“The human brain, then, is the most complicated organization of matter that we know.”
Isaac Asimov

If someone asks what you recall when you look at the following pictures, I can hear you say ‘President Obama’ and ‘Statue of Liberty’. You just see a fragment of the pictures and remember them.

So, how does it happen? This is just a simple task for the brain. It stores an image and retrieves it whenever a part of it is seen. Amazing features of the brain, especially its power to learn and make decisions, inspires computer scientists in the field of artificial intelligence.

In computer science, an artificial neuron is a simple computational model of a neuron in the brain that excludes biological properties. Artificial neural networks (ANNs) are composed of artificial neurons, and they are utilized to solve specific problems, especially those that require learning and decision-making. ANNs may not be the best solutions in various machine learning problems; however, they are accepted as strong alternatives. Although ANNs don’t claim to be so, currently they are not even close to producing a simple model of the brain. Let’s take a short journey into the world of ANNs to experience the extreme difficulty of modeling the brain.

Some Applications of ANNs

Figure 1: Overview of ALVINN structure. Images obtained from the camera installed on the vehicle are provided to the ANN, and ANN decides the steering angle.

(adapted from: http://virtuallab.kar.fei.stuba.sk/robowiki/images/e/e8/Lecture_ALVINN.pdf).

ANNs have various applications in very large spectrum of problems that require learning, such as the Autonomous Land Vehicle in a Neural Network (ALVINN). The structure of ALVINN is shown in Figure 1. The ALVINN project by Carnegie Mellon University started in 1986 and aims to make a vehicle without a driver (Mitchell, 1997). In this project, ANN learns the steering habits of a driver. A camera is mounted on the vehicle to capture the images of the road. With respect to the continuous images provided, ALVINN determines the steering level with 45 different angle positions from sharp left to sharp right. Steering is updated 15 times per second so that it allows real-time control while driving at 55 mph. The system is trained by the data obtained from a human driver in a simulator and a real vehicle. ALVINN was able to speed up to 70 mph and successfully drive at 55 mph for 90 miles.

Figure 2: Handwritten zip codes (LeCun, et al., 1989)

Another example is handwritten zip code recognition (LeCun, et al., 1989). Zip codes from US Mail written by various people with large variety of styles and sizes were used in the experiments. Figure 2 presents some examples of zip codes in the experiment database. After the ANN was trained with more than 7,000 digits in the zip codes, it was 99% successful in recognizing around 2,000 digits in new zip codes.

Learning and Decision-making in ANNs

In order to understand the challenges better, we will first examine learning and decision-making in neurons and ANNs on simple examples.

Figure 3: (a) A typical neuron (adopted from http://commons.wikimedia.org/wiki/File:Neuron_-_annotated.svg), (b) artificial neuron in computer

Figure 3(a) illustrates a typical neuron which is the constituent of brain’s complicated network structure. Each neuron receives information as signals via dendrites, then evaluates it and generates a signal that is transmitted through its axon. A neuron has many connections between its dendrites and the axons of various other neurons. Figure (b) demonstrates an artificial neuron in computer science. It is considered a function: dendrites as the inputs of the function and generated signal via the axon as the output of the function.

Let’s see an example of an artificial neuron that understands if a given produce is a red apple or not. Think about how you understand whether a produce is a red apple or not. You see the shape and the color. However, it might be an artificial one for decoration. Then you can taste it and you get the sweetness of the apple. Similarly, our neuron receives three pieces of information as the input; ‘has circular shape?’, ‘is sweet?’, and ‘has red color?’. If the output is ‘yes’, that means the neuron recognizes the produce as a red apple. Otherwise, it will be ‘no’, which means the produce is not a red apple (Figure 4). Here, the neuron’s function is defined in such a way that it only generates ‘yes’ when all the inputs are ‘yes’.

Figure 4: Example inputs and outputs for the artificial neuron.

In an artificial neuron, some of the information can be more important than the others. For instance, to have red color may be more valuable in determining the price of produce. Assume that round shape and sweetness has equal value of $1; however, having red color is $2 – twice as valuable as the other features (Figure 5).

Figure 5: Artificial neuron with different input weights. Arrow thickness indicates the importance.

So, what is the big fuss about artificial neurons if they are only functions? In fact, the main feature of artificial neurons is learning. Considering the last example above, the neuron initially does not know the importance of the dendrites, i.e. the weights of inputs are all the same. If not trained, the neuron will generate the following answers which are sometimes wrong as indicated in Table 1.

Table 1: Artificial neuron before training; highlighted answers are wrong.

In real life, a teacher trains students. For instance, the teacher asks a question and if the received answer is not correct, she provides the right answer. Students learn the right answer and use this correct information in their lives. It is similar in artificial neurons as depicted in Figure 6. When the response of the neuron is incorrect, it adjusts the importance of the dendrites with respect to the correct answer hence it answers the same question correctly next time. During the training session, the neurons will be continuously asked the values of all the produce until it learns them all.

Figure 6: The learning process of the artificial neuron.

What if the problem gets complicated? Then one artificial neuron will not be sufficient, and we will need a network of neurons; ANNs. A more complex problem, ‘learning the digits’ is indicated in Figure 7.

Figure 7: (a) Digit learning problem, (b) ANN structure that learns digits. Due to the difficulty, only the connections between the input layer and first / last neurons in the middle layer are shown.

ANN has 3 x 5 = 15 input units like receptors of an eye retina. Each input unit corresponds to one square in the digits; either filled or blank. Each input unit is connected to the dendrites of all neurons in the middle layer. The output of each cell in the middle is connected to the dendrites of all neurons in the output layer. There are 10 output neurons corresponding to the digits from 0 to 9. After the ANN is trained, it provides a correct answer to the given digit as input. When digit ‘3’ is provided to the network, the neuron labeled with number ‘3’ in Figure 7(b) is triggered and outputs ‘yes’ whereas the rest of the neurons output ‘no’.

Figure 8: Faulty digit ‘3’ with a missing black square on the top right side.

Initially, all neurons in the network have equally weighted dendrites. After a reasonable amount of training, neurons adjust their weights, and ANN is able to identify digits. Here, we have some major challenges: what does ‘reasonable amount of training’ mean? When the ANN is undertrained, it will not always answer correctly to the digits given in Figure (a). In the other case, when the ANN is overtrained, it will memorize the digits provided during the training and will not recognize the faulty ones such as the one in Figure 8.

Challenges of ANNs

Beyond the mentioned the overtraining / undertraining problems, ANNs have a bigger challenge – how to determine the structure of ANN that fits the problem? In the digit learning example, we’re lucky because the structure is provided in Figure 7(b). However, the outcome of the solution may drastically depend on the number of neurons and the connections among them which is indeed a hard problem for ANNs.

The huge capability of the brain in learning and decision making comes from the huge number of neurons – around 100 billion – and the enormous amount of connections among them – from 100 to 500 trillion. The challenge to design such a huge network requires huge computation power. With the increasing number of neurons, ANN dramatically slows down especially during the learning process. Here, our example is a simple learning task of 3×5 pixel digits compared to the brain’s acquisition capacity of hundreds of images in our daily life. 

When the number of neurons gets larger, the reliability of network also reduces. Small adjustments in weights may change the entire behavior of the network hence it is easy to lose control of ANN. In contrast, the brain has a robust system, and its fault tolerance is admirable. Although neurons die every day, this doesn’t affect its performance significantly. The training method and how to update the weights are other hard problems leading to many different approaches in the neural computation field.

We have presented some simple tasks that can be solved using a few neurons and their challenges. On the other hand, consider the thousands of problems, various and incredible amount of information we have learned, and the thousands of decisions we make. The brain is truly amazing from the computer science perspective.

Bibliography

• Hertz, J. A., Krogh, A. S., & Palmer, R. G. (1991). Introduction To The Theory Of Neural Computation. Reading, MA: Addison-Wesley.
• Hopfield, J. J. (1982). Neural networks and physical systems with emergent collective computational properties. Proceedings of the National Academy of Sciences of the USA , 79, 2554-2588.
• LeCun, Y., Boser, B., Denker, J. S., Henderson, D., Howard, R. E., Hubbard, W., et al. (1989). Backpropagation applied to handwritten zip code recognition. 1 (4), 541-551.
• Mitchell, T. M. (1997). Machine Learning. McGraw-Hill.

The cell is the structural, functional, and biological unit of all organisms. All information needed for numerous processes in a cell, including repair and division, is contained in DNA (Deoxyribonucleic acid). DNA is a huge single molecule with intriguing features. How can a single molecule have such a dominant role in preserving information essential for the continuation of life? What are the mechanisms and levels of organization during its function? What does DNA mean for a single cell or for a human being? It’s impossible to answer these great questions in a single article; however, understanding the ways DNA exerts its role, DNA’s impact on multiple levels ranging from a single cell to an organism, and coordination between various levels, can potentially open up new frontiers in our mind and in our perception of life.

