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	<title>factory &#8211; Fountain Magazine</title>
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		<title>Quest to Solve the Mystery of Life</title>
		<link>https://fountainmagazine.com/all-issues/2012/issue-86-march-april-2012/quest-to-solve-the-mystery-of-life/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Thu, 01 Mar 2012 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 86 (March - April 2012)]]></category>
		<category><![CDATA[A Moment for Reflection]]></category>
		<category><![CDATA[actions]]></category>
		<category><![CDATA[adam]]></category>
		<category><![CDATA[cellular]]></category>
		<category><![CDATA[composition]]></category>
		<category><![CDATA[creation]]></category>
		<category><![CDATA[creator]]></category>
		<category><![CDATA[earth]]></category>
		<category><![CDATA[energy]]></category>
		<category><![CDATA[Eve]]></category>
		<category><![CDATA[factory]]></category>
		<category><![CDATA[knowledge]]></category>
		<category><![CDATA[life]]></category>
		<category><![CDATA[molecules]]></category>
		<category><![CDATA[program]]></category>
		<category><![CDATA[sciences]]></category>
		<category><![CDATA[small]]></category>
		<category><![CDATA[time]]></category>
		<category><![CDATA[universe]]></category>
		<category><![CDATA[velocity]]></category>
		<category><![CDATA[water]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2012/issue-86-march-april-2012/quest-to-solve-the-mystery-of-life/</guid>

					<description><![CDATA[The quest to solve the mystery of life seems to be continuing. Where did we come from? What’s matter and what’s beyond it? Where and how did life originate? What about Adam and Eve of other organisms? Obviously, we were not allowed to witness either the creation of universe or the beginning of life on [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>The quest to solve the mystery of life seems to be continuing. Where did we come from? What’s matter and what’s beyond it? Where and how did life originate? What about Adam and Eve of other organisms? Obviously, we were not allowed to witness either the creation of universe or the beginning of life on Earth. We don’t know much about creation, but we can see the results of creation.</p>
<p><span id="more-1358"></span></p>
<p>While discussions on the education of creation in schools continue, generations grow up with lack of knowledge about the Creator and understanding of His Actions. The current education system in high schools and colleges are giving knowledge about the universe, nature, earth, and life but courses are not directed to understand the Actions of the Creator. How and where can people learn about their Creator? Although there are various means such as the internet, religious groups, and journals, it is not always feasible and enough to understand directly the Creator’s Actions without a good understanding of sciences. Fortunately, every science continuously mentions God with their unique language and speaks of the Creator, but we will need a point of view, windows to see beyond our sight and knowledge, just like we need a microscope to see microorganisms or a telescope to discover depths of the universe. With some attention, everyone can understand what sciences reflect from God’s Actions. That’s why we should listen to what sciences tell us in their own language.</p>
<p>Imagine there is a simulation program to analyze a car crash. In this program, let us say you enter different parameters such as velocity, weight, angle of hit, general structure of the car, hardness of the body, and weather information like wind velocity and its direction and so on. After you click on the OK button in this imaginary simulation program, you almost get the same results with real physical crash tests. This obviously shows us a skillful software programmer and his great knowledge in mathematics and physical events. Noticeably, nature is composed of millions and millions of parameters determining final result just like this simulation program. For instance, when you throw a stone to a lake or into water, first of all it falls down with a velocity and then you see a wave of water expanding to its surrounding from the center affected by that velocity. The velocity of this stone at a certain time and place and wave formation on the surface of water can be explained with some physical laws described with mathematical equations. Whoever put these rules for the physical events also created the universe in a perfect mathematical order. From these and the knowledge we get from computer sciences, physics, and mathematics, we can open windows to understand the ruler of the universe as Glorious Creator.</p>
