In the seventeenth century, nearly seven centuries after Ibn Sina, the Dutch scientist Anton van Leeuwenhoek (also referred to as the “Father of Microbiology”) observed microorganisms under a microscope (van Leeuwenhoek 1980). With his fundamental discovery, he showed that there were living organisms that were not visible to the naked eye. What van Leeuwenhoek did not realize was that these microorganisms (e.g. pathogen: a disease causing microbe) could actually be the cause of infections. This is contrary to the discoveries made by Ibn Sina seven centuries earlier that microorganisms could be the cause of infections despite the extremely limited evidence for the existence of microorganisms at the time. Nearly two centuries after Leeuwenhoek’s first observation of microorganisms, in 1876, Robert Koch, a German physician, postulated that microorganisms could actually be the cause of infection and therefore disease by his fundamental observation that the blood of an infected animal that contained pathogenic bacteria that, when transferred to a healthy animal caused the recipient animal to become sick (Koch 1999).

Let’s take a moment to reflect on Ibn Sina’s life story to encourage readers to learn more about him (McGinnis 2010) and his contributions to modern medicine and science.

Ibn Sina was born in 980 in in the village of Afshana near Bukhara, Uzbekistan (previously known as Khorasan) to a local governor named Abdullah, from Balkh, and his wife Setareh, a local from Afshana. Thanks to his father’s position as a governor as well as his background as a scholar, Ibn Sina had access to an excellent education in Bukhara, which at the time was the capital and intellectual center of the Samanids. Ibn Sina was taught by some of the most famous scholars of the time in the sciences and in Islamic theology. By the age of 18, Ibn Sina had already mastered the sciences of his day and had become a practicing physician. In addition to his expertise in medicine, for which he became world-renown, he was also a well-known philosopher, astrophysicist, mathematician, and theologian. He spent his life educating people, treating patients and writing books that not only enlightened the people of his age but later generations throughout the world as well.

Although Ibn Sina was considered one of the greatest Muslim philosophers of the medieval age he was a widely respected and well-known physician and was known as the “Prince of Physicians” in the West, and al-Sheikh al-Rais (Leader of the Scholars) among his students and colleagues (McGinnis 2010, 227). His gigantic medical encyclopedia al-Qanun fi al-Tibb (The Canon of Medicine), comprising of upwards of a million words, has been used as the standard medical textbook up until the seventeenth century and is still widely considered a valuable resource for the study of medicine. It was printed thirty-six times in the fifteenth and sixteenth centuries alone (Ullman 1978) and is regarded as one of the most influential books in Europe during the Middle Ages and Renaissance (Siraisi 2001).

The Canon of Medicine consists of five books with each book subdivided into various subjects, subsidiary subjects, summaries, and sections. The first book, also called al-Kulliyyat (The Collection), discusses the scientific background of medicine and anatomy such as physiology, symptomatology, and the principles of therapy. The second book has an account of the therapeutic properties of substances used in medicine. The third book is devoted to pathology and specific or localized ailments. Diseases that affect the whole body, such as fever, are discussed in the fourth book. Ibn Sina explained the mixing of drugs in the final volume, which is a book on pharmacology. Ibn Sina, in his Canon, derives his system of medicine from the Greco-Roman physician Galen (Galen of Pergamon, modern day Bergama, Izmir, Turkey, 129-200 CE) who himself based his approach on Hippocrates (460-370 BCE). Ibn Sina also benefited from ar-Razi (Rhazes in Latin, 865-925 CE) and al-Majusi (Haly Abbas in Latin, died circa 990) to present a systematized and comprehensive view of the medical sciences of the time (Prioreschi 2003).

Ibn Sina is only one of many great minds of the Muslim World during the medieval era. There were other great minds such as Ibn Rushd (Averroes in Latin), Ali Kuscu, al-Farabi (Alpharabius), Omar Khayyam and many more whose multifaceted studies encompassed diverse scholarly fields such as exegesis, law, logic, metaphysics, mathematics, astronomy, and medicine. The great Mesopotamia and Andalusia Civilizations – civilizations that were built by these brilliant scientists and philosophers – established the foundations of the science, art and philosophy of our age. The knowledge developed by the Muslim scholars was later transmitted to Europeans and enabled Europe to emerge from the Dark Ages and into the Renaissance.

A Renaissance is also needed for the Muslim world today. This can only be possible when they can raise a new generation of scholars like Ibn Sina who can lead the society with their groundbreaking findings and illuminating interpretations.

