One of the processes that occurs in the body is called “inflammation.” Inflammation occurs when a cut into the skin also punctures a blood vessel. This situation directly exposes the blood to the air. Inflammation occurs in a few steps. First, the blood vessels near the wound are expanded (which causes the swelling that we see near the cut) and special proteins called “fibrins” are brought in. These fibrins bind to each other to form a net-like structure. We are all quite familiar with this net, which we call a blood clot. This net stops the bleeding and cuts the interaction between the air and the blood within a few minutes.

Next, it is time to quickly eliminate any foreign objects that got into the tissue. Special immune cells called “macrophages” are sent to the crime scene to clean up. Macrophages are large white blood cells that “eat” microbes and other foreign objects using a process called “phagocytosis.” After the scene is all cleaned up, these macrophages excrete special molecules that induce tissue repair and return the blood flow to normal. An important note here is the specific order of these events. Like every single process in the body, they occur in the most purposeful way possible. What do I mean? I mean that, first the wound is closed urgently; second, macrophages are sent in; third comes the tissue repair. Any other order would have greatly lowered the effectiveness of inflammation. Imagine that the wound is closed after the macrophages are sent in. Then, by the time the macrophages killed all the microbes, twice as many would have entered the scene. The body seems to know every single event beforehand and plans its defense accordingly.

Our body is perfectly calibrated to keep our blood, the milk of our organ systems, absolutely pristine.

Let’s say a microbe managed to sneak into the blood before inflammation occurred, and is long gone to another region of the body. Does the microbe win? Unfortunately for the microbe, it has to pass another test. This time the tester is the lymphatic system. The lymphatic system is the sewage system of the body. When the blood transfers its nutrients to the tissue, the fluid goes through the “interstitial area” (the empty space between organs). During this process, some of the fluid stays in this area and starts to accumulate. This is where the lymphatic system kicks in. The lymphatic system consists of many tubes running parallel to the blood vessels and recollects any excess fluid and transports them to the subclavian vein near the neck. This way, excess fluids of the body and all of the molecules in them, are reintroduced into the circulation. If there is a problem with this process, an abnormality called “edema” occurs. Of course, the blood is a very sensitive fluid because it travels through the whole body and seeps into almost every single cell. If a microbe were to get into it, it would easily spread and cause disease. So, the lympatics first does a checkup on the body fluid. This checkup occurs at special nodes in the system called lymph nodes found all over the body. Two of the most famous lymph nodes are the spleen and the tonsils. Within these nodes are lymphocytes, special immune cells that “tag” bacteria and other microbes to be later destroyed by macrophages. Thus, the blood is continuously cleaned and kept safe from harmful microbes.

Last but certainly not the least, the final inspection the blood goes through takes place in the kidneys. The aforementioned two checkpoints prevent the entrance of any foreign materials into the blood, and the elimination of any microbes lucky enough to somehow make it through. So, the only task to be completed is the elimination of excess molecules formed in the metabolism. For example, the blood in the veins (the vessels that carry carbon dioxide formed by the respiration of cells) is carried to the lungs where the carbon dioxide is exhaled. But, a much more precise mechanism comes into play in the kidneys. Blood vessels that come from all around the body form a knot-like structure in the kidney called the “glomerulus.” This knot-like shape increases the surface area of filtration. The blood running from the glomerulus is then filtered into the “Bowman capsule,” which surrounds the glomerulus.

But wait! The sanitation system is not satisfied with this first filtration and “thinks” that the filtrate is not ready to be excreted by the urine. So, a more delicate filtration occurs right after the filtrate enters the “proximal tubule.” While passing through this tubule, essential molecules are immediately reabsorbed into the body. The most valuable of all these molecules is glucose, since it is the main source of energy in the body. The proximal tubule reabsorbs around 98 % of all the glucose, while the distal tubule scouts out the rest. After the tubules are done with the filtration, not a single glucose molecule is left in the urine. As a matter of fact, the presence of even a few glucose molecules in the urine leads to a diagnosis of “renal glycosuria.”

After the proximal tubule, the filtrate goes into the “loop of Henle,” where it is dipped into a high-concentration environment. Water travels passively (without the need for energy) from low-concentration to high-concentration areas. In the loop of Henle, the urine is low-concentration, so water runs back into the body. Thus, any excess water in the urine is effectively and economically reabsorbed. The big machine that consists of the glomerulus, the Bowman capsule, the tubules, and the loop of Henle is called a “nephron.” Everything described above occurs in a single nephron. The average number of nephrons in one kidney is around 1,000,000. The human bladder holds around 150 ml of urine on average. So, each nephron is actually responsible for 0.00015 ml of urine production. The kidneys filter over 1,000 liters of blood each day, so our blood is kept just as we want it. Millions of tiny nephrons work in unison to take in huge amounts of blood and they know exactly what to leave and what to keep, 24 hours a day, 7 days a week.

