question: Why do our bodies have so many "defenses" that are actually harmful or even potentially deadly?
comment: The vast majority of the time they help keep you alive, just sometimes they don't. The body isn't intelligent, it doesn't know if something it is doing is detrimental overall. These are evolved responses, not intentional strategies.
passages: The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue. In many species, there are two major subsystems of the immune system: the innate immune system and the adaptive immune system. Both subsystems use humoral immunity and cell-mediated immunity to perform their functions. In humans, the blood–brain barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system, which protects the brain.
   Section::::Brainstem.:Immunity.
  
  The brain controls immunity both indirectly through HPA glucocorticoid secretions from the pituitary, and by various direct innervations.
  
  BULLET::::- Antibodies. There is sympathetic innervation of the thymus gland. Sympathetic control exists over antibody production, and the modulation of cytokine concentrations.
  
  BULLET::::- Cellular immunity. An intact sympathetic nervous system is required to maintain full cellular immunoregulation as denervated mice do not produce and activate, for example, splenic suppressor T cells, or thymic NKT cells.
   Chemical barriers also protect against infection. The skin and respiratory tract secrete antimicrobial peptides such as the β-defensins. Enzymes such as lysozyme and phospholipase A2 in saliva, tears, and breast milk are also antibacterials. Vaginal secretions serve as a chemical barrier following menarche, when they become slightly acidic, while semen contains defensins and zinc to kill pathogens. In the stomach, gastric acid serves as a powerful chemical defense against ingested pathogens.
   Section::::Other vertebrate mechanisms.
  
  The coagulation system overlaps with the immune system. Some products of the coagulation system can contribute to the non-specific defenses by their ability to increase vascular permeability and act as chemotactic agents for phagocytic cells. In addition, some of the products of the coagulation system are directly antimicrobial. For example, beta-lysine, a protein produced by platelets during coagulation, can cause lysis of many Gram-positive bacteria by acting as a cationic detergent. Many acute-phase proteins of inflammation are involved in the coagulation system.
   Innate immune system
  
  The innate immune system is one of the two main immunity strategies found in vertebrates (the other being the adaptive immune system). The innate immune system is an older evolutionary defense strategy, relatively speaking, and it is the dominant immune system response found in plants, fungi, insects, and primitive multicellular organisms.
  
  The major functions of the vertebrate innate immune system include:
  
  BULLET::::- Recruiting immune cells to sites of infection through the production of chemical factors, including specialized chemical mediators called cytokines
   An alternative explanation is that the developing immune system must receive stimuli (from infectious agents, symbiotic bacteria, or parasites) to adequately develop regulatory T cells. Without that stimuli it becomes more susceptible to autoimmune diseases and allergic diseases, because of insufficiently repressed T1 and T2 responses, respectively. For example, all chronic inflammatory disorders show evidence of failed immunoregulation. Secondly, helminths, non-pathogenic ambient pseudocommensal bacteria or certain gut commensals and probiotics, drive immunoregulation. They block or treat models of all chronic inflammatory conditions. 
  
  Section::::Evidence.
   The danger model has not won universal acceptance. Some immunologists, following Janeway's ideas more directly, believe that the immune response is mainly fueled by innate evolutionarily conserved "pattern recognition receptors" which recognize patterns expressed by microbes such as bacteria, and do not see cell death in the absence of pathogens as a primary driver of immune responses. These ideas however, do not explain how the immune system rejects tumors, induce autoimmune diseases, or generate allergy and asthma.
  