“Double helix” architecture of DNA DNA has an elegant structure that forms the basis for all of its functions. DNA is a repeating structure of nucleotides. Each nucleotide is formed of a phosphate group, 5-carbon sugar (deoxyribose) and a nitrogen-containing base attached to the sugar from outside to inside (See Figure 1a for a schematic view of DNA). There are four types of nucleotides in DNA, differing only in bases. We can consider bases as the identity of nucleotides. These four nucleotides are shown with letters A (adenine), T (thymine), G (guanine) and C (cytosine). Thousands of nucleotides bound with sugar-phosphate covalent bonds come together to form long strings. The sugar-phosphate backbone can be imagined as the steelwork of a skyscraper. The nice thing about nucleotides is their specific match to each other in double helix. A forms a base pair with only T, and G forms a base pair with only C. These pairs are bound to each other with hydrogen bonds. This feature is the key that makes DNA a double ladder. Two strings of nucleotides form a double helix by selective interactions of As with Ts, and Gs with Cs (See Figure 1b for 3-D structure of DNA). In DNA structure, hydrophobic bases tend to stay inside of double helix and hydrophilic sugar-phosphates stay outside interacting with water in nucleus. This feature helps DNA to form a double ladder. The length of the sugar-phosphate backbone is more than the bases. To compensate for the length difference, the sugar-phosphate backbone wraps around the bases inside, as a road wraps around a mountain to climb to the top. This simple difference is the main reason for DNA to form a helix.

The double-stranded nature of DNA with specific base pairing is one of its key features as genetic material. DNA is replicated using one strand as a template. Replication machinery reads one strand of DNA and builds the second strand by putting As against Ts and Gs against Cs. If a mutation occurs in one strand, it can be repaired using the second strand. This system is like photocopying DNA from itself instead of building it from scratch every time. That is why specific base pairing of nucleotides in the double helix makes it possible to replicate DNA through generations, protecting its integrity and information content. The code of DNA, an alphabet with four letters DNA contains the information to produce nano-sized cellular machineries called proteins. We mentioned that there are four types of nucleotides. Nucleotides are like letters in DNA, three of them are code for one amino acid of protein. We can make it more understandable by giving an example: “ATG-GCC-CTG-TGG-ATG” as a nucleotide sequence of DNA corresponds to the first five amino acids of a protein called insulin (a hormone regulating blood glucose level that is important in diabetes) and amino acid sequence is methionine-alanine-leucine-tryptophan-methionine. The code is so sensitive that even a single mistake in the sequence of DNA can cause serious diseases in humans such as sickle-cell disease or cystic fibrosis. With all these nucleotides, DNA can be thought of as a book containing amino acid sequence information for thousands of proteins (about 30,000 in humans). The amount of information contained in DNA is incredible: a typical human cell contains 2 meters of DNA that is tightly packed by proteins in the nucleus. If we tried to write the information from DNA into books, the book would contain over one billion words and 1,500,000 pages. DNA-protein interdependency and the cell as a micro-factory DNA can be thought of as an instruction manual that stores information for proteins and RNAs. Proteins, as molecular machines, perform particular tasks such as energy production and synthesis of DNA and RNA (See Figure 2 for the structure of proteins). Certain proteins read the information on DNA and make a transient copy of certain regions of DNA. These copies are called messenger-RNAs (mRNAs) and mRNAs are transported from nucleus to cytoplasm (See Figure 3 for representation of mRNA production from DNA by proteins). In cytoplasm, the information on mRNAs is read by protein complexes called ribosome. Ribosomes produce new proteins processing the data from mRNAs. This information flow from DNA to proteins is called central dogma in molecular biology (Figure 4). The data that is encoded in DNA can be read, translated, and put into the form of product only by proteins. We can conclude that for a protein to be produced, DNA is essential; for DNA regions to be read into proteins, proteins are essential. So, there is interdependency between proteins and DNA. Proteins without DNA have no future and no ability to regenerate and DNA without proteins is just like an instruction and manufacture manual of a computer without the user and computer itself. We can imagine the cell as a sophisticated factory, and proteins as the machines of the factory. DNA includes the instructions for the factory to be rebuilt and for itself to be rewritten for every new factory. It has instructions on how to build every machine in the factory. It has also codes for when and how much of these machines should be produced (we will discuss more about these codes on DNA in the next section). On the other hand, the timing and control of all these productions also depend on machines in the factory. Some of these machineries read and decode the instruction manual, some of them produce new machines by reading the decoded copies of the instruction manual, some of them act as sensors for the signals, some of them transmit signals to other machines, some of them produce signals by measuring the levels of materials in the factory, some of them function in communication with other factories, and so on. As we can see, DNA and proteins are meaningful for life only when they are together in the excellent cell context. This is a perfect example of the principle that the whole is bigger than the sum of its parts, because each element of the cell system has limited potential, until it comes together with the others to blossom into life.

The famous term “Gene” We can think of genes as functional units of DNA. A gene has the information content for at least one protein. Humans have about 20,500 genes that are read by protein machineries to produce proteins. Special proteins read the information on genes and make a transient copy of these certain regions of DNA. The process of making a copy of a gene as an mRNA is called transcription.

Genes don’t only store information; they have an intrinsic architecture of design to coordinate transcription utilizing three main components: promoter, coding region, and terminator. The promoter is the gene region that signals for the start of transcription. Protein machineries bind to the promoter and activate transcription. The coding region has the information for the amino acid sequence of the protein. The terminator region gives the stop signal for transcription. There are different functional regions on DNA located between separate genes such as enhancer regions that are platforms for binding regulatory proteins to tune the transcription.

The coding region of genes has multiple reading blocks for amino acid sequences and these reading blocks are called as exons. For some genes, different combinations of exons can be put together to give rise to different proteins. This mechanism allows one gene to be able to produce multiple proteins, increasing the efficiency of genetic material. A similar mechanism is used to produce antibodies (proteins recognizing foreign antigens) by the immune system. Different regional genes come together by a mechanism of DNA rearrangement (V(D)J recombination) and their differential combinations form many different antibodies. For example, a part of the antibody that is called a heavy chain is produced by a DNA region containing 65 variable (V) genes plus 27 diversity (D) genes and 6 joining (J) genes (5, 6). This produces a combination of 65 V genes x 27 D genes x 6 J genes = 10,530 heavy chains. There is a similar mechanism of rearrangement for light chain and variable region of antibodies, which result in millions of different antibodies for host antigens. A single example in the immune system shows us that DNA not only has a decent design for the coding system, but it also has ingenious and creative mechanisms to maximize its potential.

Gene expression is orchestrated during development and formation of organs The human body which consists of more than 1013 (ten trillion) cells is generated from a single cell called the zygote (see Figure 5). This tells us that, in a single cell, all the information and instructions to build and coordinate the systems of human body is encoded. Different tissues and organs including muscles, nerve cells, connective tissue, and eyes are fruits of one single cell. They all contain the same genetic information. Then what makes them different?

Promoters, enhancers, and repressors located in and nearby genes are important in spatial and temporal control of gene expression in different cell types of the body. Each cell type in our organs expresses a different subset of genes; this is what gives a cell its identity. For example, in muscles, myosin is expressed and in the eye’s retina, rhodopsin is expressed. Myosin functions in contraction and rhodopsin functions in vision. What determines the expression of rhodopsin in the eye but not in a muscle? The determination process occurs during development by programmed interactions of specific proteins called transcription factors, and restricted regions of DNA including promoters and enhancers. During development, certain regulatory proteins in a specific cell type, bind to DNA regions of only some genes (for example, in future retinal cells of the eye, rhodopsin gene would be activated but not myosin) and this predetermination orchestrates differential expression of genes to give rise to hundreds of different types of cells.

Different layers of complexity and organization related to DNA

There are different layers of function for DNA—each subtitle of this article tries to focus on a certain layer of function. DNA as a molecule has a double helix structure and is replicated through generations to preserve genetic information. It stores genetic information and has a four-letter alphabet for the expression of proteins. In the second layer, DNA has an informational unit called gene and thousands of genes are encoded in DNA to contain information for proteins. Each gene is controlled individually by making use of promoters and enhancers. In the third layer, all processes in the cell micro-factory as an entity are performed through interactions of DNA and proteins with each other and among themselves. Proteins read DNA code and work as cellular nano-machineries. In another layer, temporal and spatial expression of genes on DNA are orchestrated and different subsets of genes give rise to different cell types and organs. Organs communicate with each other to function properly and keep the balance and homeostasis of the body. The information stored in DNA not only coordinates highly sophisticated processes of a single cell, it simultaneously projects the whole body system of a human being, which is billions times bigger than a single cell.

DNA functions in all these different layers and keeps a great harmony in coordination between various layers of function. After grasping this complexity, organization and communication from a single molecule, to proteins, to a single cell, to tissues and organs, and to a human being by utilization of DNA, should not we ask ourselves, “can these elements come into existence by random forces and collisions?

References

1. Calladine, C. R. et al. 2004. Understanding DNA: The Molecule and How It Works, Academic Press

2. http://www.genome.gov

3. Li A, Rue M, Zhou J, et al. 2004. “Utilization of Ig heavy chain variable, diversity, and joining gene segments in children with B-lineage acute lymphoblastic leukemia: implications for the mechanisms of VDJ recombination and for pathogenesis.” Blood 103 June (12): 4602–9.

We are now approaching the end of the series of organs that told you about themselves. They have been pointing out the seal of God on them, and celebrating themselves as they manifest the beauties and the delicacies of God’s art. Thus, they have not only expanded your knowledge, but also guided people to the truth of God’s Oneness, stressing that natural and biological causes alone can never be an explanation for their splendid creation.

