maps of the various switches and routes.   Above 2-graphs are cutting edge 2016 road maps for aging and anti-aging.  “Many studies have demonstrated that AMPK is inhibited in many pathological conditions, such as inflammation, diabetes, aging and cancer, and that activation of AMPK can be beneficial to treat such diseases.” [3]  However, merely turning on AMPK with a drug, given the complexity of functions, will likely have dire consequences, much like that of statins which down regulate the mevalonate pathway—especially among the elderly who have MTDD.  Drugs that intervene in autophagy given its complexity are likely to have a net negative, though some natural supplement are of value such as the salicylates and some of the sex hormones (6:2), that is a result of evolution.  With our current ownership of data and the failure to open major data banks kept by government, health insurances, and medical facilities, the long-term and short-term harm is consistently grossly under estimated.  Perversely, industry does hatchet jobs on off-patent drug or the salubrious hormones.  Marketing rules.   

The body has evolved mechanism for stress.  “We have recently shown that autophagy is induced by ischemia and reperfusion in the mouse heart in vivo. Ischemia stimulates autophagy through an AMP activated protein kinase (AMPK)-dependent mechanism, whereas reperfusion after ischemia stimulates autophagy through a Beclin 1-dependent, but AMPK-independent, mechanism.” [4] This and much more confirms Oliver Wendell Holmes: “Drugs are what you take while you wait for your body to heal.” 

12.  Autophagic lessons:  “A decrease in the rate of protein turnover and the intracellular accumulation of altered proteins in cytosol and membranes are features common to all aged cells. Diminished autophagic activity plays a major role in these age-related manifestations.”[5]

The repertoire of routine housekeeping functions performed by autophagy includes the elimination of defective proteins and organelles, the prevention of abnormal protein aggregate accumulation, and the removal of intracellular pathogens. Such functions are likely critical for autophagy-mediated protection against aging, cancer, neurodegenerative diseases, and infection. Although some of these functions overlap with those of the ubiquitin-proteasome system—the other major cellular proteolytic system—the autophagy pathway is uniquely capable of degrading entire organelles such as mitochondria, peroxisomes, and ER [endoplasmic reticulum] as well as intact intracellular microorganisms. Further, the relative role of the autophagy-lysosome system in protein quality control—i.e., in preventing the intracellular accumulation of altered and misfolded proteins—may be greater than previously anticipated[6]

The important point is that there are many systems in the cells and tissues designed to maximize performance and deal with the stresses, many of these systems are arbitrary group under the label of autophagy.  Whether RAGE (receptors for advanced glycation endproducts) are under the autophagy umbrella or outside is arbitrary, a man-made classification.  The importance lies in knowing that there is sufficient glycation with adverse consequences to justify the evolution of a major system with special receptors for the damaged.  This indicates that fructation has major health consequences, and thus one more brick of evidence for its role in CAWD.  The general knowledge about system of repair including replacement acts as a guide through the pirate water of the sea of pharma; a sea that pharms doesn’t want mapped.[7]