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Lecture for year 2 medical students on July 6, 2001 by Professor Omar Hasan Kasule Sr.



The miracle of the human body is more startling when seen in its interaction with the environment. Internal and external environments: Although we talk about two environments, it is actually one environment with 2 compartments that are intimately linked. The interaction between the internal and external environments is purposive and is not a product of chance.



The nervous and endocrine system ensure that the human body can adjust to rapidly changing circumstances of the external environment. This even includes changes on anticipation of external changes. Claude Bernard said that animals live in two environments: internal and external. Physiological adaptation to the internal environment: GIT, lungs,



The interaction between humans and their external and internal environments is part of Allah’s grand design and is not by mistake. This implies that this interaction has to be harmonious and follows the laws of Allah sunan llah fi al kawn. The human body is programmed to interact with the environment in the most efficient way. However humans because of their free will can behave in ways that produce unhealthy interactions.



There are some phenomena like disease or drought that may bring adversity to humans. These are part of the grand design to ensure that there are checks and balances in the eco-system that ensure equilibrium. The adversities are therefore not created for punishment of humans.



The universe was placed under the humans (taskhir). They control and change it as they want. However this control is sometimes not proper resulting into imbalances and problems. The crucial question is to determine what changes are bad because the derange the permenent fixed laws of nature, al sunan. A decision must also be made on what changes must be made for purposes of building a civilization.

Genetics: Phenotype is the final shape after interaction of the environment with the genotype.




The human body is able to adapt to all types of physical environments. Humans live in the hot Sahara desert but also live in the permafrost of the tundra. Humans in the southern hemisphere have darker skins with more melanin for protection against dangerous radiations from space. Humans who live in the cold northern hemisphere have smaller nostrils than those in warmer areas of the world because inspiration of the cold air must be limited. The distribution of body hair also is affected by the geographical region. Sun’s rays are needed to synthesize vitamins A, K, and D in the skin. Human eucaryotic cells are less dependent on the external chemical environment that pro-karyotic cells. They have in a way created their own environment in their internal environment



Human can change environment  by prayer like prayer for rain (Muslim #1947, 1948, 1949, 1950, 1951, 1952, 1953). Prayer for protection during violent storms (Muslim #1961, 1962, 1963, 1964). Salat al kusuuf (Muslim # 1966, 1968, 1969, 1970, 1972). Humans are also able to engineer major changes in their air, acquatic, and terrestrial environment. Some of the changes are for the good of the aco-system while some others are definitely harmful. Industrialized countries are currently suffering from several environmental problems due to air pollution (tobacco, industry, indoor, radon), non-biodegradable wastes, depletion of the ozone layer, and global warming.



Humans can sustain injury from the environment. Mechanical injury is due to tissue danage caused by abrasion, laceration or other types of mechanical trauma. Both excessively high and excessively low temperature can cause tissue injury. Humans can not live at high altitudes because of low atmospheric pressures. Blast injuries are due to temporary exposure to high air pressure. Air emboli can also cause damage when they enter the blood stream. Other forms of physical injury are: electrical and radiactive energy.



Water in a basic need of life. Fresh and salty water. Oceons source of food. Humans can drown in water but can also swim. The soil is a nutrient for plants that are part of the human food web. Violent movements of the earth such as earthquakes, landslides can cause physical injury to humans and their property. Elements of the earth provide shelter from bad weather and assure privacy. Physical location is an important consideration. Some places are special like Makka, Madina, Uhud (Muslim #3207, 3208). The Prophet talked about the mutual love between Muslims and the mountain of Uhud (KS p. 61). On one occasion the mountain of uhud trembled and the prophet addressed it not to be afraid because the messenger of Allah, a siddiq and two martyrs were on it (KS 62). Abubakr complained about the fevers of Madina. Companions were weakened by the fever of Madina (KS p. 501). 


Weather phenomena such as heat, cold, rain, clouds, thunder, and lighting can cause injury. Humans ask Allah for protection from wind, rain, and clouds (KS p. 79)



The Sun is a source of energy. Its movements control the diurnal rhythm and the seasons.


The moon is the basis of the lunar calendar and its movements moderate the sea tides.


Space. Time dimension:



Humans and parasites have evolved a mutual adaptation. This takes several forms: symbiosis, commensalism, parasitism. Parasites undergo antigenci change to avoid host immune defences. Acute and chronic conditions. Plants are a source of food. They are involved in the oxygen, carbon dioxide, and nitrogen cycles that are necessary for human confort. Human are able to eat some plants or parts of plants for which they have the appropriate digestive enzymes. Plants or parts of plants indigestable by humans still provide human food by being eaten by herbivorous.