References

• Colgan, Richard. 2009. Advice to the Young Physician. Springer, New York.
• Koch, Robert. 1999. A Life in Medicine and Bacteriology. ASM Press, Washington, D.C.
• Life and work of Anton van Leeuwenhoek of Delft in Holland; 1632-1723. Municipal Archives, Delft, 1980.
• McGinnis, Jon. 2010. Avicenna. Oxford University Press, New York.
• Prioreschi, Plinio. 2003. Medieval Medicine vol. 5: Medieval Medicine, Horatius Press, Omaha, Nebraska.
• Siraisi, Nancy. 2001. Medicine and the Italian Universities 1250-1600. Leiden, The Netherlands.
• Ullman, Manfred. 1978. Islamic Medicine. Edinburgh University Press, Edinburgh, United Kingdom.
• United States National Library of Medicine, MS A 53
• http://www.pbs.org/wgbh/globalconnections/mideast/themes/science/index.html

Digestion in grain-eating birds

The digestive system of the chicken, which is a representative of the world of birds, is comprised of organs lined up in straight line succession: a beak, mouth, gullet, craw, front stomach (with gland), gizzard, small intestine, caecum, large intestine, cloacae and anus. In addition, enzymes secreted from the pancreas, liver and gallbladder also have digestive duties. Ending in a sharp point, the beak was created especially to be able to pick up single pieces of feed. Chickens do not have assisting organs like the palate, cheek, tongue or teeth that are normally found in the mouth, the first door of digestion in most animals. Ruminating animals like cows, sheep, goats and camels use the tongue instead of a beak for taking food into their mouths, and then their teeth are used to begin the breakdown of food. In chickens, however, this breakdown is initiated with the bottom and top beak. In ruminants there are taste buds in different shapes on the tip, sides and middle of their tongues which also function as the organ for the sense of taste. Since such taste buds are not found in chickens, there is also no perception of taste like that experienced in ruminating animals.

The structure and function of the gullet, or food pipe, has similar characteristics in chickens and other animals. However, just as in all birds that eat single seeds and grains, there is another digestive organ in chickens in the shape of a bag opposite to where the gullet expands. Called a craw, this tiny pouch is a place for the storage, wetting and softening of feed, and it serves the purpose of bringing food to the consistency needed for further digestion; consequently, it lightens the burden of the stomach (just like when we leave food that is difficult to cook, like chick peas or beans, standing in water overnight before we cook it).

A chicken’s stomach is composed of two different sections, the front stomach and the gizzard. The feed the chicken eats passes from the gullet and the craw to the front stomach, where digestive secretions are made. The food is stored here briefly and mixed with the special fluids of the stomach. Found in this secretion are both the pepsin enzyme, which starts the digestion of proteins, and hydrochloric acid, which is secreted to generate the pH level that makes this enzyme effective (and which also helps in the dissolution of minerals). These two important secretions are produced by different glands in the stomach. Like the craw, the gizzard, which comes after the front stomach, is the place where mechanical digestion, which is particular to all birds that eat grains, takes place. The gizzard is called the stomach with muscles because it is comprised of a pair of thick and strong muscle layers. As a result of these muscles constricting strongly, feed is broken down mechanically and ground up. While gathering feed, the chicken usually also swallows small pieces of sand, stone and limestone as if it knows how its digestive system works. Although many of us think that chickens swallow stones because they cannot distinguish them from feed, it is obvious that there is a purpose why they are doing it. If these stones, which are like “mill stones” for the digestive tract, are not found in the gizzard, the feed is not fully ground; consequently, it will pass to the small intestine in a form that will not be fully beneficial to the body.

Depending on its characteristics, the feed eaten can stay in the gizzard for a few minutes or several hours. The small intestine, which comes after the stomach, is comprised of the duodenum (twelve-finger intestine), the jejunum and the ileum. The small intestine is similar in grain-eating birds to those of other animals. The duodenum empties the secretions coming from the pancreas and the bile coming from the gall bladder. The digestion and absorption of the feed actually takes place in the small intestine due to these secretions. Final digestion and the absorption of carbohydrates and protein are effected by bacteria found at the point where the small intestine ends, in the 10-15 centimeter-long, V-shaped caecum.

The large intestine and the cloacae are found in the advanced sections of the digestive system. The role of the large intestine, which is twice as large in diameter as the small intestine, is to temporarily store the waste from the digested food and to maintain the balance of water in the body. The cloacae is a small orifice with a structure formed by the widening of the large intestine towards the anus and where the digestive, defecation and reproduction tracts open up.

While giving grain-eating birds the above mechanisms in order to nourish them, God equipped ruminating animals with different oral, dental, gastric and intestinal structures as well as different digestive strategies.

Digestion in ruminating mammals

While secreting saliva is essential for ruminating animals, it is not necessary for chickens because of differences in their digestive system. As a result of the secretion of saliva the fodder of ruminants is softened and dryness of mouth is prevented. Ptyalin (or alpha amylase), which is found in saliva, has antibacterial properties that protect animals from infections in addition to playing a role in digestion. The mother cows constantly licking their newborn calves is both an expression of compassion and also of wisdom in protecting the newborn from probable infections (Similarly, animals like dogs and cats licking their wounds and thus speeding up healing is no coincidence, but a sign of universal wisdom and mercy). This wisdom shows that saliva, of which cows secrete 90-180 liters and sheep 5-8 liters per day, is not a waste.