<p>We are at the time of great advancements in gene technology and huge increase in knowledge about molecular biology; even individual structures of biological molecules are known and many more discovered about cellular mechanisms. The more we learn, the more we face complexity and organization in the tiniest compartments of cell. Cell is no longer a small room filled with a gel-like structure in our minds, it is a massive factory that contains all required machinery and it is automatic, well balanced, and continuously renewed. Things are in constant motion; uptake follows release of substances and signal from outside results in a response produced inside. With increase in understanding of how living things are working and necessity to answer how these things originated caused discussions in scientific research. Some scientists like to talk only at scientific platforms or on so-called testable scientific subjects, but this does not change the reality. We wonder about the beginning and we wish to live forever. We are finite but dream of infinity. How can we think of eternal life if we were a product of something that is not eternal?</p>
<p>Imagine there is a high-tech, but small self-working factory producing highways and trucks to carry items, fuel engines for the energy that can be used in many different processes and containing solar energy collectors. There are great photocopy machines for the production of a new factory, feedback systems to control and repair any problems as well. Without any concern, control of all these events and thousands of machines, engines, highways in such a small sized factory without any problem involves a perfect engineer, scientist, architect, and chemist. Similarly, believe it or not, the cell is an excellent composition of around one million molecules, thousands of machines, and energy producing engines. There are highways, trucks, feedback systems and more in an arranged and fine control in such a small size. Mitochondria, for instance, is one of the most essential cellular organelle and produces ATP molecules as carrier of energy obtained from organic molecules for energy requiring cellular processes. In addition, cellular requirements vary by time and vesicles carry required molecules as cargo on molecular motors using microtubule pathways to different places. Those and many other examples we learn from biological sciences point to the Glorious Creator of the Earth.</p>
<p>When you consider a cell coming into existence by causes other than the hands of a Creator with numerous levels of regulation, coordination of subcellular compartments like organelles, information storage in DNA, and use of this information required for their specific function, it means molecules come together under the effect of natural causes and form an artistic cellular structure in a wise-manner. Actually, this reminds us of a very famous experiment by Stanley Miller to make amino acids, the building blocks of proteins, to demonstrate that life on earth has originated by natural causes and chance. Miller, in his experiment, took molecules which were supposed to represent the major components of the early Earth&#8217;s atmosphere and put them into a closed system. He used methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O) in his experiment and ran a continuous electric current to stimulate lightning storms and to drive these unfavorable reactions. He found that three amino acids have been synthesized in these conditions. Later, it was found that this composition was different from the early Earth&#8217;s atmosphere and arguments raised to his experiment due to continuous energy input not possible in nature. However, this was exciting at that time and some used headlines like &#8220;Miller created life.&#8221; On the other hand, what Miller had managed to synthesize was only a few inanimate lifeless molecules.</p>
<p>People who do not believe in God also do not believe in creation. That’s why they tend to conclude that &#8220;nothing is created out of nothing, and nothing goes to nothing; there is only composition and decomposition.&#8221; But, the All-Powerful One has two ways of creating. The first way is through origination and invention and the second way is through composition and through art. He creates from out of nothing together with everything necessary for, again, nothing. In the second way of creating, He forms beings from materials of universe in order to show his delicate wisdom, perfection, and the manifestations of His Names. &#8220;O people! be careful of (your duty to) your Lord, Who created you from a single being and created its mate of the same (kind) and spread from these two, many men and women&#8230;&#8221; (Quran 4:1)</p>
<p>When we think about the lessons learnt from these examples and natural sciences with their special focus areas, we realize that every science somehow declare the Glorious Creator of this universe. However, there may not be an opportunity in school to discuss and go deep into the understanding of the Actions of the Creator. With the window of what sciences open to us about God, we can uncover the hidden truths.</p>
<p><em>Ali Fethi Toprak is a PhD candidate at Southwestern Medical Center, Texas University, Dallas.</em></p>
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		<item>
		<title>Functional Art in the Nucleus: DNA</title>
		<link>https://fountainmagazine.com/all-issues/2011/issue-82-july-august-2011/functional-art-in-the-nucleus-dna/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Fri, 01 Jul 2011 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 82 (July - August 2011)]]></category>
		<category><![CDATA[cell]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[double]]></category>
		<category><![CDATA[factory]]></category>