Mammals as a source of food: competition. Humans omnivorous but meat is best food (Ibn al Qayim p. 357). Transmission of disease parasites. Animals diseases rarely affect humans. When they do it is a dead-end. Humans are rerely victims of animals as food. Humans must be kind to animals (KS p. 211). A woman entered hell for mistreating a cat (KS p. 556). Birds provide food and also,play a part in spreading pollen and seeds.





Insects are the most successful biological species. They can be food for humans but also are parasites or vectors of parasites. They help in plant pollination. Insects sing. Insect colour is part of esthetic beauty in the environment. Mosquitoes have changed the course of history. The malaria mosquito prevented the colonisation of the interior of Africa by Europeans. Insect-transmitted trypanosomiasis has depopulated many parts of the world.



The food web and the food chain.  Malnutrition may occur due to physical forces beyond human control or may be due to human injustice (maldistribution of food). Under-nutrition manifests as protein energy malnutrition or deficiency of specific micro-nutrients like vitamins. Over-nutrition manifesta as obesity and associated diseases.






3-classes: A rough 3-way classification of micro-organisms can be made into: viruses, pro-karyotes, and eucaryotes. The following are the commonest groups of micro-organisms encountered in medicine: viruses, bacteriophages, plasmids, transposons, bacteria, rickettsiae, mycoplasma, bacteria, chlamidae, fungi, protozoa, helminths, ectoparasites. Micro-organisms are divided into 3 major groups depending on the complexity of their celliular structure: viruses, prokaryotes, and eucaryotes.


Viruses: Viruses are the smallest infective agents with only 1 nucleic acid, either DNA or RNA, as the sole genome. Viruses are obligate intracellular parasites that depend on the host for survival. They can replicate only in the host's cells. This replication may be fully or partially expressed and in either case pathology results. They have no ribosomes for metabolic processes. Viruses have very few enzymes.  They take over  control of cell protein and nucleic acid synthesis in infected cells. They are the smallest structures with the basic properties of living organisms (reproduction). Viruses vary in size. The pox virus is large enough to be seen by the light microscope. Others can only be seen by the electron microscope. In structure some are isometric, others are helical while others have more complex shapes.


Prokaryotes. Their DNA is not bound in a membane. There is no separation between the nucleus and the cytoplasm. They can be divided into: bacteria, spirochetes, mycoplasmas, and rickettsieaie. Pathogenic bacteira are erobic only a few like clostridium ae anerobic. Examples of mycoplasmas are M.hominis and M,pneumonia. Chlamydia are obligate intracellular parasites.


Eukaryotes (protists): have their DNA separated from the cytoplasm. Eucaryotes can be unicellular or multi-cellular. Unicellular organisms, also called protozoa, consist of sporozoa (eg plasmodium and taxoplasmosis), mastigophora (eg trichomonas, giardia, trypanosomiasis, leishmaniasis), sarcodina (eg entamoeba, dientamoeba), ciliophora (eg balantidium coli, pneumocytis carinii), and fungi. Multi-cellular protists are of 2 types: helminths and arthropods. The helminths are classified as nematodes or round worms (eg ascaris lun\mbricoides), plattyhleminths or flat worms. Flatworms are either trematodes, flukes, eg schistosomiasis or cestodes, tapeworms, eg teania solium. Arhropods can be obligate parasites such as body lice (P.corporis), head lice (eg P. capitis), P. humanus,  crab lice (eg phthimus pubis) or scabies (eg sarcopteri scabei).



Classification: Viruses are classified as DNA or RNA viruses depending on the nucleic acid that they have. The major viral groups are: parvo, adeno, herpes, pox, haptitis, picorna, rhino, rota, arbo, orthomyxo, and paramyxo viruses. The following are the commonest members of each of the groups above. Common herpes viruses are varicella-zoster, cytomegalovirus, Epstein-Barr virus, and the herpes simplex virus. Small pox which has been eradicated in its wild form is an example of a pox virus. There are 5 forms of the hapatitis virus: A, B, C, D, and E. Polio and cocksackie viruses are examples of picorna viruses. Yellow fever, dengue, encephalitis are examples of arbo viruses. Influenza is an example of an orthomyxo virus. Mumps and measles viruses are paramyxo viruses.  


Viruses are very vulnerable to enviromental elements outside their hosts. Heat, ultra-violet light, and x-rays inactivate viruses. Viruses infect plants, animals, and bacteria (bacteriophages). Viral transmission can be direct human to human, animal to animal or can be arthropod-borne.