The stomachs of ruminants are comprised of four sections; the first three are the rumen, the reticulum and the omasum. These three sections are called the front stomach. The section that does the real work is called the abomasum. Because the nutritional value of grass is very low in comparison with meat, it is obvious that a large bodied ruminant will need a lot of grass. Consequently, the capacity of rumen being 150 liters is a wise and fitting design. In addition, the cellulase enzyme that digests the cellulose walls in plant cells is not produced in the tissues of any mammals. The possessor of infinite knowledge and power, God placed high concentrations of bacteria, protozoa, yeast and fungus-all of which can produce the cellulase enzyme needed to break down cellulose-in the rumen of ruminating mammals. The rumen acts as a fermentation factory because of these microorganisms. Breaking down the cellulose-rich food consumed by ruminants, these microorganisms both fulfill their own nutritional needs and help to meet the host’s energy, protein and vitamin (especially B12) needs within a symbiotic relationship. I wonder where the microorganisms in the rumen learned about this synthesis and assistance mechanisms!

What a magnificent engineering wonder is the “sulcus esophagus,” a semi-duct structure in the shape of a canoe that extends from the end of the food pipe in newborn ruminants to the abomasum where the essential stage of digestion takes place. Due to this structure, milk drunk reaches the last stage of the stomach without passing through the rumen, for there is no matter like cellulose in the content of milk that needs to be broken down. Consequently, there is no need for the milk to go to the rumen. If it were not like this, the milk would go directly to the rumen where it would be ruined by microorganisms, lose its nutritional quality and be like a bribe given in vain to the microorganisms in the rumen.

And surely in the cattle (feeding on the pastures of the revived earth) there is a lesson for you: We give you from that which is within their bodies, (marvelously distinguished from) between the waste and blood, milk that is pure and palatable to those who drink. (Nahl 16:66)

Ruminants, probably the most abundant of the herbivores such as cattle, sheep and goats, are foregut fermenters with a four-chambered stomach (rumen, reticulum, omasum and abomasum) and are an essential component of utilizing marginal land in the world in a sustainable way.

In the verse above from the Qur’an, the Creator and the Sustainer of the universe draws our attention to many of the benefits we get from domestic animals. While the main message of the verse is easily understandable to the general reader, it also contains some concise hints, even descriptions about the physiological details of milk production in ruminants that would be fully understood and explained by science only centuries after the Qur’an was revealed. The purpose of this article is to explain this process in a general sense and milk production in some detail.

Mammals are generally categorized according to the dietary habits into three classes-flesh-eating (carnivore), plant-eating (herbivore) and both flesh and plant-eating (omnivore). In a sense, humans (omnivores) and carnivores depend on herbivores for their nutrition. Generally speaking, all humans and animals in the world have directly or indirectly benefited from the plants. The ability of herbivores to utilize plants as their main energy source is dependent on symbiotic microorganisms which live at various sites within their gastrointestinal tract. The animal provides the microorganisms with food and habitat for growth and the microorganisms provide the animal with fermentation acids and microbial protein.

Herbivores are divided into two types, those with post-gastric (hindgut) fermentation and those with pre-gastric (foregut) fermentation. Fermentation is a chemical process during which microorganisms obtain energy from organic products. Ruminants, probably the most abundant of the herbivores such as cattle, sheep and goats, are foregut fermenters with a four-chambered stomach (rumen, reticulum, omasum and abomasum) and are an essential component of utilizing marginal land in the world in a sustainable way. Rumen and reticulum contain millions of microorganisms, which form about 3 to 10 percent of rumen fluid.

A major reason why human beings keep ruminants is their ability to convert food which humans find inedible-or at least unpalatable-to food (meat, milk) which humans can eat. They play an important role in the livelihood of farmers throughout the world, providing sustenance such as milk and meat, manure for crop production, cash income from sales of their products and a safety net of capital assets to face risks and misfortune in harsh environments. Currently, humans obtain about fifty percent of the meat and most of the milk they consume from ruminants. Scientists who have conducted studied on ruminants have developed cow breeds, which have higher milk and meat production than traditional cow breeds, and thus supplied an important development to meet the nutritional requirements of humans.

Pre-gastric fermentation provides three important nutritional advantages to the host animal.

First, cellulose and other plant polysaccharides are brought into solution and become available as energy sources. Cellulose is the most abundant natural carbohydrate polymer in nature, but mammals do not produce enzymes that can degrade it. Ruminant animals utilize cellulose via a symbiotic relationship with ruminal cellulolytic microorganisms. During ruminal fermentation, microorganisms ferment the carbohydrates to produce energy, gases (methane and carbon dioxide), heat, and volatile fatty acids (VFA) in the rumen. Effective digestion of plants requires a means of dealing with cellulose, the most important structural material of plants, which is extremely insoluble and remarkably resistant to a chemical attack. Cellulose digesting enzymes that are called cellulases and produced by microorganisms are also present in the intestinal tract of several invertebrates that feed on wood and similar plant products. Rumen harbors the different functional groups of the microbial population, which is responsible for about seventy percent of total digestion in ruminants, and the ability to digest cellulose has been ascribed to a large number of bacterial, fungal and protozoal species isolated from the rumen.

The energy content of plants is low, and the herbivore must consume a large quantity in order to satisfy its energy requirements. Therefore, herbivores spend a lot of time eating; eight or more hours per day may be spent eating.