Our blood is our life source. It is the milk of the organs, and our organs would dry up without it. Believe it or not, our organs are quite picky. If they are to receive anything they don’t like, they will start acting up. In order to keep the organs happy, the three mechanisms mentioned above have to work hard and not make a single mistake. These mechanisms are, of course, also made up of cells. These miniscule cells “know” exactly what their clients on the ends of the body like and don’t like, and prepare the blood composition accordingly. Only one word can describe these wondrous mechanisms: Impeccable.

Brian Turk is a medical student from New Jersey. He writes on medicine, health, and biology on a freelance basis.

The harmful foodstuff eaten is spat out quickly through vomiting and so damages of such foodstuff is minimized. Occurring upon taking of any poisonous food or alcohol, vomiting directly contributes to treatment by ensuring a quick disgorge of the harmful stuff. Variations in amounts of estrogen and progesterone hormones during pregnancy helps in noticing even the least amount of toxins (poisons) found in the blood by way of increasing sensitivity of the chemoreceptor trigger zone within the brain stem. When this zone of the brain takes notice of toxins in the blood, it immediately activates feeling of nausea and vomiting. Margie Profet, a researcher from the University of California at Berkeley was the first person who drew attention to this issue in 1995. She asserted that food craving is a divinely merciful mechanism aiming at protection of the miraculously developing embryo against probable dangers within the human body. She also asserted that food craving protects the embryo from natural toxins in foods. Vomiting may also happen to travellers and sufferers of migraine. Certain psychological factors such as unpleasant smell and excessive fear may result in vomiting as well.

If, however, vomiting recurs and turns out to become a habit, one should be careful, for vomiting causes new problems such as electrolyte losses and dehydration while irritating the alimentary canal, throat, mouth and teeth through which vomited matter passes. In addition to these, regurgitating might be inadvisable and indeed should be avoided in certain cases of poisoning which develop due to ingestion of petroleum products and burning chemicals like hypochlorite and ammonia which are used in house cleaning. The reason for this is because petroleum products may cause pulmonary infection of chemical origin in the lungs and burning chemicals may cause scalds on the tissues they touch during regurgitating.

Just like all the systems that our bodies are equipped with, vomiting also happens in accordance with a plan and program during which a wonderful co-ordination is displayed. The vomiting center in the brain is responsible for such co-ordination.

Rapid increase in salivation and nasal secretion prior to vomiting plays a key role in alleviating damages of the highly acidified vomited matter over the interior surfaces of the mouth and nose. Increased salivation helps with the protection of tooth enamel too. The pushing process of the foods eaten normally occurs from the intestines towards the bowels during the course of digestion. However, it reverses and occurs from the intestines towards the stomach during which the muscles of gastrointestinal tracts relax, open and the contents of the intestines are thus gathered in the stomach. Taking deep breaths prior to vomiting decreases the need for breathing during vomiting and blocking of the air passage by vocal cords’ converging prevents aspiration, that is, the passage of contents of stomach to the lungs. If such mechanisms did not exist, every vomiting attack might have ended catastrophically. Breathing attempts apply negative pressure on the rib cage and convulsion of stomach muscles applies positive pressure within the abdomen in spite of the converging of vocal cords. A pressure decrease is observed in order for contents of the stomach to be regurgitated. Muscles of the gastrointestinal tract tighten while muscles of the gate between alimentary canal and stomach relax just before vomiting. So, regurgitating via alimentary canal occurs without passage of stomach contents to intestines. Upon completion of vomiting, there is the disappearance of abdominal convulsions and the secretion of endorphin in the blood, so a person breathes sigh of relief.

In conclusion, although vomiting is perceived as something which is seemingly unpleasant, it is indeed a fine product of Divine artistry like all other systems and mechanisms of our body. Vomiting, as one of the proofs that God has created nothing useless and unnecessary, is certainly a great blessing bestowed upon us.