Each of your organs told you about its perfect structure and how it functioned within your body system. Let us think that each organ is a musical instrument. No matter how splendid and artful a musical instrument is, its true value is understood only among other orchestra instruments as they perform a wonderful concert. Your body is like that orchestra, where hundreds of instruments play together. In addition to the perfect structure of each organ, more importantly all the organs have to work together perfectly as a team. The success of an orchestra depends on how the instruments play in harmony with each other. The conductor of an orchestra is the person who ensures that harmony. The orchestra members carefully watch the conductor and play according to his arm movements, sometimes louder or softer, sometimes pausing or breaking into a very loud introduction. That is how a perfect concert can be performed.

In order to achieve such harmony, the organs in your body need a system that works just like a good orchestra conductor. This “regulating system,” which has to maintain the perfect harmony and order of the ongoing activities in your body, has two sub-units: One is the brain and the nervous system, and the other is me; your endocrine system (hormonal system). Since I work as a system that consists of many organs, from now on I will refer to myself as “us.” Each of us adjusts itself to the whole system by carefully watching the movements and works of the other organs. At our head are the brain and nervous system, which act as the general control center. However, it cannot carry out the regulating and controlling task alone; it needs our help.

The most basic principle that your body has to follow in order to maintain its health is keeping the inner medium stable in a dynamic balance while responding to varying environmental conditions properly. This is also known as homeostasis. For the inner medium to be kept stable, it is first of all important to be aware of the changes that are happening in the outer world, which is initially done by your sense organs. The signals related to the changes in the outer world are sent to your brain and nervous system through the sense organs. Afterwards, the signals are evaluated, and then they are sent to the related organ so that the proper reaction is produced and the inner balance can be regained. While all the activities regarding growth and reproduction are carried out, the inner medium should be kept stable at the same time (homeostasis). In order for all these activities to be performed continuously, you need inner secretion glands, which are small, but highly important.

The most important of all your organs that constitute the endocrine system is called the Pituitary (hypophysis) gland, which is recognized as the commander of all these organs and situated in your brain. The other secretion glands included in my system are the thyroid, parathyroid, suprarenal (adrenal) gland, epiphysis, pancreas, testicles, and ovarium. Now, these small but very important organs of mine will respectively talk about themselves and demonstrate the perfect program and the sensitive balance within which they work. You are the one who will draw the necessary lessons from this.

In all tissues, there are specific recipient molecule groups that respond to a particular hormone. Each hormone is programmed to stimulate its target cells, which contain those special recipient molecule groups that start doing their specific work. The principal functions of my endocrine system are: to enable growing; to regulate the necessary reproduction process in an ordered manner; and to carry out the physiological processes in the body in a relatively stable medium. I guess your amazement, admiration, love, and apprehension will increase when you hear about my secretion glands. Now, here comes the hypophysis.

My name is Hypophysis (the Pituary Gland)!

I am appointed as the commander of all your glands. Therefore, I am situated in a very firm place at the lower brain. I am an organ that is as small as a bean and that weighs only a few grams, but I have got so many talents. I have two parts. The first is my frontal lobe (adenohypophysis) which secretes most of the hormones. Our Creator has given key roles to the hormones of my frontal lobe to direct secretion activities of other endocrine glands. For example, thyrotropin hormone is arranged in such a way that it affects the thyroid gland and stimulates it for secretion. The unbalance in my thyrotrophic secretion affects the function of Thyroid gland negatively. If it is secreted too much, hyperthyroid; if it is secreted too little, hypothyroid illnesses emerge. In both cases, some problems occur during metabolism. Adrenocorticotropic hormone is created to arrange the activities at the adrenal cortex. Follicular stimulating hormone has two very important roles. The first one is regulating the secretion of estrogen, which is one of the female hormones. The second one is maintaining the physiological activities in the maturation of sperm cells in males, as well as the egg cells in females, for the continuation of human generation. The Luteinizing hormone together with the Estrogen stimulates the secretion of other sexual hormones (progesterone and testosterone).

When you were born, you were 20 inches tall. Now you are almost 6 ft tall. Both your height and your hands and feet grew. Meanwhile, your head and body got bigger proportionally. Another important secretion of yours that controls your growth appropriate to your age is somatotropin hormone. If, for some reason, my working balance got deteriorated, and this hormone secreted less, you would be like a dwarf, or some of your parts would be unbalanced with your body and abnormally short. If this hormone were secreted too much, then you would get into gigantism due to abnormally large growth. Together with gigantism illness, several problems occur; i.e., heart and blood pressure problems, muscle weaknesses, and problems regarding immunity and general metabolism.

Other hormones that are secreted from my frontal lobe are prolactin hormones, which help milk glands develop in expecting mothers, and melanocyte stimulating hormone, which stimulates the pigment cells that give color to your skin. However, these two hormones have no relation with the other hormonal glands.

The lipoprotein molecule of my melanocyte stimulating hormone helps the morphine substances, known as encephalin and endorphin, to be synthesized. You can call these two substances naturally inherent drugs. These secreted substances help you to bear several physical pains. The secretion of my hormones has direct relation with your nervous system and psychological well-being.

Although formed in the hypothalamus part of the brain, one of the hormones that is secreted after being stored in my back lobe (Neurohipofiza) is oxytocin, and the other one an antidiuretic hormone called vasopressin. Oxytocin makes the smooth muscles work. In particular, it stimulates the contractions at uterus during labor and delivery, and it also stimulates the secretions of milk canals by making them contract. Vasopressin enables blood vessels to shrink, causes the blood pressure to increase, and also reduces the production of urine by increasing the transition of water to blood through the kidneys. Hence, it prevents dehydration in hot and dry weather. In the deficiency of the secretion of this hormone, an illness called diabetes insipidus will occur and water metabolism will be deteriorated. I have more amazing features to tell, but I should not be selfish. I think it is time for Thyroid to speak.

My name is Thyroid!

I am placed in your neck, right at the two sides of the trachea (air tube) and below the larynx (voice box). I consist of two pieces that are attached to each other with a thin tissue. Inside me, there are many little saccules called Follicules which are densely surrounded by a capillary network. Following their innate program my cells produce three important hormones in the cavities of those saccules. The two of them are thyroxine and triiodothyronine, which contain iodine atoms and the other one is calcitonin. My hormones have highly important impact in your body. Our Lord God has appointed me, the hormones secreted by a very small piece of flesh, with regulating the oxygen use of all of your cells, and thus the speed of your metabolism which all affect your body’s overall performance. In addition to that, I also adjust your cholesterol level by lowering it in your blood. My iodine-containing hormones are vital for children’s growth. In the case of their deficiency, conditions like growth failure, dwarfism and mental disorders appear. If there is not enough iodine in the earth or water, it becomes more difficult for me to produce hormone and I start to work harder, which causes me to enlarge. This is a disease called goiter. When I secrete excessive hormone, your eyeballs become bulged, a disease called exophtalmic goiter or Basedow syndrome.

My iodine hormones and the stimulating Thyrotropin hormones secreted by the Hypophysis work together; they watch and control each other. If I get lazy and slow down secretion, the Hypophysis immediately warns me. If I secrete too much, this time Hypophysis stops warning me and waits for me to “calm down.”

Do you see what a wonderful system I am? Not only between us, but also all other systems have the same feedback organization between themselves and the Hypophysis. The Hypophysis is an organ as big as a chick pea, and we are only a small piece of flesh. Peter, look at the great jobs we are doing! Can coincidence play any role in this, do you think?

Lastly, I will tell a little about Calcitonin, a hormone which works to adjust the calcium level in the blood serum. That is not an easy job at all. This hormone is vital in the healthy growth of your bones; otherwise your bones will empty, get weak and they might even break for no reason at all.

My name is Parathyroid!

As my name suggests (“para” is a prefix signifying alongside of, beside), I am located just behind the Thyroid, consisting of four small parts. I have so many important functions beyond what is commonly known. My foremost duty is to delicately adjust the amount of calcium between your skeletal bones and your blood. Moreover, I am also assigned with controlling the phosphate and magnesium metabolism. In order to do that, I produce a hormone called parathormone. Of course, I have no idea about the chemical composition of this hormone; but I am just doing my job by producing it and working as I am programmed. When the level of phosphate in the urine and the level of calcium in the blood are measured, you can understand whether I am working well or not. The decrease of calcium in your blood leads to the stimulation of your nerves, thereby causing muscle spasms or titanic contractions that occur along with dotage. The healthy function of your heart and muscles highly depends on this calcium. Who knows, Peter, what other functions of me you human beings will discover in the future!

My name is Adrenal gland!

I consist of two little parts located on top of the kidneys, one on each side. Do not underestimate me by just looking at my size! You will be amazed to learn what crucial functions I perform. Each of my parts has an inner (medulla) and an outer (cortex) section. Those two sections differ quite markedly from each other in their structure, functions and in the origin of the embryonic layer where they form. But despite those differences, our God Almighty has put them one within the other. The two important hormones that my inner section secretes are Adrenaline and Noradrenaline. My adrenaline secretion speeds up the conversion of glycogen (in your liver) into glucose, and thus the sugar level increases in your blood depending upon your energy needs. This increases the power and the speed of your heart contractions and constricts the diameter of the blood vessels, thereby causing the blood pressure to increase. I assist in dilation of the narrow bronchioles of your lungs so that you can get more oxygen. When you become nervous, quarrel with somebody, face a danger or experience any stressful moment, I cause all those activities to happen by secreting more hormones expeditiously. That is how I help in protecting your body. All in all, 80% of my secretion is adrenalin, whereas the 20% is noradrenalin. Noradrenaline has less impact on your heart and metabolism.