  Section::::Research.:Pattern recognition and a tissue-driven immune system.
   The adaptive immune response is the body's second line of defense."Adaptive immunity has evolved to provide a broader and more finely tuned repertoire of recognition for both self- and nonself-antigens. Adaptive immunity involves a tightly regulated interplay between antigen-presenting cells and T and B lymphocytes, which facilitate pathogen-specific immunologic effector pathways, generation of immunologic memory, and regulation of host immune homeostasis." The cells of the adaptive immune system are extremely specific, because during early developmental stages the B and T cells develop antigen receptors that are specific to only certain antigens. This is extremely important for B and T-cell activation. B and T cells are extremely dangerous cells, if they are able to attack without going through a rigorous process of activation, a faulty B or T cell can begin exterminating the host's own healthy cells. Every B and T-cell is different, making way for a diverse community of cells ready to recognize and attack a full range of invaders. This response is much slower than the body's innate response because its cells are so specific and require to be activated before it is able actually act. "In addition to specificity, another principal feature of adaptive immunity is the generation of immunologic memory. During the first encounter with an antigen (pathogen), sets of long-lived memory T and B cells are established. In subsequent encounters with the same pathogen, the memory cells are quickly activated to yield a more rapid and robust protective response". This feature of the adaptive immune response is responsible for the development of vaccines as well as other modern day medicines targeted at disease prevention. Immunologic memory is the basic concept behind the modern day flu shot. The flu shot basically is giving the recipient a dormant flu virus. This activates the recipient's immune response. After the immune response, immunologic memory is activated, so if the individual ever comes into contact with the flu virus again the body will be prepared to deal with it accordingly, this time faster, and more efficiently.
   Section::::Mechanism of action.
   threat : What constitutes a "threat" as it pertains to "defense physiology"? A "threat" may be consciously recognized or not. A physical event (a loud noise or car collision), a chemical or a biological agent which alters (or has the possibility to alter) body function (physiology) away from optimum or healthy functioning (or away from its current state of functioning) may be perceived as a "threat" (also called a stressor). 
   As first responders, the innate immune cells cannot afford to be specific, and must respond to foreign substances in a generic way. Neutrophils, for example, contain toxic substances in their granules that kill or hinder the expansion of pathogens. The cells attack pathogens by releasing strong oxidizing agents including hydrogen peroxide, free oxygen radicals, and hypochlorite. Although the attack is effective against bacteria and fungi, the response can inadvertently inflict severe damage to the surrounding host tissue. The misregulation of innate immune cells plays a key role in promulgating inflammatory conditions.
   Overactive immune responses comprise the other end of immune dysfunction, particularly the autoimmune disorders. Here, the immune system fails to properly distinguish between self and non-self, and attacks part of the body. Under normal circumstances, many T cells and antibodies react with "self" peptides. One of the functions of specialized cells (located in the thymus and bone marrow) is to present young lymphocytes with self antigens produced throughout the body and to eliminate those cells that recognize self-antigens, preventing autoimmunity.
  
  Section::::Disorders of human immunity.:Hypersensitivity.
   The immune response can be transferred via serum antibodies introduction from sensitized to desensitized individuals. It is highly specific for given antigen, and it is normally directed against foreign protein substances.
  
  Section::::Innate.
  
  Innate response is the first line of defense when it comes to defending an organism from an foreign invader. Foreign invaders include bacteria, viruses, and parasites. The protection an innate response offers is beneficial because it attacks all foreign invaders that are not part of the cell’s self. 
  
  Section::::Adaptive.
   Section::::Layered defense.
   The immune system is involved in many aspects of physiological regulation in the body. The immune system interacts intimately with other systems, such as the endocrine and the nervous systems. The immune system also plays a crucial role in embryogenesis (development of the embryo), as well as in tissue repair and regeneration.
  
  Section::::Physiological regulation.:Hormones.
   Microorganisms or toxins that successfully enter an organism encounter the cells and mechanisms of the innate immune system. The innate response is usually triggered when microbes are identified by pattern recognition receptors, which recognize components that are conserved among broad groups of microorganisms, or when damaged, injured or stressed cells send out alarm signals, many of which (but not all) are recognized by the same receptors as those that recognize pathogens. Innate immune defenses are non-specific, meaning these systems respond to pathogens in a generic way. This system does not confer long-lasting immunity against a pathogen. The innate immune system is the dominant system of host defense in most organisms.
   Section::::Immunologically privileged sites.:Central nervous system.
   Section::::Background.
   Section::::Role in physiological processes.:Immune-privileged sites.
  