		<category><![CDATA[functions]]></category>
		<category><![CDATA[gene]]></category>
		<category><![CDATA[genes]]></category>
		<category><![CDATA[information]]></category>
		<category><![CDATA[nucleotides]]></category>
		<category><![CDATA[nucleus]]></category>
		<category><![CDATA[produce]]></category>
		<category><![CDATA[protein]]></category>
		<category><![CDATA[proteins]]></category>
		<category><![CDATA[read]]></category>
		<category><![CDATA[region]]></category>
		<category><![CDATA[regions]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[single]]></category>
		<category><![CDATA[specific]]></category>
		<category><![CDATA[structure]]></category>
		<category><![CDATA[sugar]]></category>
		<category><![CDATA[transcription]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2011/issue-82-july-august-2011/functional-art-in-the-nucleus-dna/</guid>

					<description><![CDATA[Volumes of books and hundreds of articles have been published about the structure and functions of DNA, since the day two renowned scientists from Cold Spring Harbor laboratories, who would later win the Nobel Prize, described the double helix structure of it. Perhaps one common element that shines through all the publications is their emphasis [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>Volumes of books and hundreds of articles have been published about the structure and functions of DNA, since the day two renowned scientists from Cold Spring Harbor laboratories, who would later win the Nobel Prize, described the double helix structure of it. Perhaps one common element that shines through all the publications is their emphasis on the numerous specific functions of DNA, if not the fascinating harmony of these specific functions in a living organism. In this article, we will take a look at a few small droplets from the vast ocean of information about the multi-layered functions of DNA that are orchestrated in an awe-inspiring manner.</p>
<p>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.</p>
<p>“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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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?</p>
<p>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.</p>
<h3>Different layers of complexity and organization related to DNA</h3>
<p>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.</p>
<p>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?</p>
<h3><b>References</b></h3>
<p>1. Calladine, C. R. et al. 2004. Understanding DNA: The Molecule and How It Works, Academic Press</p>
<p>2. http://www.genome.gov</p>
<p>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.</p>
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		<title>The Onerous Journey of a Meatball</title>
		<link>https://fountainmagazine.com/all-issues/2011/issue-81-may-june-2011/the-onerous-journey-of-a-meatball/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Sun, 01 May 2011 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 81 (May - June 2011)]]></category>
		<category><![CDATA[acid]]></category>
		<category><![CDATA[acids]]></category>
		<category><![CDATA[body]]></category>
		<category><![CDATA[carbohydrates]]></category>
		<category><![CDATA[cells]]></category>
		<category><![CDATA[energy]]></category>
		<category><![CDATA[factory]]></category>
		<category><![CDATA[fat]]></category>
		<category><![CDATA[fats]]></category>
		<category><![CDATA[leaf]]></category>
		<category><![CDATA[liquid]]></category>
		<category><![CDATA[Meatball]]></category>
		<category><![CDATA[proteins]]></category>
		<category><![CDATA[red]]></category>
		<category><![CDATA[room]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[tube]]></category>
		<category><![CDATA[walls]]></category>
		<category><![CDATA[water]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2011/issue-81-may-june-2011/the-onerous-journey-of-a-meatball/</guid>

					<description><![CDATA[I was once a delicious meatball. I should, in fact, say &#8220;we,&#8221; not &#8220;I,&#8221; for I was a foodstuff with such ingredients as fats, carbohydrates, proteins, and vitamins. Humans – especially kids – loved me very much. Imagine: I have just been cooked, and I am now waiting on a dish. Oh, what&#8217;s that? A [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>I was once a delicious meatball. I should, in fact, say &#8220;we,&#8221; not &#8220;I,&#8221; for I was a foodstuff with such ingredients as fats, carbohydrates, proteins, and vitamins. Humans – especially kids – loved me very much.</p>
<p>Imagine: I have just been cooked, and I am now waiting on a dish. Oh, what&#8217;s that? A metal thing with four prongs has just stuck itself into my chest, and it threw me into a shaking room with a gate moving up and down. There are, in this room, 32 flat and occluding rocks, some of which are sharp, while some are like millstones, all being lined up in a U-shape row. The frontal rocks have divided me into large pieces by squeezing and cutting. My pieces are pushed backwards by a soft shovel underneath. The rear rocks have made me almost like a paste, thoroughly mashing my pieces. Meanwhile, many taps on the right and left sides and in bottom of the room began flushing water upon me, and the carbohydrates within me have began dissolving by the pityalin enzyme (alpha amilaz) in this water. The flushing water contains substances such as lyzozym and antichore to eliminate any probable microbes within me.</p>