My cortex (outer section), where steroid types of hormones are produced, secretes aldesterone, cortisol, and some androgens (a male hormone). Aldestrone regulates the water and salt levels (especially sodium and potassium metabolism) of your body. Cortisol meets your glucose needs if you are starving by breaking down the proteins into amino acids; it is also responsible for preventing the infections and allergies. Although the testicles (male reproductive glands) are the main organs that produce the male hormones, I also supply them. My androgens help in the development of male characteristics such as voice changes, beard and moustache growth and hair growth. When women get older, the androgens that I secrete causes the voice to deepen and hair to grow on their bodies.

My name is Epiphysis (Pineal gland)!

I am a small gland that is situated at the roof of the dieencephalon (“interbrain”). As it is most commonly known, I secrete the melatonin hormone. This hormone helps the melanin (the black or brownish pigment that gives your skin its color) to aggregate or dissolve in the special skin cells called melanophore. Thus, it senses the intensity of the light that changes according to the seasons and day length, and adjusts your skin color by lightening or darkening it. Moreover, I work as your biological clock, regulating your sleep-wake cycle. It is also thought that I arrange the different working periods of your organs.

Our Name is Testicles!

We are male reproductive glands. Our God Almighty has created us for the continuation of human generation. Each of us is oval-shaped and located in a pouch that weighs 25 grams and facing to each other. Each of us is protected by a case of skin and muscle. This case extends into our internal part where it is divided into 200-400 lobules. Each lobule consists of fine coiled tubes. The reproductive cells and the sperm cells which contain a group of your genetic program are produced in those tubes.

When you reach puberty, upon responding to the stimuli that comes from the hypophysis, we start to produce sperm, as well as Testosterone, a type of androgen (male) hormone. Testosterone is necessary for your male appearance; it helps in the developing the characteristics that distinguish you from females in terms of appearance.

A special cell division called meiosis is needed for sperm production. Along the layer that make up the walls of the coiled tubes lie the cells that are called Spermatogonium. Each of these contain 46 chromosomes (23 maternal and 23 paternal). As a result of serial divisions and crossover of those cells, new cells are created with new characteristics. From one Spermatogonium, four sperms are formed and each of them has 23 chromosomes.

Each sperm differs from one another, and each of them contains a mosaic composed of the different characteristics you possess. Among the millions of sperms that are produced, not one of them is identical to another. The reason is the interchange of sections between pairing homologous chromosomes (that you take from both your mother and your father) during the process of meiosis. For example, in one sperm, your nose traits that come from your father might come together with the ear traits that come from your mother. In another sperm, for example, the fingers traits that are inherited from your father might come together with the eye traits that are inherited from your mother. When so many different traits can be mixed in so many different ways, you can imagine the great potential of variety for human beings.

We are private organs that some people see as “obscene” to talk about and which generates “dirty” sperm-containing fluid. However, as you have seen, we are given to you as a gift from God, wrapped with so many beautiful meanings, one of which is the important task of continuing human generations.

My name is Ovarium!

Dear Peter! My duty is particularly relevant to women; I am the female reproductive organ. Therefore, I should begin by saying something like ‘I am Jenny’s…’ this time. Just as the Testicles are the male reproductive system, the ovaries are the woman’s organ. It cooperates with the male productive system in order for human generation to continue. We, the two ovaries, are located in the lateral wall of Jenny’s pelvis, one on the left and one on the right, and we measure approximately 1x 0.60 x 0.60 inches and weigh between 4 and 8 grams. Even before Jenny was born, we contained an amazing 150–500 thousand immature egg cells inside us.

During childhood, the follicles which contain the eggs diminish continuously, and by the time a young girl reaches puberty, only 35,000 of these follicles remain in each of her ovaries. Throughout the woman’s reproduction lifespan, usually between the ages of 13–50 years, a mere 300–500 of these follicles actually transform into mature eggs. You will certainly realize that you have reached puberty when I begin to produce the estrogen and progesterone hormones. As the estrogen I produce stimulates the development of the female’s sexual characteristics, progesterone prepares the wall of the uterus, making it more receptive to the implantation of a fertilized egg. If the egg I produce is not fertilized by sperm, every month (in approx every 28 days), it will degenerate and then be discharged from the body together with the lining of the uterus during menstruation. Then another one of my eggs matures, and patiently begins to await sperm.

The principle event of chromosomal change in my eggs and their diminishment in numbers is the same in the development of sperms. The only difference being that every spermatogonium produces four sperms, whereas only one mature follicle is produced from the mother cell (Oogonium) that produces my eggs. The remaining three are degenerated. You would have thousands of eggs awaiting fertilization if this was not the case. However, due to the fact that your bodies are not capable of harboring and protecting so many eggs, our Creator provided you with the mechanism of reducing the number of these eggs, and therefore relieved you of any difficulties.

I must take this opportunity mention another two of my organs, one of which is the pancreas, who described itself previously (see The Fountain # 67). As you may recall, the pancreas is a compound gland. The pancreas previously described how it produces digestive enzymes, and also how it produces insulin and glucagon to deal with the metabolism of carbohydrates. As this is a very complex organ, we allocated the pancreas the opportunity to describe itself and explain its functions in a previous edition of the magazine. For more information you may refer to the issue listed above.

An organ which is a part of your immune system, and also considered part of the endocrine system, but an organ you are probably unfamiliar with, is the Thymus gland. If the immune and lymph systems feel the need to describe themselves to you in the future, the Thymus gland will inform you that it resides at the same level as your heart, behind your breastbone (sternum). Then it will go on to define its specific duties. But for the moment, the only thing I am going to inform you of is the most important duty of the Thymus gland.

The Thymus gland produces soldiers called T lymphocytes (T cells) and special antibodies which fight the invasion of diseases, illnesses, and also attack cancer cells and any foreign antigens. The Thymus gland is recognized as a part of the endocrine system because it produces hormones and antibodies. The special lymphocytes and antibodies that are produced in such a complex process by other organs of the immune system are transformed into T cells as they pass the Thymus gland. Then, gaining new characteristics, they secrete specific hormones which in turn stimulate the development and differentiation of T lymphocytes.

Whatever the system may be, the Thymus gland, to the contrary of other organs, is at its largest and most active during the embryonic and neonatal periods. During adolescence, the Thymus gland begins to shrivel and shrink, and continue to shrink gradually into old age. The reason why the Thymus gland is large during the early stages of life is because it must constantly generate new antibodies to enable the body to fight against new germs and diseases, which the body encounters every day.

I may have extended the topic slightly this time because every organ of my endocrine system described themselves individually, and then we got onto the subject of Jenny’s special case, as wel as the different aspects of Peter’s case. All the organs I mentioned today are small, but as you may have noticed, these small organs behold great mystery and wisdom. In addition to this, all of these organs’ individual duties are connected, in particular the Pituitary gland (Hypophysis), and have been arranged and regulated in such a way that they control one another. Can such a magnificent hormone system and bodily activity working in such harmony be explained as a mere coincidence?

Irfan Yilmaz is a professor of biology at Dokuz Eylul University, Izmir, Turkey.

Conventional water and wind turbines cannot function properly in a whirling current; the working of turbines depends on the existence of a steady and regular flow. In order to be able to obtain energy from vortices, turbines would need to mimic the movements of fish, adjusting their position to the differing angles of flow. A mechanical device to be developed in this respect should perceive the angle of the current flow instantly and adjust itself accordingly.

Normally, wind turbines are set up in high and open places. However, in cities the eddies that are formed by winds moving around buildings and roofs prevent conventional turbines from working efficiently. In order to overcome this challenge, scientists are aiming to develop turbines that benefit from the dynamic principles apparent in the movement of fish, though without imitating the fish exactly. They hope that in this way it will be possible to produce energy from turbulent currents as well. The projects being devised aim to develop different types of turbines to work in air and water. The energy production of these turbines will naturally be relatively low in comparison to common wind turbines operating in strong winds. However, these new types will make it possible to produce energy from winds moving at less than 32 feet per hour, when conventional turbines do not function. So, the total annual energy they are expected to produce will be no less than the regular wind turbines. If scientists can successfully model the admirable engineering applied in the bodies of fish, they will be able to boost the efficiency of these devices dramatically.

Notes

1. For further information see Liao J. C. et al., “Fish exploiting vortices decrease muscle activity,” Science 302, 1566–1569, 2003.
2. Dabiri, J. O., “Renewable fluid dynamic energy derived from aquatic animal location,” Bioinspiration and Biomimetics 2, L1-L3, 2007.

There is no similarity between the systems through which insects produce or receive sounds. Furthermore, even the frequencies of the sounds they produce or hear may not be the same. The wisdom behind this might be that the receptors of some insects are devised in a way that will enable them to detect sounds produced by their enemies. Moths can be given as a typical example of this. They can detect sounds between 1,000-140,000 Hz. Their sensitivity is best between frequencies of 20,000-40,000 Hz, but interestingly, most moths do not have any organs to produce sounds at these frequencies. In other words, moths do not seem to use their tympanal organs in order to communicate with one another. Discovering the real function of the tympanal organ of the moths has taken researchers quite a long time.