References

• “Sickening sounds – research to make your ears cringe.” University of Salford. January 28, 2007.
• Lunsden, K, and Holden WS. 1969. “The act of vomiting in man.” Gut 10: 173-179.
• Margie Profet (1995) Protecting Your Baby-to-Be: Preventing Birth Defects in the First Trimester. Reading, MA: Addison-Wesley. pp. viii, 312.
• Flaxman, S.M. and P.W. Sherman 2000. “Morning sickness: A mechanism for protecting mother and embryo.” Quarterly Review of Biology June 2000. 75:1-36.

We live in a world full of technological devices, instruments and machines. Even if we buy them from good retailers, our cars we use to commute, or our CD-players and nowadays the mp3-players we use to listen to music one day break down, and eventually we change them. Can you imagine a TV which never gets old and can be used forever? The answer is obviously no. But we human beings have a miraculous system that always repairs itself-a system called DNA Repair. The proteins which are produced using DNA as a template, are also used to repair DNA when necessary. Before going into details of DNA repair, let us look at what DNA is, what DNA damage is, and how it occurs.

DNA (deoxyribonucleic acid) is one of four major macromolecules (the others being carbohydrates, lipids, and proteins) that constitute living things. DNA mainly contains genetic information encoded by a combination of four different DNA building blocks, nucleotides, to produce proteins. These proteins in turn play a role in cellular reactions. Genetic material is faithfully copied and passed on from generation to generation, perpetuating the characteristics of the parent and providing children with the information necessary for existence. Our sex, most of our personalities, as well as physical traits (eye color, hair color) are dependent on DNA as a part of the biological order established in our body. Moreover, even aging is a result of the shortening of the packed DNA (chromosome) through time. DNA is crucial for our body, but having such a unique molecule can come at a cost. In particular, cancer and many other disorders are thought to be caused by a lack of proper DNA-handling in cells, due to a defect in DNA repair.

DNA is a fairly stable molecule made up of two strands. Along each individual there are covalent bonds which hold sugar and phosphates together, and the two complementary strands of DNA are bound by hydrogen bonds. But, are these bonds strong enough? Are they unbreakable? To be able to function properly is DNA ever in need of maintenance? Like everything in this world, DNA too can be fragile in extreme conditions (Figure 1). Physical or chemical agents that might cause changes in DNA are commonly known as DNA-damaging agents or mutagens. Mutagens can be either endogenous (like free radicals which are produced from normal metabolic byproducts) or exogenous (like UV radiation or some toxic food chemicals). In addition, DNA can be damaged when synthesizing itself before cell division. These changes may be caused by enzymatic errors or mis-incorporation of nucleotides. Studies have shown that DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day. While this constitutes only 0.000165% of the human genome’s approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell’s ability to carry out its function and appreciably increase the likelihood of cancer formation.

Although there are many ways that DNA can be damaged, we are equipped with DNA repair mechanisms that can reverse the process. As soon as damage occurs to the DNA, it is detected by sensor proteins. These proteins scan the DNA all the time for any bulges or breaks. Once damage is identified the proteins tag it and DNA repair is initiated. A second precaution against damage is provided by a process called DNA Damage Checkpoint (Figure 1). Once this has been activated, cell division is delayed or comes to a halt in order to prevent the change from being passed on to any new cells.

Damage can occur on a single strand or on both strands. Depending on where or how the damage has been introduced, we have different repair systems for each type of DNA damage (Figure 2). In figure 2 we can see the difference between the original, undamaged DNA and the damaged DNA. The DNA repair systems responsible for repairing different defects are also shown in the figure to give a better idea of different DNA repair systems. Of particular interest is the fact that there are more than 150 genes that have been identified to date as being related to DNA repair. When we consider the number of possible defects that can threaten the DNA, this number is surprisingly low in comparison to the total number of genes (~ 30,000 as estimated by the Consortium of the Human Genome Project). Related to that, research in recent years has started to show that the genes which are important for one particular type of DNA repair are in fact required for different repair systems too. When we think about the enormous number of defects introduced into the DNA as opposed to the very few number of proteins involved in DNA repair (as compared to the whole genome), we can easily appreciate the perfection of the system. To give an idea of how DNA is repaired a nucleotide excision repair is shown in figure 3. At the top of the figure, UV exposure causes damage to the DNA. After that, DNA repair is initiated and recognizes the damage. The proteins (represented by circles in different colors) which are responsible for the repair act one after another to bring the DNA back to its original, intact shape.

If damage in DNA is not repaired at all, then the cells with the damaged DNA are either eliminated via a process called apoptosis or mutation occurs. The term mutation refers to permanent changes in the DNA. Although most people assume mutations are harmful, they can be silent or even beneficial depending on the region of DNA in which they occur. In the worst case, when they are deleterious, they can cause many genetically related disorders as well as cancers (Table 1). In this table, we can see different disorders which are caused by lack of appropriate repair systems.