<p>I was fully softened and turned into something almost like gruel, when suddenly I was impelled by the actions of that soft shovel to an extremely tight tube inside of which movements continuously push me downward. A gate opened while I was being brought down and, as I was hoping to enter into a more spacious room and be saved from the compressive movements, I suddenly flopped into a well containing a light-colored liquid. I have come to know, while I was expecting to have some refreshment, that the liquid I flopped into was an acid capable of eroding marble (pH=0,8). I cried ‘Oh My God!&#8217;, but it was too late. This acid began to break my proteins down. The pepsinogen which was simultaneously being secreted by some cells over the walls of this large room and which were ineffective within an acid-free environment, became instantly activated by this acid and began to thoroughly break me up. Most of my proteins were broken. While I was wondering and asking ‘how come the liquid I flopped into is capable of eroding the marble but not capable of breaking up this well?&#8217;, I have come to notice that walls of the well were coated with a thin layer of mucous substance (membrane) which is unbreakable by acids.</p>
<p>I said ‘Oh My God! As long as you do not permit, these acids, which can erod marble, are not capable of damaging a soft tissue!&#8217;. Together with other foodstuff, I have been both blended and broken in this well-like room for about an hour. Later, the outer walls have again squeezed us, and we have been ejected yet again, this time into a new tube at an opposite direction to the one we were just pushed out of, by a sudden loosening and opening of a valve. This tube (called duodenum in Latin) has a length of about 15-18 cm and, appears as if lined up side by side. Here too, we felt wretched and were faced by a basic secretion (sodium bicarbonate) being ejaculated from a tap. This liquid was inactivating (neutralizing) the acids mixed with us, i.e., preventing them from damaging the unprotected walls of the tube which we were in.</p>
<p>Here again the amylaz, lipaz, trypsin, kymotrypsin and carbocsypolypeptidas attacked me, all of which break up, in a respective order, carbohydrates, fats and proteins of my ingredients, along with a lot many other enzymes, and they broke me up to my smallest constituents. Meanwhile, I started pondering the reasons why these enzymes, which are making mincemeat of me, are not damaging the tap (pancreas), which are composed of the same proteins, fats and carbohydrates that they come from. Then, I have come to realize that these enzymes could not become activated in pancreas tissue, since it does not have any activating factors, but they gained shredder features only after we arrived in the tube we are in, and only with the help of such factors which are being secreted from the intestinal walls.</p>
<p>After having been fully shredded within this narrow tube, a green liquid (bile), was poured on us as we were approaching its end. This detergent-like liquid was particularly responsible for shredding the fats in my ingredients. I understood, after all of this, that I was passing through a very excellent factory. As I and my fellow meatballs proceeded inside this narrow tube of approximately three meters long, no part of us remained un-shredded, except the cellulose fibers of plants such as parsley and onion which accompanied us. They continued their journey until arriving at a very thick and short tube. I have found out that their sap have been absorbed and their leftovers, after being amassed for some time, have been thrown into a cesspool called a toilet.</p>
<p>In the meantime, we have noticed that the walls of this tube are plicate and protuberant. These walls are apparently the places where our particles penetrate into another realm through two different ways. We understood that, via rather thin capillary channels situated inside these protuberances, we were being transferred into narrower tubes which contained two different (red and white) types of liquids (blood and lymph vessels). Now, there isn&#8217;t ‘me&#8217; anymore, instead, there is only an ‘us&#8217; which is composed of very smaller particles. While glucoses, the simplest forms of carbohydrates and aminoacids, the simplest forms of proteins are being transferred into the red liquid, our fat acid siblings are transferred into the white liquid of lymph vessels. Our glucose and aminoacid siblings have been carried by the red liquid to a factory called a liver. They are being returned to the red liquid after having passed through certain processes and being equipped with some useful characteristics here. But, the fats (lymphs) of the white liquid are, for some reason or another, being separately transferred into the red liquid, bypassing this factory. I learned the reason later: if the fat acids came to the liver together with glucoses and aminoacids, they would spoil this factory and kill its workers.</p>