The mysterious relation

Every being in nature is created to assume a role in the ecological balance and no creature has been equipped with a useless organ. Researchers have discovered that the tympanal organ plays an important role in defense. Moths spend the day resting in corners and only become active after sunset. Researchers have come to the conclusion that they are not searching for food, since the nutrition they need is stored in their bodies during the larva stage. Thanks to this blessing, moths do not spend their short life span in search of food. The aim of their night flights is reproduction.

The essential duty of moths is to find the plants where they will lay their eggs and on which their larvae will feed. As slow moving animals, it is almost impossible for the moth larvae to go and find their own food. As all creatures are provided in accordance with their need, these helpless larvae are born on their food. Another amazing fact about their nutrition is that the moth larvae eat their own protein-rich eggshells before eating leaves. Research has shown that those larvae which eat their eggshells are more resistant to environmental conditions.

As the moths try to continue their species by laying their eggs in the darkness, some other creatures try to continue their own existence by feeding on the moths. Bats eat insects and are also active at night. As is well known, bats fly comfortably in the dark thanks to the radar system they have been equipped with. This innate system is perfectly devised to enable bats to pinpoint a tiny insect flying through the darkness, and moths are a prey that is easily spotted by bats. The astonishing fact is that the moths’ sensitivity to the sound waves is perfect for picking up the sounds emitted by bats. The moths are able not only to detect the bats, but also to judge their distance from the frequency of the waves. If the distance is greater than 30 meters, the moth leaves the area immediately. If the bat is closer however, the moth takes a zigzag course or tries to avoid danger by plunging down and staying still.

The balance here is so perfect that while bats are skilled enough hunters to obtain provision, the moths are good defenders and are able to continue their existence. Both species fulfill their roles in balance with creation. Some bats are able to catch some moths, but there is no excess on either side. Nothing is left to blind chance in nature; not only did the Creator equip the bat with a perfect radar system, He did not leave the moth helpless but granted them perfect receptors to rescue themselves from bats. If it were not for the Power that established the mysterious balances in the universe, how would a bat find its way through the darkness and how would moths be protected from extinction?

Every different type of moth which forms another ring in the chain of food in nature lays its eggs on different plants. If moths did not feed on certain fast-growing plants and if their growth is not kept under control, these plants would invade the space of other plants and wipe them out. The moths and other creatures that feed on plants ensure that no one plant is allowed to upset the balance of the chain of nutrition. Similarly, the perfect balance established between bats and moths prove that nothing in this universe is left on its own. When confronted by the perfect order in nature, one cannot help but think about the verse:

You do not see any fault or incongruity in the creation of the All-Merciful. Look yet again: can you see any rifts?

Then look again and yet again, (and however often you do so, with whatever instruments to aid your looking) your sight will fall back to you dazzled (by the splendor of God’s creation), and awed and weakened (being unable to discern any flaw to support any excuse for claiming that there could be any sharing in the dominion of the universe). (Mulk 67:3)

It is worth contemplating that humans are in need of microorganisms to survive and that living things as insignificant (!) as bacteria are necessary to synthesize B12 vitamin. Why our so-called bacteria ancestors (!) from which we evolved – as some claim – lost this ability to synthesize B12 vitamin which was, and still is, vital for survival, is a challenging question for those scientists who support the theory of evolution.

The journey of B₁₂ in our body

Cobalamin, which is taken in with food, is absorbed by the final section (ileum) of the small intestine and transported into the blood by receptors on the cell membrane. For B12 to be absorbed into the blood, it is necessary to have an “intrinsic factor” bound to this vitamin. The intrinsic factor is a glycoprotein produced in parietal cells that secrete gastric acid. After the absorption, the vitamin binds to transcobalamin, a carrier protein found in the blood, and it is then being bound with transcobalamin II so that it can penetrate the cells. B12 can be stored in the liver to meet the needs of our body for a long time. A deficiency in cobalamin due to a poor diet (e.g., vegetarians) or a failure to produce the intrinsic factor in the stomach may result in pernicious anemia, which is fatal. Cobalamin deficiency negatively affects DNA synthesis, which is necessary for production of new cells, particularly in the division of the stem cells that are assigned to construct new red blood cells. This is followed by the circulation of cells that will generate underdeveloped red blood cells; these cells will not be able to function properly and will have larger diameters.

The training of parietal cells

If the stomach is removed or cannot produce the intrinsic factor, it is impossible for B12 to be absorbed. It is worth reflecting on the wisdom of why an organ like the stomach, the main duty of which is to partially digest food and convey it to the intestines, synthesizes intrinsic factor. How can the stomach know that our body is in need of this protein? How did it become able to synthesize this very special composition of glucose and protein which is so necessary to absorb intrinsic factor through the gastrointestinal tract? Why doesn’t our body produce the vitamin in the first place, instead of binding it to such a complex molecule? And how do the parietal cells know what is necessary to bind this vitamin, the use of which they cannot understand, although they have never been trained in bio-chemistry, physiology, or pharmacology? In which laboratory did these cells synthesize and test this compound?

The intrinsic factor

In order to decompose proteins into amino acids, the stomach secretes hydrochloric acid and an enzyme called pepsinogen. Parietal cells that secrete acid also produce a protein (intrinsic factor) which is not damaged by the acid or the pepsinogen enzyme. How were these cells able to develop a synthesis in which proteins do not decompose, which can protect them from the acid in the stomach, and bind themselves to a vitamin like B12, which is absorbed only in very small quantities?

The hydrochloric acid secreted in the stomach is like bleach and it irritates anywhere that it goes other than the stomach. Should even the slightest quantity of this acid pass into esophagus (reflux, diaphragm boiling) it can cause severe burning. It is amazing that B12 is found and bound in a cauldron like the stomach, but is not damaged by the acid produced when the stomach is filled with food and drink.

The intrinsic factor bound with the vitamin goes on its journey and it reaches the absorption region in the last section of the small intestines. During absorption, the gates on the cell membrane of the intestines open up only to allow the B12 intrinsic factor compound. Maintained in the intestinal cell for a while, the B12 vitamin binds to the transporter transcobalamin and is conveyed to the cells through the blood. After reaching a cell, the vitamin, needed by the entire body, is bound to another transporter: transcobalamin II.

Some components, although they appear to be very simple, must be supplied from outside our bodies if we are to survive. B12 vitamin is one such component, and it certainly deserves to be studied well.

The second leading cause of death in the United States, after heart diseases, is cancer, claiming around half a million lives every year.(1) People today are concerned more than ever about cancer and its terrible consequences. However, in the light of recent scientific findings, a very different picture can be seen: In an environment with increasing carcinogens, it is actually surprising to find most populations are cancer-free. This is because our bodies are equipped with systems to prevent cancer formation.

Cancer research over the last two decades has shown that cancer is a disease of the genome.(2) Changes in the DNA, called mutations, disrupt the regular cellular networks that control a state of delicate balance. People are continuously exposed to varying amounts of chemicals that have been shown to cause mutations in the genome which may lead to cancer formation. Exposure to harmful chemicals can occur due to being in an environment where these agents are present in the food, air or water, and also due to our own metabolism which may produce these chemicals. It has been estimated that exposure to environmental chemical carcinogens may contribute significantly to the formation of the majority of human cancers.(3)

Even though some of the mutations caused by these agents hit cancer-critical genes, cancer does not immediately develop. Furthermore, cancer is mostly seen in old age, when many mutations have accumulated in the genome. The reason why we are protected from developing cancer, even though our DNA is under numerous types of attacks everyday, is that our cells are equipped with several lines of defense against cancer formation. These built-in defenses include DNA damage repair systems, external and internal controls of cell division rate, and the programmed death of cells. All of these defenses have been given to our cells in order to protect us from getting cancer. If we were not to have these defenses, cancer would be a daily occurrence for every one.

It is possible to say that a cell’s first defense against cancer is similar to the regular maintenance of a car. One has to replace the brake pads, change the oil, etc., so that the aging of the parts will not cause failure that may lead to an accident. Similarly, chemical carcinogens from environmental pollution, ultraviolet rays from the sun, radiation from various sources, etc. all cause multiple types of damage in the DNA molecule. Therefore, our cells and genome need maintenance as well. This function is carried out by groups of proteins called DNA repair complexes. DNA repair mechanisms have been designed to correct the DNA damage before it can lead to inheritable mutations.(4)

If the DNA damage repair systems are intact, most of the damages to the genome are dealt with before they can cause problems. We observe the extent of attacks that can damage the DNA on our genome in many types of cancer where the DNA repair mechanisms are known to have been inactivated. In these cancer cells, mutations accumulate at a very fast rate, leading to more aberrant behavior. Also, individuals with defective DNA repair systems are more susceptible to developing various types of cancer.(4,5) Therefore, the first line of defense given to our cells against cancer is the ability to check and correct the integrity of our genome.