Viral disease: Over 300 viruses are known to infect humans. There is no relation between viral morphology and the disease produced. The same disease may be produced by more than one virus type. Viral infection goes through several stages. After entry into the body, there is primary replication that is followed by viremia. Cell injury may result into clinical illness followed by recovery and shedding the virus to the outside environment. In many cases there is no clinical disease at all. Most viral infections are self-limiting. However some of them go on to become chronic infections, latent infection, or slow viral infections. The range of host response to viral infection is non-response through cytopathology to neoplasia. Most viral disease is subclinical. Cell-mediated and not humoral immunity is important for recovery from viral infection. The following non-immune methods are involved in immunity against viral infection: interferon, phagocytosis, body temperature, age, nutrition, and hormones. Interferons are host-coded proteins that inhibit viral replication. Viruses cause many human diseases. Small pox killed 50 million people in Europe in the 18th century alone. There is no effective chemotherapy against viruses. The best approach is still immunisation. Lady Monatgue introduced variolation against small pox in England. Unethical trials were carried out on condemned prisoners and orphans before the practice was widely adopted. Many persons did contract the full-blown disease and often died. Modern immunisation uses live attenuated or killed vaccines. The attenuated vaccines are rendered harmless without loss of immunogenicity. These avirulent strains are obtained by passaging the species through man and by selecting avirulent mutations. Mutation is about 1 in a million replications. Recombinant viruses do occur.



Classification: On morphological grounds bacteria are divided into gram positive and gram negative. The following are the major morphological groups of bacteria with examples of each. (1) Gram positive spore-forming bacteria living as saprophytes in soil or water: B. anthracis, Cl. tetani, and Cl. botulinum. (2) Gram positive non-spore forming: C. diphtheriae and L. monocytogenes. (3) Staphyloccoci are gram positive spherical: S aureus, S. epidermis. (4) Streptococci are gram positive spherical eg S. pyogenes, S viridans,  and S pneumonae. (5) Enterobactariacae are gram negative rods: E. coli, Shigella spp, Salmonella spp, enterobacter spp, klebsiella spp, serratia spp, and proteus spp. (5) Pseudomomas and actinobacter are gram negative (7) Vibrios have characteristic shape: V. chlerae, H.pyloris. (8) Hemophilus: H.influenzae, H. ducrey. (9) Bordetella: B. pertussis. Brucella eg B. melitensis (goats), B.suis (pigs), B.abortus (cattle), and B. canis (dogs).  (10) Gram negative with animal reservoirs: Yersinia spp, Fransicella spp, Pateurella spp. (11) Neisseria: N. gomorrorhoea, N. meningitidis, M.leprae, M.bovis. (12) Spirochetes: T. pallidum,  L.interrogens, Borelia spp.  

Phages and plasmids transfer genetic material from one bacterium to another.



Fungi: are protists which ae eucaryotic. Most fungi are saprophytic but a few are parasitic. The parasitic fungi may be topical eg dermatomycoses or systemic eg candidiasis or aspergillosis


Helminths: Worm infestation is common in poor countries. The mouth is the main portal of entry. Transmission related to poor hygiene. Humans are genrally internediate hosts


History: Human interaction with micro-organisms has been left undisturbed for all human history.  Only in the past 100 years have humans been able to change transmission of organisms with microbial therapy and changes in the habitat such as draining and spraying swamps. Chemotherapy only started in the early 20th century with the discovery of sulfonamides (1935) and penicillin (1940). With this they have been able to distort the normal balance among organisms. Genetic engineering is promising further dislocations by introducing new organisms unknown before into the environment. 


Parasite-host relations: There are 3 basic types of host-parasite relations: symbiosis, parasitism, commensalism. Both eucakaryotes and prokaryotes are able to live on their own without being parasitic. Bacteria may be pathogenic such as TB or saprophytes (free-living). Some bacteria are opportunistic pathogens such as E.coli.  Yet other organisma are accidental pathigens like Y.pestis which infects humans accidentally. Some micro-organisms may cause disease by being in the wrong part of the body eg S. pneumonae is a comensal in the nose but a pathogen in the lungs. Human is an  intermediate or definitive host.  In malaria the human is an intermediate host. Sometimes he is accidental. In Wuchereria bancrofti and B. malayi the human is an accidental host. Normal flora inside the body and also on the surface membranes such as the mouth, the respiratory tract, the gastro-intestinal tract, the urethra, the vagina, the eye (conjuctiva). They may be resident commensals or may be transient. Micro-organisms ensure their survival and transmission by not killing the host outright Some manifestations of disease ensure spread of infection for example diarrhoea and coughing.