Secondly, the rumen microorganisms can utilize non-protein nitrogen for growth, converting it into microbial protein which becomes available to the host. Proteins provide the amino acids needed for maintenance of vital functions, reproduction, growth and lactation. Non-ruminant animals need pre-formed amino acids in their diets, but ruminants can utilize many other nitrogen sources because of their rare ability to synthesize amino acids and protein from non-protein nitrogen sources via a symbiotic relationship with ruminal microflora.

Ruminants possess a rumeno-hepatic nitrogen circulation mechanism, which does not exist in non-ruminant animals, in order to save nitrogen. By this mechanism, ruminants can be fed non-protein nitrogen sources such as urea and nitrate when nutrients are in short supply to obtain high quality milk protein. Feed proteins are degraded by microorganisms in the rumen via amino acids into ammonia. Ammonia is used by bacteria to build their proteins and any excess of it is absorbed through the rumen wall into the blood and then converted to urea in the liver. When a diet is low in nitrogen, large amounts of urea (which is normally excreted in the urine) return to the rumen where it can be used by the microbes. In non-ruminants, urea is always entirely lost in the urine. If ammonia levels in the rumen are too low there will be a nitrogen shortage for bacteria and feed digestibility will be reduced. Too much ammonia in the rumen leads to wastage, ammonia toxicity, and in extreme cases, death of the animal.

Thirdly, vitamin synthesis by the microbial population makes the ruminant animal virtually independent of dietary sources of all vitamins, except for vitamins A and D.

However, rumen fermentation also brings some disadvantages. First of all, rumen metabolism causes environmental pollution. Methane is produced as a natural consequence of the anaerobic fermentation; it is a potent greenhouse gas. Dairy farming is the largest agricultural source of methane, one of the greenhouse gases. Furthermore, the major environmental concern associated with the animal industry is ammonia volatilization, which increases atmospheric acid deposition because of the impact of nitrogen-rich excreta on the environment. Therefore, worldwide, scientific research projects have been carried out to find sustainable strategies for reducing emissions of the greenhouse gas methane and ammonia volatilization from domestic ruminants to the environment.

In conclusion, the symbiotic relationship between ruminants and ruminal microorganisms plays an important role in the recycling of nutrients between humans and plants. This relationship also contributes to human life by converting low quality nutrients (grass and hay) to high quality food (meat and milk). Humans will benefit more from ruminants as scientific knowledge about relationships between ruminants and rumen microorganisms advances.

Zubeyir Altuntas has a PhD in Molecular Medicine. He is a research associate in Immunology Department of The Cleveland Clinic.

More specifically, groundwater represents 98% of the available fresh water on earth. The contamination of groundwater has increased significantly due to industrial developments over the last century. To illustrate how the modern human has had an impact on the environment, let us look at some numbers: In the United States alone, yearly 100 million tons of hazardous waste is generated and 4 million tons of toxic chemicals are released into streams; in addition, 1.2 million tons of toxic waste are emptied into landfills and 1.5 million tons are injected into deep wells for disposal. Again in the United States, of the 2 million underground storage tanks in gas stations, 450,000 are leaking gasoline and petroleum products to the subsurface. If these numbers do not impress you, remediation costs for contaminated sites in Europe are expected to exceed $1.5 trillion in the near future. These are only some of the impacts of heavy industrialization of which we are aware. The contaminants that are released into the environment severely threaten drinking water, agricultural, and surface waters.

The pollution process of the subsurface environment is ironically simple. Leaks from various contamination sources seep into the groundwater from where they travel and infiltrate the soil with which they come in contact. Contaminated soils and sediments slowly release these pollutants, which over long period of time have become a continuous source. Of course, all these contaminants can potentially cause cancer or have detrimental effects on the ecosystem or on human health. To give an example of how these pollutants easily spread around the globe, in a recent study of dairy products that were collected from countries all around the world, the same type of organic contaminant (PCB:

Polychlorinated Biphenyls) was found in those products that, for the most part, originated in the USA, although the usage and production of this contaminant has been banned since 1976. How have these pollutants managed to persist in the environment and travel all the way from USA to the rest of the world, even as far as Australia? There are several ways this can be done; first the released contaminant volatilizes into the air and travels, through atmospheric depositions of large quantities onto the grass that is eaten by the cow. Another way is that a fish swimming in contaminated fresh water is caught and becomes food at a dairy farm. This research exemplifies how the pollution of the environment can affect us, regardless of where we live on this planet.

It seems like a very gloomy picture though, if nobody is going to take any action against the contamination or clean up the toxic chemicals from vulnerable targets like drinking water sources or terrestrial lands. There are, of course, many precautions that have been undertaken to clean up the environment. This article is about one of the interesting ways in which we utilize microorganisms to clean up contaminated groundwater or drinking water.

It sounds a little strange for engineers to be dealing with bacteria that naturally exist and utilize them in cleaning up the environment. But this is what they are doing, using a technique called bioremediation, wherein natural microbes become stewards for destroying the pollutants in the environment. The simple technical description of bioremediation is the intentional use of the biodegradation process to eliminate environmental pollutants that have been intentionally or inadvertently released. The biodegradation used here is the microbial transformation process of toxic chemicals into nontoxic forms and sometimes mineralization into inorganic elements like carbon, oxygen and hydrogen.