  Certain body tissues are able to tolerate antigens without an inflammatory immune response. Immune privilege is thought to be an evolutionary adaptation to protect the most vital sensory organs and reproductive structures that would be otherwise severely impaired during an inflammatory response. Although these locations are often physically isolated or segregated from access by immune cells, there are some functionally significant characteristics of such environments that are unique, and could potentially be replicated to keep immune cells away from targeted areas. Known immunologically privileged sites include the:
  
  BULLET::::1. Brain and central nervous system
  
  BULLET::::2. Eyes
   Body reactivity
  
  Body reactivity is usually understood as the body's ability to react in a proper way to influence the environment. Resistance of an organism is its stability under the influence of pathogenic factors.The body reactivity can range from homeostasis to a fight or flight response. Ultimately, they are all governed by the nervous system.
  
  Section::::Nervous system divisions.
   These mechanisms include sensory processes through which cues connoting the presence of parasitic infections are perceived (e.g., the smell of a foul odor, the sight of pox or pustules), as well as stimulus–response systems through which these sensory cues trigger a cascade of aversive affective, cognitive, and behavioral reactions (e.g., arousal of disgust, automatic activation of cognitions that connote the threat of disease, behavioral avoidance).
   An immune system may contain innate and adaptive components. The innate system in mammalians, for example, is composed of primitive bone marrow cells that are programmed to recognise foreign substances and react. The adaptive system is composed of more advanced lymphatic cells that are programmed to recognise self-substances and don't react. The reaction to foreign substances is etymologically described as inflammation, meaning to set on fire. The non-reaction to self-substances is described as immunity, meaning to exempt or as immunotolerance. These two components of the immune system create a dynamic biological environment where "health" can be seen as a physical state where the self is immunologically spared, and what is foreign is inflammatorily and immunologically eliminated. "Disease" can arise when what is foreign cannot be eliminated or what is self is not spared.
   Section::::Inflammation.
  
  Inflammation is one of the first responses of the immune system to infection or irritation. Inflammation is stimulated by chemical factors released by injured cells and serves to establish a physical barrier against the spread of infection, and to promote healing of any damaged tissue following the clearance of pathogens.
   Physical structures surrounding privileged sites cause a lack of lymphatic drainage, limiting the immune system's ability to enter the site. Other factors that contribute to the maintenance of immune privilege include:
  
  BULLET::::- low expression of classical MHC class Ia molecules
  
  BULLET::::- expression of immunoregulatory nonclassical, low polymorphic class Ib MHC molecules
  
  BULLET::::- increased expression of surface molecules that inhibit complement activation
  
  BULLET::::- local production of immunosuppressive cytokines such as TGF-β
  
  BULLET::::- presence of neuropeptides
  
  BULLET::::- constitutive expression of Fas ligand that controls the entry of Fas-expressing lymphoid cells.
   BULLET::::- Acting as a physical and chemical barrier to infectious agents; via physical measures like skin or tree bark and chemical measures like clotting factors in blood or sap from a tree, which are released following a contusion or other injury that breaks through the first-line physical barrier (not to be confused with a second-line physical or chemical barrier, such as the blood-brain barrier, which protects the extremely vital and highly sensitive nervous system from pathogens that have already gained access to the host's body).
  
  Section::::Anatomical barriers.
  
presuppositions: The body is intelligent and the bodies defenses are intentional.
corrections: The body is not intelligent and the bodies defenses are evolved responses not  intentional strategies.
raw_presuppositions: The body is intelligent and the bodies defenses are intentional. The body's defenses should be strategically designed to be helpful.
raw_corrections: The body is not intelligent and the bodies defenses are evolved responses not  intentional strategies. The body's defenses are evolved responses rather than intentional strategies.