Concept of disease vectors:


Virulence and disease causation: The following are bacterial virulence factors: adherence, invasion of host tissues, toxins, and enzymes.

Host defences to infection:

Host immune responses:

Bacteria overcome host resistance and barriers:


Interaction of micro-organisms with the physical environment: The  following can regulate bacterial virulence: temperature, iron, osmolality, acid-base balance pH, ions, and nutrients.


The balance sheet: The benefit vs the harm of micro-organisms



The specific toxicity of chemical agents is due to inhibition of essential metabolic processes in the parasite, inhibition of cell-wall synthesis, changes in the plasma membrane permeability, and impairment of protein synthesis (inhibits nucleic acid synthesis). Development of chemical agents toxic to viruses has been difficult because they are obligate intracellular parasites. Drug resistance develops in situations of ndescrminate use of anti-microbials. Such excessive use causes sensitization, change of the microbial flora, toxicity, and drug resistance. Micro-organisms resist drugs using various methods. They can produce ebzymes that destroy the drug. They can change their cell wall permeability to the drug. They can develop altered structural targets. They can develop altered metabolic pathways. They can also develop altered enzymes. Drug resistance may be genetic or non-genetic. Genetically-determined drug resistance may be chromosomal or extra-chromosomal (eg plasmids). Non-genetic drug resistance is said to occur when the organism is dormant or non-developing.



CONTAGION, al ‘adwah:

Hadith literature for and against contagion: hadith for (MB #1003). Hadith against (  ).


Islamic teachings about avoiding infections: Many hadiths have reported many teachings about avoiding microbiological infections. acts of fitrat and hygiene (Muslim #495, 496, 497, 498, 499, 502). wiping turban and fore-lock (Muslim #531-536), shaving hair for head lice (Muslim # 2732, 2734, 2735, 2736, 2727, 2738, 2739). wiping over socks (Muslim #522… 530). covering vessels (Muslim #4987, 4989, 4990, 4991, 4993, 4995, 5000, 5002, 5003), breathing into vessel (Muslim #5028). Covering vessels to prevent shaitan from entering KS p. 43, prevention of breathing into vessels KS p.43, washing a vessel if a fly falls in it KS p.44, drinking urine of camels KS p.48, camel urine as medicine KS p.124, istinjah from urine KS p.81, rinsing is part of fitrat KS p. 82, rinsing the inside of the mouth after drinking milk KS p. 81, rinsing the mouth after vomiting KS p. 82, wiping the nostril is fitrat KS p. 82, forbidding breathing into a vessel KS p.86, undesirable to put hand in a vessel before washing it (Muslim #541, #544), cutting nails KS p. 92, cleaning after urine KS p.123, forbidding urinating in stagnant water KS p. 123, washing urine from mosque (Muslim #557, 558, 559). Forbidden to urinate in stagnant water (Muslim #553, 554, 555). contamination of a cloth by urine of a baby boy ot baby girl KS p. 124, avoiding urinal contamination KS p. 124, forbidden to drink human urine KS p.124, putting a hand on the mouth when yawning KS p. 135, forbidding use of skins of wild animals KS p. 152,  saliva of a cat is not najasat KS p. 555, superiority of using miswak KS p. 287, washing the miswak KS p. 287, circumcision is fitrat KS p. 214. if a dog puts saliva in utensil throw away and wash 7 times (Muslim #546, 548, 549, 551),




Water is 45-75% of body weight. Components of tissues: inorganic, carbihydrates, lipds,and proteins. Elements higher concentration in humans than earth: H, C, I. Elements the same concentration in humans and human body and the earth: P, S, Cl, K, Ca. Humans take elements from the earth as food, drink and through respiration. C is the basis of organic compounds. Natural vs man-made chemicals



Interactions at molecular level

Ability to metabolise and excrete all chemicals

Humans do not release dangerous chemicals into the environment eg ammonia is detoxified and turned into urea.



Drugs have different effects and behavior on the elderly and the neonate



Humans have complicated the simple chemical environment bequeathed to them. The following are examples of adverse health effects following human introduction of newe chemicals in the environment. Many drugs have adverse drug reactions. Exogenous estrogens are suspected causes of breast cancer, uterine cancer, myocardial infection, and osteoporosis. Oral contraceptives are suspected causes of venous thrombosis, myocardial infarction, and breast cancer. Anti-neoplastic agents cause immune suppression that facilitates infection and neoplasia. Ethanol, the oldest and most commonly ingested drug has adverse effects on the liver, the CNS, and the PNS. Street drugs like marijuana, cocaine, and heroin have various physical and psychological adverse effects.

Professor Omar Hasan Kasule Sr. June 2001