This transformation, which is essentially a process of destruction, first requires the presence of microorganisms. These microorganisms almost always exist in nature, unless there are harsh conditions that prevent microbial growth. The microorganisms use inorganic or organic contaminants as their nutritional and growth source in the life cycle. For example, a commonly encountered organic contaminant, benzene, is composed of six carbon atoms and six hydrogen atoms. During the degradation process, the microorganisms synthesize enzymes that stimulate the breaking down of benzene into carbon dioxide and water or sometimes the simple elements of carbon and oxygen. These enzymes ease the reactions that produce cellular energy and the building blocks for the synthesis of new cells. In essence, the contaminant serves as a nutrient – food – so that the microorganism can continue its life.

The electron acceptors

During the process in which the microorganism feeds on the contaminant (the degradation process), the key issue is the electron acceptors, the complementary part of the chemical reaction that occurs during the biodegradation process. During the breaking down of the large organic molecules into small elements, excess electrons are released into the environment and therefore an electron acceptor is required to maintain the chemical equilibrium and continue the reaction mechanism. This necessity for oxygen or iron dioxide resembles the need for oxygen in our liver to break down the complex molecules that occur during energy production and new cell generation. The process is as simple as this: we breathe oxygen to live and so do microorganisms. Oxygen molecules act as convenient electron dumps for bacteria that usually lie near the soil surface. Depending on the electron acceptor types, degradation reactions are categorized as aerobic (using oxygen) or anaerobic (using nitrate, manganese, iron and sulfate as electron acceptors). Humans can only inhale oxygen, but most insects can utilize other molecules, like iron oxide or sulfur as well.

Moreover, in order to have a successful clean up, scientists need to satisfy chemical and nutritional requirements and this is challenging for engineers. As these electron acceptors are not always readily available, engineers supplement the electron acceptors in the contaminated environment by methods like pumping air into the ground. Sometimes the microorganisms that are necessary to degrade the potential pollutant do not exist and the engineers must first inject the bacteria so that they can consume the pollutants as food.

Geobacter

One of the microorganisms most frequently studied for its degradation potential for organic and inorganic contaminants is Geobacter metallireducens, or the geobacter. Since it was first discovered, more than 20 years ago, researchers at the University of Massachusetts have been studying this incredible creature; however, they admit that there are many things that they still do not know about it. The geobacter was the first organism found to oxidize organic compounds to carbon dioxide using iron oxides as the electron acceptor. In other words, the geobacter gains its energy by using iron oxides (a rust-like mineral) in the same way that humans use oxygen. The main nutrient for the geobacter can be organic or inorganic pollutants for, and it breathes iron oxide in the way the human inhales oxygen. The geobacter can consume soil and groundwater contaminants like benzene and the gasoline additive MBTE, even in an oxygen-free environment. The geobacter, which has been found almost everywhere, even living in the dental spit-sinks, also flourishes in uranium-contaminated sites, converting soluble radioactive material to a material that is insoluble in groundwater, therefore making it easier to isolate for cleaning up. At present the geobacter is being put to work in actual clean up projects. As our understanding of the functioning of the species has improved, it has become possible to use this information to modify environmental conditions in order to accelerate the rate of contaminant degradation.

More interestingly, researchers have discovered that the geobacter spits out unwanted electrons into the circuit while consuming contaminants for energy. The geobacter exhales electricity through 20 to 30 hair-like structures, just 3 to 5 nanometers in diameter, to its surroundings. Although there is hardly enough microbe-produced electricity generated to solve the world’s energy problems, a fuel cell measuring a cubic meter would generate 2 kilowatts, and some engineers are talking about powering sewage treatment plants with a type of geobacter that harvests off the sewage itself. Just to give an idea about the direction of future research, researchers are now working on a selected gene of the geobacter. The gene that limits electricity production will be modified so that electricity production can be boosted during the degradation process. Given that, it would not be surprising if there were technology that created energy while cleaning contaminated soil or groundwater.

Clean water is a basic need for every human being, and it is our moral obligation to work as stewards for the environment; the first thing we must do is to stop contaminating the planet. However, we are faced with resources that have been previously contaminated. As one result of an increasing sense of responsibility toward nature, we are at a point where we can use natural microorganisms or plants as clean-up tools. Although mankind harshly contaminates the environment while creating an industrial and technological world, it is quite ironic that we still rely on the marvels of such divinely ordained solutions to sustain life.