Every cell type in our body has been designed to proliferate at a certain rate that is suitable for the function of those cells. For example, neurons or muscle cells almost never divide after reaching adulthood, whereas the epithelial cells lining the interior of the intestines or under the skin divide at a fast rate continuously throughout our lives. The rate of division of a cell is mainly controlled by extra-cellular cues, i.e. a normal cell doesn’t grow or divide unless it receives growth and proliferation signals from neighboring cells.

There is a safe rate at which a cell must divide – just as a car needs to be driven at a safe speed. The requirement of cells for external stimuli in order to grow and divide is like the car’s need for someone to step on the gas pedal in order to accelerate. Normal cells cannot grow without control as neighboring cells produce growth signals when they are necessary and stop producing them in a regulated manner. A good example of the control of cell proliferation rate is seen in the wound healing process. When there is a cut in the skin, the cells adjacent to the wound are stimulated to divide rapidly by signals given from the injured cells; they divide and close the wound as soon as possible. However, when there are no wounds, there is no signal to divide and the skin cells only divide at a very slow rate, just enough to replace dying cells; this is a much slower process than wound healing. Cancer cells, on the other hand, are known to produce their own growth signals and proliferate abnormally fast and in an uncontrolled manner.(6) Therefore, the environmental control of cell division is an important barrier against cancer formation.

Cancer cells cannot divide uncontrollably unless they are independent of the external stimuli to divide. However, cancer cells can produce their own growth and proliferation signals, so they are free from external constraints. But even then, all is not yet lost. This situation of uncontrolled and rapid cellular proliferation is like a car in which the accelerator has become jammed– the car accelerates continuously and an accident is impending. In this situation the way to prevent too much speed is to step on the brake of the car. Similarly, in a cell, there are a set of genes called tumor-suppressor genes, which are responsible for stopping cell division upon excessive growth stimuli.(7) These genes act like brakes in cell division and prevent further progression into a malignant state. In many cancers,(8) it has been shown that these genes have been inactivated. If the brakes of the car are functional, you can safely bring your car to a stop and fix the problem that caused the accelerator to jam. Similarly, if a cell starts to divide too rapidly, it can stop dividing and repair the damage that caused the uncontrolled growth. Therefore, tumor suppressor genes represent a third line of defense.

If all the previous safety valves fail, there is one more defense to cancer. A situation in which a cell with harmful mutations promotes its own proliferation and cannot abort the division process is similar to one where the accelerator of the car is jammed and the brakes don’t work. In this case, in order to prevent greater damage, one can choose to hit a wall or a tree to stop the car– this will total the car, but will prevent further damage to others. Similarly, if a cell begins to grow uncontrollably and can’t slow down its rate of division, a process called apoptosis, or programmed cell death is initiated. In apoptosis, the cellular DNA and cellular compartments, like lysozomes, Endoplasmic Reticulum, and Golgi are degraded, and the cell shrinks in size. In the end, the cell dies and is absorbed by neighboring normal tissue. Therefore, the programmed death of an aberrantly behaving cell is another way that the body is protected from cancer. As expected, in cancer cells defects in this last line of defense are observed as well.(9)

These four mechanisms, i.e. DNA repair, external/ internal cell division suppression, and programmed cell death, are only the ones that we are aware of at this time. In addition to these, there are multiple levels of other redundant safety checks. All these safety features work without our knowledge or will. Findings from cancer research show that the design of cells was carried out so intelligently that even the carcinogenic environment which we produce today was accounted for within the genes of the very first human being.

Notes

1. Cancer Statistics 2006. 2006, American Cancer Society.

2. Vogelstein, B. and K.W. Kinzler, “The multistep nature of cancer.” Trends Genet, 1993. 9(4): p. 138-41.

3. Wogan, G.N., et al., “Environmental and chemical carcinogenesis.” Semin Cancer Biol, 2004. 14(6): p. 473-86.

4. Dixon, K. and E. Kopras, “Genetic alterations and DNA repair in human carcinogenesis.” Semin Cancer Biol, 2004. 14(6): p. 441-8.

5. Jiricny, J., “The multifaceted mismatch-repair system.” Nat Rev Mol Cell Biol, 2006. 7(5): p. 335-46.

6. Brattain, M.G., et al., “Growth factor balance and tumor progression.” Curr Opin Oncol, 1994. 6(1): p. 77-81.

7. Hanahan, D. and R.A. Weinberg, “The hallmarks of cancer.” Cell, 2000. 100(1): p. 57-70.

8. Coleman, W.B. and G.J. Tsongalis, “Molecular mechanisms of human carcinogenesis.” Exs, 2006(96): p. 321-49.

9. Dlamini, Z., Z. Mbita, and T. Ledwaba, “Can targeting apoptosis resolve the cancer saga?” Future Oncol, 2005. 1(3): p. 339-49.

Indeed, We have offered in this Qur’an every evidence and lesson by way of parables and examples for people so that they may think and take heed (Zumar 39:27)

So God propounds parables for human beings, that they may reflect on them and infer the necessary lessons. (Ibrahim 14:25)

Parables are short stories that may or may not represent an actual event that are designed to convey a truth or a moral lesson (Flexner 92). If we accept this definition of what a parable is then there are approximately 40 parables in the Qur’an. Some scholars define parables to include other narratives, such as stories of past prophets and their people, and thus find more parables in the Qur’an.

Parables help people understand abstract concepts by alluding to shared experiences and by allowing the readers to emphasize with participants or to feel as if they are direct observers in these experiences. By using carefully selected or crafted parables, remote and abstract truths can be made nearer and more comprehensible. Topics with a variety of sub-topics can be organized into a harmonious unity (Risale-i Nur).

Human beings are visual creatures. About 80% of the input to our brain comes through our eyes. Hence, important parts of the brain are dedicated to the processing, storage, and recall of visual information. Parables help activate our imagination, the eye of the mind, and enable us to comprehend a general truth or principle in a particular circumstance (Ozsoy). Parables help the power of imagination and inner senses to assist the mind/intellect in comprehending or internalizing the message. The parables of the Qur’an are another way in which the Qur’an uses human language to explain things that are beyond human capacity; this has been recognized even by non-Muslim experts, such as one of translators of the Qur’an, N. J. Dawood, who calls the Qur’an a “literary masterpiece.”

Those Who Associate Partners with God

The most important message of the Qur’an is the unity of God. As God is one and has no partners, there can be no partners associated with Him nor can any worship, including prayers, be directed toward others to seek help and protection. The very first chapter of the Qur’an emphasizes this fact in the form of a prayer; believers are instructed to say: You alone do We worship and from You alone do we seek help (Fatiha 1:5). In many verses, God challenges those who worship other objects or beings to bring proof that these are worthy of worship, and asks what those objects have produced that can be understood as a sign of their status. The following parable is an example:

O humanity! A parable is set forth, so pay heed. Those whom, apart from God, you call upon as gods will never be able to create even a fly, even if all of them were come together to do that. And if a fly snatches away anything from them, they cannot recover it from the fly. Powerless indeed is the seeker, and (powerless) the sought! They have no true judgment of God as His being God requires. God is certainly All-Strong, All-Glorious with irresistible might. (22:73-24)

Another example emphasizes the same message:

To Him alone is made the call to truth and the true prayer. Those (powers and persons) to whom they pray and call others, apart from Him, cannot answer them in any way-meaning nothing more than the action of he who stretches out his open hands in dire need toward the water so that it may reach his mouth; yet the water never reaches him. The prayer of the unbelievers is destined to go to waste. (13:14)¹

Those Who Forget God and Think of Themselves as Self-sufficient

In the Qur’an the reason why humanity was created is to worship God. According to this teaching, humans have been created to recognize their Lord, to strive to learn His attributes, to learn what code of conduct is pleasing to Him and to worship him in the way He desires. An important aspect of this worship is thanksgiving. Various verses of the Qur’an emphasize the importance of recognizing God’s bounties and being thankful for them. In particular, the chapter Al-Rahman (The All-Merciful) the following verse is repeated numerous times: Then, (O humankind and jinn,) which of the favors of your Lord will you deny? (Rahman 55:13) In the following parable, the Qur’an illustrates the events that happen to two people, one of whom is a grateful believer, and the other who abstains from recognizing the Giver of all bounties:

“…Tell them as an example the story of two men: for one of them We made two vineyards and surrounded both with date-palms, and placed a field of grain in-between. Both of the vineyards (including the date-palms and grain) yielded its produce, without failing in the least therein. We had also caused a stream to gush forth in their midst. So both of the vineyards including the date-palms and grain) yielded its produce, without failing in the least therein. We had also caused a stream to gush forth in their midst. The man had fruit in abundance, and one day he said to his friend, bandying words with him: “I am more than you in wealth, and more esteemed and stronger in respect of men.” He went into his vineyard in self-wronging (puffed up by worldly successes which had led him to conceit and unbelief). He said: “I deem not that all this will ever perish. Nor do I deem that the Last Hour will ever come. Even if (it should come, and) I am brought back to my Lord, I shall surely find (there by virtue of my own abilities and as my deserts) something even better than this as a resort.” His friend said to him, in the course of the argument with him: “Do you blaspheme (in such ingratitude as this) against He Who has created you out of dust, then out of a sperm-drop, then fashioned you into a complete man? But I believe for my part that He is God, my Lord, and none can I associate with my Lord as partner (in His Lordship-His bringing up, providing, sustaining and protecting). Alas, if you had but said, on entering your vineyard, “Whatever God wills will surely come to pass. How perfectly He creates and how mercifully He provides! There is no strength save with God.” Though you see me as less than you in wealth and children, (this is no problem at all, for it is God Who does what He will, and He is All-Compassionate toward His servants). Yet it may well be that my Lord will give me something better than your vineyard, just as He may send a calamity upon your vineyard from Heaven, so that it becomes a barren waste. Or its water sinks deep into the ground, so that you will never be able search for and find it again.” So eventually all his produce was encompassed by ruin, and there he was, wringing his hands with grief over all that he had spent on it, when now it was all ruined on its trellises, and he could but say, “Oh, would that I had never associated anyone with my Lord as partner (in His Lordship).” And he had, apart from God, none, no troop of men to help him, nor could he be of any help to himself. For thus it is: all protective power and authority essentially belongs to God alone, the True One. He is the best to reward, and the best to determine the end of things. (Kahf 18:32-44)