If the rate of DNA damage exceeds the capacity of the cell to repair it, the accumulation of errors can overwhelm the cell and might also result in premature aging. Biologically, aging is an irreversible state in which the cell no longer divides, and is a protective response to the shortening of the DNA ends (telomeres). The telomeres are long regions of repetitive DNA that undergo partial degradation each time a cell is divided. Aging in cells may serve as a functional alternative to apoptosis in cases where the physical presence of a cell is required by the organism, thus serving as a “last resort” mechanism to prevent a cell with damaged DNA from dividing inappropriately. Since inappropriate division might lead to cancer, the induction of aging and apoptosis is considered to be part of a strategy to protect against cancer.

On the other hand, there is an interesting example for researchers where we see a proficiency of DNA repair activity in an organism called deinococcus radiodurans, the most radiation-resistant organism known to date. Specifically, it exhibits a remarkable resistance to radioactivity (which in turn causes double strand breaks on DNA) most likely due to enhanced DNA repair.

In this article we have tried to answer the question of what DNA repair is, how it is regulated in the cells and what the results of a deficiency in DNA repair are. Studying wonders like the DNA of our biological system is a means of contemplation that leads us to deep reflection on the intricacies of the universe. But one question remains unanswered, how has DNA learned to repair itself?

Hasan Altinbasak is a researcher at the National Institutes of Health.

References

• Lodish H, Berk A., Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipursky SL, Darnell J. (2004). Molecular Biology of the Cell, p. 963. WH Freeman: New York, NY. 5th ed.
• A physical map of the human genome. The International Human Genome Mapping Consortium. Nature 409, 934–941 (15 February 2001)
• http://www.riken.jp/engn/r-world/info/release/tress/2005/050609_2/index.html
• Wood RD, Mitchell M, Lindahl T. Human DNA repair genes, 2005. Mutat Res. 2005 Sep 4;577(1-2):275-83.
• Tom Strachan, Andrew Read. 2003. Human Molecular Genetics. John Wiley & Sons Inc.
• http://bbrp.llnl.gov/repair/html/overview.html
• http://biology-pages.info

Thus, the nitrogen molecule is inert and stable. However, in spite of this fact, nitrogen molecules undergo oxidization in the presence of water; in other words, nitrogen molecules are unstable in the presence of H2O and more easily form other compounds. This is expressed in the following equation:

This reaction occurs quite slowly. If this reaction did not occur so slowly, all of the nitrogen and oxygen molecules in the atmosphere would immediately combine with ocean water to form nitric acid. If this were to occur, an extraordinarily terrifying scenario that would lead to a global catastrophe would occur: The earth’s oceans would change into nitric acid, the most powerful and harmful acid in both its oxidizing and its acidizing effects! Such an event would entirely consume the nitrogen and oxygen of the atmosphere. The only more devastating global calamity imaginable is the apocalypse and the end of time itself! Of course, this chemical reaction cannot be entirely eliminated, even if its rapid occurrence would result in a terrifying global catastrophe. On the contrary, this chemical reaction must continue to occur slowly, as it has in the past, in order to ensure the proper formation of nitrogen compounds in the chemistry of the ocean; this is crucial to the continuation of life on earth. It is interesting that this phenomenon can show us how misguided some philosophers and philosophical movements, who have not based their thinking on religious principles, are in their attempts to demonstrate that humankind is God-like.

Although humankind is the most perfect creation in the universe, we are nonetheless almost entirely helpless in the face of the dangers that threaten us. The chemical reaction, summarized briefly above, has been taken from a basic chemistry textbook. The rate of the chemical reaction we described-in which nitrogen molecules in the presence of water can result in oxidation and the formation of nitric acid-in fact occurs in such a measured way that it is beneficial rather than harmful. This fact, along with the regularity at which the rate of this reaction occurs, clearly demonstrates the helplessness of the human condition.

Fortunately, the slow rate at which this reaction occurs ensures that the terrifying global catastrophe described above does not occur. Entire oceans do not turn into nitric acid, and the oxygen and nitrogen in the atmosphere, which is so crucial to our survival, is not consumed in this apocalyptic fashion. Should we not, therefore, learn the chemistry behind this good fortune? Even more importantly, should not we wonder Who calibrates the rate of this reaction, and continues to ensure that this careful calibration is not disturbed?