References

• Martin Alexander, Biodegradation and Bioremediation, 199, Academic Press, San Diego CA USA
• Pedro J. Alvarez, Walter A. Illman, Bioremediation and Natural Attenuation: Process Fundamentals and Mathematical Models, 2005, Wiley and Sons, NY, USA
• www.geobacter.org Geobacter project, University of Massachusetts, Amherst Environmental Biotechnology Center
• Jana Weiss, Olaf Papke, and Ake Bergman, A Worldwide Survey of Polychlorinated Dibenzo-p-dioxins, Dibenzofurans, and Related Contaminants in Butter, AMBIO: A Journal of the Human Environment Volume 34, Issue 8 (December 2005), pp. 589–597

Immunity can be divided into innate immunity and acquired immunity. The mechanisms of innate immunity are given to us by our Creator as a tool with which to protect ourselves. These are used to fight against every kind of microorganism. These ever-ready forces do not need to have met the enemy microorganisms to fight them off. Acquired immunity comes about after the infectious microbe has been encountered; this is usually as a result of infection or vaccination. Such immunities only protect the body against a specific harmful organism. T and B lymphocytes and antibodies belong in the acquired immune system, whereas other mechanisms are part of the innate immune system. We can classify the very intricate immunity mechanisms as follows:

A – Layers that cover the inner and outer surfaces of the body: These are the physical structures that carry out the task of protection by covering the tissues like a shield or fortress.

1. Skin: Our skin is an organ in its own right. It is created with such perfect characteristics that no microorganism can penetrate our body if there are no flaws, like gashes, scratches, or wounds.

2. Oral mucous membrane: If the epithelial layer covering the interior walls of our mouth is healthy, microorganisms cannot infiltrate the blood.

3. Areas around the sexual organs: The sexual organ in males is, even at birth, more protected than that of females. For female children, the epithelium covering the interior face of the organ turns into a multi-layered structure due to the impact of estrogen (sexuality hormone) that starts being secreted after adolescence. That multilayered structure blocks infections that can result from sexual intercourse. Female children before adolescence do not have estrogen, thus their genital organs have a thinner layer of epithelium and are more likely to be infected. This is why cleansing after urination should be done from the front to the back and the genital organs should not come into contact with feces. Our God of infinite mercy also gives girls a hymen in order to protect girls from germs.

B – Flora bacteria (beneficial bacteria): These do not serve as mechanical obstacles, but are assigned tasks. There are some bacteria that do not cause illnesses in the urine and in the proliferation canals, the skin, throat, intestines, and the eyes. Those beneficial bacteria located in our body work for us and hinder other infectious bacteria from settling in these zones. Those places are sterile in the body of a fetus; no beneficial bacteria exist there. Protector bacteria are positioned in those places right after the birth; this is a revelation of God’s infinite compassion. For instance, a baby’s first feces are sterile because there are no bacteria in his intestines. As time passes, a baby adopts protector bacteria through his mouth by nursing, from bottles, and pacifiers. Parents should be careful about the purity of pacifiers, feeding bottles, water, and additional nourishments, particularly in the first couple of months, until the bacteria flora have been established in an infant’s body. Otherwise, babies can easily suffer from diarrhea. God equipped beneficial bacteria with some special peculiarities to be able to deter other microorganisms from settling in the body. Here are some of these peculiarities:

1. They compete with infectious bacteria on the consumption of nutrients, so they restrain the reproduction of other bacteria.

2. They emit bactericides that kill only pathogenic (harmful and infectious) bacteria.

3. Some flora bacteria are assigned a mission to impede the reproduction of pathogenic bacteria so as to reduce pH (increase acidity) in the environment. For example, the lactobacillus in the female genital passage produces lactose by breaking down the glucose in the uterine canal in order to acidify the secreted matters in that canal. Reproduction of fungi is also obstructed in the same way. Due to that fact, some fungal diseases might emerge in genital areas or in the ears, among other places, after antibiotic treatment. Antibiotics kill not only pathogenic bacteria, but also flora bacteria. Thus, desultory usage of antibiotics should be avoided.

Today, beneficial intestinal bacteria are taken orally in capsules, and infectious bacteria in the intestines are killed by supplementing the flora bacteria in that organ without the use of antibiotics.

C – Mechanical cleansing:

1. Secretions:

a.Saliva: Secreted continuously from the glands behind the ears, beneath the chin and beneath the tongue, saliva expels the intruder pathogenic bacteria by cleansing our mouths. It also prevents tooth decay and gum inflammation by cleaning leftover food on which bacteria could feed.

b. Tears: Tears are charged with the duty of cleaning the conjunctiva (the mucous membrane that lines the inner surface of the eyelids and that continues over the forepart of the eyeball) and the cornea (the transparent part of the coat of the eyeball that covers the iris and pupil and admits light to the interior).

2.Cilia: These are feather-like cell extensions of microscopic size.

a.Nasal Cilia: Covering the nasal mucous membrane, mucus (a slimy substance) grasps dust particles and microbes in the air due to its adhesive nature. Lumpy folds inside the nose do not let the air flow straight. Therefore, a turbulent air current occurs in the nose. This turbulent current causes the particles in the air to come into contact with this slimy substance and to get stuck there. Epithelial cells also have cilia expanding toward the nasal cavity. Every cell has nearly 200 cilia. These cilia push mucus and the dust particles attached to it toward the pharynx with an up and down whipping action (10–20 strokes per second) so as to keep them away from the lungs.

b.Cilia in the lower respiratory passages: The upper surface of epithelium that is spread on the trachea, bronchi, and bronchioles is also covered with mucus. Epithelial cells in this area have cilia, too. These cilia do the same whipping action to push particles and microorganisms in the mucus toward the pharynx. They are pushed into the pharynx and expelled by coughing. One of the damaging impacts of nicotine on the respiratory system is that it paralyzes these cilia and disrupts the discharging process of harmful particles. As a consequence, smoking leads to many lung diseases.