The Transience of the Bounties of the World

The Qur’an presents three views of this world: (1) As a place to plant good deeds as seeds that will blossom in the Hereafter, (2) as a wonderful display of God’s names, and (3) as a place of enjoyment. While the world carries enormous significance with respect to the first two aspects, with the third it carries little weight in God’s sight. This is illustrated by the following parable:

The present, worldly life (which you pursue) is like this: We send down water from (the direction of) the sky, and with it the plants of the Earth grow rich and dense, mingling so that human beings and animals can eat of them, until, when the Earth has taken on her ornaments and has been embellished, and its inhabitants believe that they can do with it whatever they want, Our command comes upon it by night or day unexpectedly, and We cause it to become like a field mown down, as if it had not flourished the previous day. Thus We display in detail the signposts of Our way and the relevant Revelations (included in the Qur’an) for a people who will reflect (on them and draw the necessary lesson). (Yunus 10:24)²

Sincere Charity versus the Pleasure of Acknowledgement

The Qur’an encourages spending in the way of God to help the poor and the needy without embarrassing or insulting recipients. Any feeling or display of pride in giving nullifies its meaning. These are made clear in the following parables: The example of those who spend their wealth in God”s way is like that of a grain that sprouts seven ears; in every ear there are a hundred grains. Thus God multiplies for whomever He wills. God is One Who embraces all (with His mercy), All-Knowing. (Baqara 2:261) O you who believe! Render not in vain your almsgiving by placing under obligation and taunting like he who spends his wealth to show off to people and to be praised by them, he who does not believe in God or the Last Day. The example of his spending is that of a rock on which there is soil; a heavy rain falls upon it, and leaves it barren. They derive no gain (pertaining to the Hereafter) from their almsgiving, nor do they succeed in preserving it if they can derive any. God guides not such people of the unbelievers (to attain their goals). (Baqara 2:264) The example of those who spend their wealth in pursuit of where God”s good pleasure lies and who strive to make belief firmly established in their hearts is that of a garden on a hilltop; a heavy rain falls upon it, and it yields its produce twofold; even if no heavy rain falls upon it, a light shower suffices. Whatever you do, God sees it well. (Baqara 2:265)

The Good Deeds of Disbelievers are in Vain

One aspect Islamic belief that is misunderstood is the relationship between faith and deeds. In Islam, faith is the essential ingredient for success in this world and in the Hereafter. Deeds are important and have a symbiotic relationship with faith. Deeds both reflect and affect our faith. Through sincere worship we can connect with God in a way that would be impossible through intellect on its own. Conversely, a person who constantly behaves in opposition to their belief may risk losing their belief. As important as deeds are, they cannot qualify anybody for eternal success. In other words, nobody can “earn” Paradise through good deeds alone. In particular, those who do not believe in God or life in the Hereafter will receive the reward for whatever good they do in this world. The following parable illustrates these concepts very clearly: This is a parable to be set forth for those who disbelieve in their Lord: all their work is as ashes which the wind blows hard on a stormy day. They have no control of anything that they have earned (from which to benefit). That indeed is straying very far and extreme failure. (Ibrahim 14:18)³

The Ability of Humans to Transcend their Environment

The Qur’an gives examples of women who transcend their environment (both in good and bad ways) to choose a course of action. In the first example, the wives of Noah and Lot are shown as examples of people who, despite being in an environment of enlightenment, chose falsehood over the truth. The other examples illustrate two women who transcended the conditions of their environment to accept truth and live piously. While these examples are not exactly the same as the previous parables, nevertheless the iconization of the women as prototypes follow the same literary and educational style: God propounds the wife of Noah and the wife of Lot as an example for those who disbelieve. They were married to two of Our righteous servants, yet betrayed them (by rejecting the Messages they brought from God and collaborating with the unbelievers). But they (their husbands) availed them in nothing against God and it was said to them: “Enter the Fire with all those who enter it!” And God propounds the wife of the Pharaoh as an example for those who believe. She prayed: “My Lord! Build for me a home in Paradise in nearness to You, and keep me away and save me from the Pharaoh and his deeds and save me from the people of wrongdoing.” And also Mary, the daughter of “Imran, who guarded her chastity and so We breathed into him out of Our Spirit, who confirmed the words of her Lord (manifested as His Revelations—commandments, promises and warnings—to His Messengers), and His Books, and she was one of those who are devoutly obedient to God.” (Tahrim 66:10-12)

The Infinite Knowledge of God

In the Qur’an some historical accounts and important lessons are repeated; there are a variety of purposes for why this is done. Since most people find it hard to frequently read the Qur’an in its entirety, the major messages are repeated throughout the Qur’an. Also, the fact that the Qur’an serves not only as a reminder, but as a book of prayer, a book of remembrance, and a book of invitation/prohibition (in addition to its other roles), the repetitions fulfill subtle functions. These repetitions are not verbatim in each case, but rather, depending on the context, they display a subtle variance that emphasizes a certain aspect of the message in addition to the others or reveal a meaning that might not be obvious in other contexts. The following parable for instance, responds, in part, to the pagan Arabs” attribution of the frequently repeated messages or historical accounts being caused by the scarcity of God”s knowledge. If all the trees on the Earth were pens, and all the sea were ink, with seven more seas yet added to it, the words of God (the acts of all His Names and Attributes manifested as His commandments, and the events and creatures He creates) would not be exhausted in the writing. (Luqman 31:27)

Parables on Other Topics

In addition to the examples given above, parables in the Qur’an discuss such topics that depict God as the light of the Heavens and the Earth (24:35), the persistence of the truth and the transience of the falsehood (31:17), the Messenger of God and his Companions (48:29), the abundance of good and scarcity of evil (14:24), the hypocrites (2:17, 59:15), the responsibility that comes with knowledge (62:5, 7:175), the peoples who have slandered their messengers (16:112), the weight of the message of the Qur’an (59:21), belief versus unbelief (6:122, 7:58, 11:24, 16:75, 28:61), the hardening of the hearts (2:74), the attitude of unbelievers against the message (2:171), the situation of those who have forgotten God and have refrained from spending in good causes (68:17-33), and the resurrection and life after death (2:259, 35:9).

Conclusion

The parables of the Qur’an exemplify the unique literary aspects of this miraculous book. The parables are there to help readers understand complex and abstract topics. They also facilitate the involvement of the human imagination and inner senses to internalize the messages within the stories. Such characteristics are among many that made those who opposed the Qur’an in the early days of Islam resort to violence; the Qur’an puts forward the challenge to the non-believers to produce something similar if they are intent on proving that the Qur’an was written by a human. They were unable to produce the like, so instead they used violence to try to suppress the Muslims at that time. If they had been successful, the Qur’an would have become irrelevant for society. The fact that they preferred opposition by sword to a verbal or written response illustrates the fact that they were unable to challenge the Qur’an on the grounds of language.

Notes

1. For other parables on this topic, see Qur’an 22.31, 29.41, 30.28, and 39.29.
2. Other parables on this topic include 18.45 and 57.20 of the Qur’an.
3. Other parables on this topic include 3.117 and 24.39.

References

• Flexner, S. B. et al., The Random House Dictionary, Random House, NY: 1992.
• Ozsoy, O., Guler, I., Konularina Gore Kur’an, Fecr Yayinevi, Ankara: 2003.
• Celik, M., Kur’an’in Ikna Hususiyeti, Caglayan, Izmir, 1996.
• Nursi, S., Risale-i Nur Kulliyati (The Risale-i Nur Collection), Sikke-i Tasdik-i Gaybi.
• Dawood, N. J., The Koran, Penguin Classics, Penguin Books: 2000.

Our Creator has solved every potential problem which living things might experience by creating one optimal solution among every alternative.These perfect solutions open new horizons for men, and they also act as guides in the development of science and technology. The book titled “Engineering in Nature” details many striking examples.1

In recent research, it has been discovered how the thread of a spider can contribute to fiber-optic technology. A crucial challenge in photonic technology is to produce the tiny optic fiber that is used as a conductor for a light beam in nano-scaled optic circuits. Yushan Yan, of the University of California in Riverside, has taken an important step forward in this technology by covering the thread from a spider web with a glass-like material and then removing the thread after the material has hardened. By utilizing this technique, it is possible to produce threads that are 1/50000th the diameter of human hair and that have a radius of 2 nanometers (1 nanometer being one billionth of a meter).