D – Enzymes, acids and antibodies in body secretions:

1.Lysozyme: This is a substance found in body secretions (saliva, perspiration, tear, genital organ secretion etc.) that kills bacteria.

2.Stomach acid (Hydrochloric acid, HCl): Being emitted through stomach glands, HCl is a strong acid that can destroy bacteria that are able to reach as far as the stomach with the food we eat. Although we usually have our meals without cleaning our hands sufficiently or without washing them thoroughly, we rarely (except for situations where we are exposed to a high density of microbes like food poisoning or dirty drinking water) get infected via this route. The actors in this perfect protection are lysozyme and stomach acid.

3.Antibodies: Being present in the blood and body secretions, antibodies play a role in the defense against microorganisms. Antibodies in breast milk are passed from the mother’s blood to her milk via a very special mechanism, and are significant in the protection of an infant from infections.

E – Defender Cells: Resembling special operation forces, each of these cells is trained in different parts of the body and sent into the blood circulation. Those troop-like cells, which protect us against diseases by struggling fiercely with germs that can reach the blood after overcoming many obstacles, cannot have come about merely by chance, without the participation of the All-Knowing Designer.

1.Macrophages: Monocytes, a kind of leukocyte in the blood, pass from the capillaries to the tissue and turn into giant cells called macrophages that can phagocytose (swallow microbes) at a great rate. Macrophages swallow and tear down every kind of bacteria and virus that invades the body. These cells constitute the first defense line of the body and serve like advance guards. For instance, the first force to start fighting against the germs that can penetrate the skin through a scratch is the macrophages found just beneath the skin are called histiocytes. Germs that can infiltrate the blood through the intestines and reach the liver via the portal vein are eradicated by another type of macrophage. Therefore, almost no bacterium can pass from the intestines into the general blood circulation system. Germs that enter the body orally are destroyed by macrophages stationed in the lymph nodes on the tonsils. The ones that manage to reach the lungs through the respiratory paths are killed by the macrophages in the alveoli. Those cells also cause T-lymphocytes (very specially equipped cells) to proliferate by stimulating them. 2.Neutrophils: These are the most common type (60-70%) of leukocytes. These cells participate only in fights against bacteria. When bacteria enter a tissue, some poisonous matters emitted by them cause a chemical reaction called chemotaxis; this reaction attracts the neutrophils toward the infected tissue. In this case, the neutrophils leave their capillaries for the infected tissue and find and destroy the bacteria. How can germ-eating cells, like macrophages and neutrophils, distinguish normal body cells from microbes? Undoubtedly, the Creator of such an excellent defense system does not make us worry about such a problem; it was for this purpose that God created opsonins. Opsonins are similar to adapters in that they are able to attach two different parts together and connect themselves to a specific place on the germ. Thus, macrophages and neutrophils carry out their germ-eating job perfectly, connecting themselves to those opsonins. Since our own body cells do not have receptors that can handle opsonins, they cannot be eaten. 3.Lymphocytes: These are the troops of the immunity system with the most complicated organizations and strategies. These troops are categorized as T and B lymphocytes. They are the most important and powerful of the immunity mechanisms and constitute about 20-30% of the leukocytes in blood. They are regarded as the last defense line against those germs with which the other mechanisms cannot cope. a.T lymphocytes: When T lymphocytes are stimulated by macrophages, T cells that are a form of T lymphocyte secrete a matter called lymphokine. Lymphokine stimulates cytotoxic (microbe killer) T cells and B lymphocytes into action. Unless auxiliary T cells exist, the acquired immunity system collapses. Likewise, the HIV virus destroys auxiliary T cells and renders a person susceptible to disease. Even very simple infections can turn into a catastrophe for those patients. Cytotoxic T cells assault bacteria and particularly virus-infected body cells. They deliver porphyrins (proteins to make holes) into cell membranes by attaching themselves to the cells. In that way, a huge amount of water enters the cells and they get torn, due to over-swelling. Thus, viruses in the infected cells are dispersed and are neutralized by specific antibodies produced for that purpose with their infecting ability being impeded. (Viruses have to enter body cells to be able to proliferate. Only in this way can they protect themselves against antibodies and proliferate. Viruses that proliferate in cells use matters in those cells and cause them to eventually break apart, then move onto other cells.) b.B lymphocytes: These cells are stimulated directly by microbes. However, they need lymphokines to be completely stimulated and activated. Lymphokines are created capable of causing B lymphocytes to proliferate and transform themselves to Plasmocytes. Plasmocytes also emit antibodies to the blood. c.Killer cells: These play a role in the innate immune system, so they do not need stimulation like T and B lymphocytes. In particular, they assault body cells that are virus-infected or show a tendency to cancer. In this way, they establish a first defense line against viruses and block cancer development. Even though the working principles of lymphocytes are not known, they are related in some way to spiritual values such as love, enthusiasm, and peace of mind. Likewise, it is known that the immune systems of people whose spirituality has been weakened by depression and stress are more susceptible to break down. Unless those people recover by activating their spiritual dynamics, like faith in destiny, they are under a greater threat of cancer. Yet, this world is a place of examination. We cannot claim that every cancer is due to a damaged spirituality; we should not forget that cancer might occur due to different reasons. 