Not only will this discovery be applicable in photonic technology, it will also increase the resolution in optical microscopes, or, alternatively, these threads could be turned into nanoscale test tubes in a new breed of sensors that can suck up single molecules of a particular chemical.

A research group at the University of California cut a thread 1 centimeter long from the web of the giant spider of Madagascar, the Nepila Madagascariensis, and pasted the two ends of the thread to a card. Then they repeatedly dipped this thread into tetraethyl orthoslicate solution. After this, the thread that had undergone this process was dried and heated to a temperature of 420 Celsius. The string decreased by one fifth of its original radius and the process resulted in the production of tiny tubes with a radius of one micrometer.

There are plans to make use of the web of the Stegodyphus Pasifiu-a spider which uses a thread of a radius of 10 nanometers and which is found in the Middle East and Southern Asia. This will enable scientists to use thinner fibers. After heating, a thread with a radius of 2 nanometers is attained. Until this latest finding, it was only possible to produce fibers with an interior radius of 25 nanometers.

Fiber optic researchers do not hide their enthusiasm for this new simple and cheap technology. It is expected that it will be used in the field of supra-molecular chemistry; that is the study of very miniature environments. In these environments the reaction-speeds increase and completely different reactions occur. For such experiments carbon nano-tubes are being used at the present time. The tubes made from fibers obtained from spider webs will enable scientists to create more sensitive environments. It is also thought that it will be possible to create microscopes with a higher resolution by using tinier fiber optic catheters.

Such microscopes would be used to observe events that are shorter in duration than the wavelength of light, yet at the same time, these microscopes would not cause the sample to be harmed. Electron microscopes harm the sample since the features of the technology used necessitate this. Currently, these microscopes use a scope that has been made from very thin glass tubes. These fibers are relatively thick, measuring about 100 nanometers in radius. Yet, by means of this new technology, these new microscopes can be developed and biologists will have brand new opportunities to study events that have not been visible before. Surely, it is not possible to say that the immaculate biological structure and incredibly small thread employed by the spider can be explained by simply putting its creation down to chance or by stating that it is a product of nature.

These perfect examples that can be observed in nature will lead to fundamental changes in our understanding of the universe; they will enable great leaps in terms of making our life more comfortable and, most importantly, they will be helpful in realizing how the Divine Power and Art can be present together and be in harmony.

References 

• M. Sami Polatoz, Tabiatta Muhendislik [Engineering in Nature], Kaynak, Istanbul: 2003.
• Danny Penman, Spiders Weave a Web of Light, New Scientist,
• 22 March 2003, p. 20.

“Surely, those whom you invoke, apart from God, will never create a fly even if they combine together for the purpose. If the fly takes something from them, they cannot rescue it from him.”; (Qur’an 22:73)

Good day my dear friends! I know you are tired of me, I bother you so often, especially in hot weather; but would you mind listening to me a little? I don’t understand why you are so proud! Did God create just you, and someone else created me? Some people do claim that I and all the other creatures evolved just by chance, in a process they call evolution, but I wouldn’t pay attention to them if I were you. Our Lord, God, created you and me, and the whole universe. Then why do you see me as being so unimportant? Of course, my Lord made humans superior and gave them an honorable place in this world, but this is only for those humans who recognize God Almighty and who pray to Him. If someone does not recognize the Creator, then this person will fall lower than me; I know my Lord, and I do not change my behavior. I don’t do anything but what He taught me. True, I am not tested as you all are, but I am happy with my lot. I carry out my duties obediently.

Although I do many useful things, most of you (except for the zoologists among you) aren’t aware of what my uses are. Some people even say, “Why has this black bug been created? It is of no use.”

If you just look at my wings, you can see that they are like a perfect work of art. Think about it, what would be more difficult, producing a large watch or a small and sophisticated one? Obviously producing a small watch is much more complicated. But one must remember that nothing is easy or difficult for God, He just says “Be” and He can create anything. By saying, “Be” He can create a microorganism or an elephant in an instant.

Just as you have organs that carry out the biological functions in your body that are necessary for your survival, I also have organs and systems in my body which carry out similar functions. The only difference between yours and mine is their structure and working principle. For instance, we both have hearts. Your heart pumps the blood to the body via the veins, and my heart pumps the blood to the spaces between my organs. You use your lungs for breathing while I have capillary tubes called trachea which transfer air directly to my tissues. The organs in my head are composed of many small particles. Each one of my eyes is created from hundreds of small hexagonal structures called ommatidia. Each has its own lens, a pigment cell that isolates it from the others, and a crystal cone. A special protein called chitin covers my body. Each one of my hairs acts as a special receiver, allowing me to detect all vibrations. Chitin is made up of a protein, which is durable and not permeable to water.

My mouth is shaped like a tube, while my tongue is like a sponge, helping me to taste my food. My feet, made up of chitin, are very thin and formed of many parts with a hook at the tip, making it easy for me to climb vertical surfaces.

There are hollow tubes in my wings, making them very light and strong. The hammer-like organs (halter organs) under my wings help me to balance while flying. There are some know-it-alls out there who claim that these organs were secondary wings that lost their function during evolution, but they seem to forget that there are many insects that have secondary wings. If this is so, why did I need to “lose” mine? It is hard to understand why these people do not try to understand reality. Actually, God created me with one pair of wings and two organs to help with balancing. These organs have nothing to do with mutations, adaptation, selection or evolution. Although my ancestors did mutate at times as all living things have done, we have never changed or evolved. Some of us are weak and some are strong; this is a rule of God. This rule is necessary for the ecological balance to be maintained. Some flies will be food for other living creatures, while some will survive to produce more flies. I have not heard of any other flies evolving into a new living creature.

I can fly better than you. You have imagination and knowledge, and you have the ability to improve yourselves, yet you still have not been able to invent a machine that can fly as well as I can. I can turn a somersault in a tight space. I can walk on the ceiling. I can sense the approach of your hand. I can take off so easily that I do not even need a “runway” like airplanes do before taking off. Airplanes can be used for destroying other things, but us flies help to build a better world. My Creator (God) has given me coordination in flight; I do not crash into other things and do not cause any damage while flying. The Qur’an (22:73) says: “Oh mankind! A parable is set forth, so listen to it: Surely, those whom you invoke, apart from God, will never create a fly even if they combine together for the purpose. If the fly takes something from them, they cannot rescue it from him.”

The Qur’an is a miraculous book; yet, unfortunately some people do not understand this yet. Even if all human beings were to work together, they would not be able to build a small “fly”. If I take something from you, you cannot get it back from me. For example, when I snatch a piece of your food, I simply pour digestive enzymes on it and it melts. These enzymes break the food into pieces and make them liquid. Then I am able to drink this liquid. Well now, it would be impossible for you to convert this food back to its original form. Let me show you my nutrition cycle on the right.

When someone mentions the words “flight and insect”, it is most normal to think of only one insect, the common house fly, but there are in fact many species of flying insects: approximately 90,000. Since we have wings, we are all called “diptera”. There are many of us on the earth; from this one can conclude that there will be useful as well as harmful insects among us. Some of our friends take pollen from flower to flower, making honey for you to eat. We eat a variety of foods; some eat meat, some eat vegetables, while others eat fruit.

My friends and I who belong to the Musca type are the most frequently encountered flies in your neighborhood. We, like the other species of flying insects, increase our reproduction rate with increases in temperature. We produce large numbers of eggs. The maggots that you see in rotten food are in fact my larvae. The female fly leaves her eggs on the food you leave out in the open. These eggs hatch in a few days, the time being longer or shorter depending on the temperature. The larvae have a great appetite for everything and they grow fast as they eat everything they encounter. Then they enter a dormant period and retreat into cocoons. After a short while, they come out with bodies that are totally different anatomically. If you were to tell this to someone without a great deal of know-ledge, they would never believe that these crawling larvae will turn into flying creatures one day. It is hard to predict or understand such a huge change. There lies a great wisdom in both our forms. For example, if we did not exist, only bacteria would be able to help decay the dead and this would take too long. But, thanks to my larvae and their presence everywhere in large numbers, this process is completed in a matter of few days. Due to their speedy consumption of decaying matter, maggots have been used often in medicine. They have been used to get rid of decaying tissue on the wounds that aren’t healing, and in this way they speed up the healing process.

Now, I also want to remind you of an unfairness that you do to me and all other flies. As you know, our eggs develop and spread fast during the warm summer season; each of us can produce hundreds of eggs. We go all over the place to find food and sometimes we find it in your trash or in animal droppings. Those who see us in these places mistakenly accuse us of carrying and spreading disease. But the reverse is true; we consume the germs that spread quickly in hot weather. These germs grow on food all by themselves, we don’t produce them. Germs are living creatures too, and they use their abilities bestowed on them by God to grow everywhere. All we do is clean the environment by eating them as we feed. We are able to digest germs thanks to the strong digestive enzymes that we carry. Despite what is believed, I am a clean animal. I clean myself all the time, using the digestive enzymes in my saliva. If it weren’t for me, the germs would grow and spread faster.

I hope that from now on you won’t try to shoo me away when you see me on your hand. Instead, I hope that you will watch how I move and observe me more closely; witness the fine art in me. When you think about me, consider what I have told you. Don’t you think that you should change your opinion about me?