4. Eosinophils: These are a kind of leukocytes that can kill some sort of parasites. They cling to parasites and release the granules in their cytoplasm into the parasites. These granules contain enzymes which destroy parasites. 5. Mast cells and basophils: Mast cells and basophils play a central role in inflammatory and immediate allergic reactions. They are able to release potent inflammatory mediators. Mast cells function out of the veins and protect the tissues in the body, whereas basophils are similar cells found in the bloodstream. F – Factors in plasma: 1.Antibodies: These are secreted into the blood by plasma cells. They fight against the germs that have stimulated them. They show their impact directly (neutralizing bacterial poisons, gathering and precipitating bacteria, neutralizing viruses, pulling microorganisms into pieces) or by activating a very special system called a complement. 2.Complement proteins: When inactive complement proteins in plasma are stimulated by antigens and an opposing antibody complex, active complement compounds are brought to life. These compounds have various effects like chemotaxis, opsonization, development of inflammation as a result of stimulation of mast cells and basophils, and the destruction of microorganisms. The complement system can be stimulated by microorganisms without a need for antibody development (without a need for lymphocytes); this can be seen as a manifestation of our Creator”s name Mudabbir (managing, administering, controlling every being in balance and order). This ensures the stimulation of a complement system under conditions that lack antibody production. Hence, the body is never left completely undefended. Is it really possible that such an amazing defense system, that requires unlimited knowledge and power, and that consists of every kind of alternative action, can come into existence by itself? 3.Interferons: Viruses invade body cells and synthesize proteins that contribute to their proliferation. Interferons, secreted by lymphocytes or other leukocytes, are created so that they can attach themselves to virus-infected body cells and obstruct the production of those proteins. Hence, these viruses cannot proliferate. 4.Lysozyme: Mentioned in the earlier part concerning body secretions, lysozyme is also available in the blood and kills bacteria there. 5.Properdin: This is a kind of protein available in the plasma which can neutralize viruses and destroy some bacteria types. 6.Acute phase proteins: These are a large number of serum proteins (C-reactive protein, etc.) that are swiftly synthesized by the liver and that are employed in defense during infections. 7.Beta-lysin: A substance that destroys some types of bacteria. G – Events caused by infections: 1. Inflammation: Inflammation is a response that is designed to protect tissues against tissue destruction, caused by factors like infection, excessive heat, and trauma. When a tissue is invaded by microorganisms, it starts to be destroyed; certain matters come out of those tissue cells (as mast cells) and lead to certain reactions in that zone. a.Vasodilation: As the little veins transporting blood to a tissue widen, more blood rushes in and more neutrophils are carried to that zone. Meanwhile, a color enhancement (blushing) occurs in that place. b.Increase in permeability of the capillaries: Neutrophils can penetrate into the tissues more easily. Plenty of water also passes through tissues, so some edemas (swelling in tissues) develop. Finally, coagulation proteins in the plasma, which can rarely infiltrate from capillaries to the tissues because of their large molecular structures, pass to the tissues and clot the liquid here. Hence, lymph veins, which are responsible for returning the liquid to the blood circulation, are plugged by clots. Consequently, inflammation detains microorganisms in that specific zone and prevents them from spreading throughout the body. Microorganisms are also destroyed by tissue macrophages in the inflammation zone and the migrant neutrophils working there. (The more a bacterium causes tissue damage, the harder it passes to blood.) Then, remnants of dead bacteria, damaged tissue cells, and neutrophils that are also destroyed after the phagocytosing of between 5 and 20 bacteria soften the inflammation by dissolving and creating some pus in that zone. The pus streams out by itself or is relieved by an incision being cut in the covering skin. 2. Fever:Toxins coming out of some bacteria and some secretions of microbe-phagocytosing cells lead to an increase in body temperature. Fever stops reproduction of microorganisms and kills them by ruining their structures. Within this framework, the occurrence of fever is beneficial; it indicates that the body is resisting and struggling to kill the microbes. Therefore, fever should not be reduced as long as it is not too high to cause brain damage (especially for children). 3. Cough: A cough helps the body discharge the microbes in the respiratory paths. Thus, cough medicines should not be used immediately, except in cases of whooping cough. 4. Diarrhea: This helps the body rid itself of feces quickly, so medicines to stop diarrhea should not be used, either. However, in cases of cough and diarrhea, a person should know their own strength and the strength of their immune system well and take medication accordingly. When we consider all these defense mechanisms, this question occurs in our minds: Do we protect ourselves against infections or is there someone who operates various immunity mechanisms in our bodies and controls them at every moment with His infinite knowledge and power?