<p>Finally, the red liquid carried us to tiny cell chambers numbering almost 100 trillion. Each of our tiny particles were sent to separate cells. Here, water, carbondioxide and energy were being produced by primarily coupling of our sibling glucose with oxygen. I learned that energy was needed for the functioning of these cells. Our fat siblings were also being utilized (consumed) for producing energy if glucoses were found insufficient for that purpose. Our amino acid siblings were being utilized (consumed) in the production of sound (strong) proteins and glucoses, and of energy in cases of the unavailability of fat sources for use in the cells&#8217; structures. Excessive amounts of fat and glucose were being stored in these tiny cells. That is to say, I, who was a meatball at the beginning, was converted into water, carbondioxide and energy at the end of this painstaking journey. I was promoted (exalted) to the degree of humanness and rewarded a great deal of honor, as some parts of me became constituent of and some other parts of me assumed responsibility in vital cell functions of the human body.</p>
<p>After all these disintegrations and absorptions, some parts of us took their share in the structure of the body, while some others which were used in energy production including me were converted into a choky and dirty gaseous state called carbondioxide. We have been thrown back into the red liquid again since we would perhaps choke the cells we are within should our density increase very much. We have been brought to a marvellous and sponge-like factory named a lung, and composed of millions of vesicles, by being placed onto a molecule called hemoglobin, which is being pushed by a big pump. We have replaced the oxygen of the fresh air arriving to the lung vesicles. Now is the time for bidding farewell the human body. I thanked God, for I regained my freedom as a carbondioxide passing through and escaping from very dark and narrow places.</p>
<p>However, I was placed upon the leaf of a green plant after aimlessly roaming in the air for some time. After being filtered through the little windows (stoma) over the leaf, I was brought inside by the chlorophyll factory marvelously functioning inside these cells. Here, they forced me to unite with the water brought by tubules from the soil. Upon telling them that I cannot afford to do that, they instantly changed my true nature with solar rays and turned met into a chemical energy depot. I was no more a simple carbon atom; thus, I found a place for myself within an energy-emiting glucose molecule. I was in a position suitably convertible to starch, protein or fats in accordance with the true nature and genetic program of the plant I was within. Something incredible happened while I was swinging around on a green clover leaf. The leaf I was in has been eaten by a cow with real pleasure.</p>
<p>A new chapter has now opened inside the cow&#8217;s body. I was assigned with certain duties within the muscle proteins of my new host after having passed through a number of chemical processes. And I really enjoyed them. I was feeling myself more as an animal protein than a simple grass. By leaving the grass for a cow&#8217;s body, I was promoted (exalted) one more degree on the way to becoming manifestations of the divine attributes of God.</p>
<p>This blessed animal in whom I was assigned has been sacrificed during a Muslim feast of sacrifice, its meat ground into a meat grinder, and I have been served to you once again as a meatball.</p>
<p><em>Ali Uguz is a teacher of biology. He lives in Turkey.</em></p>
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		<title>Factory of Future</title>
		<link>https://fountainmagazine.com/all-issues/1993/issue-3-july-september-1993/factory-of-future/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Thu, 01 Jul 1993 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 3 (July - September 1993)]]></category>
		<category><![CDATA[1990]]></category>
		<category><![CDATA[1991]]></category>
		<category><![CDATA[aided]]></category>
		<category><![CDATA[automated]]></category>
		<category><![CDATA[cad]]></category>
		<category><![CDATA[cam]]></category>
		<category><![CDATA[capp]]></category>
		<category><![CDATA[computer]]></category>
		<category><![CDATA[control]]></category>
		<category><![CDATA[design]]></category>
		<category><![CDATA[factory]]></category>
		<category><![CDATA[integration]]></category>
		<category><![CDATA[intelligent]]></category>
		<category><![CDATA[knowledge]]></category>
		<category><![CDATA[manufacturing]]></category>
		<category><![CDATA[planning]]></category>
		<category><![CDATA[process]]></category>
		<category><![CDATA[production]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[system]]></category>
		<category><![CDATA[systems]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/1993/issue-3-july-september-1993/factory-of-future/</guid>

					<description><![CDATA[Artificial Intelligence is a promising approach to automating process planning. Expert Systems or Intelligent Knowledge Based Systems are able to automate the reasoning activities to capture logic, experience-based reasoning and knowledge in a computer environment. CAD/ CAM IN AUTOMATION The developments of manufacturing can be categorized in two stages, namely the mechanization stage and the [&#8230;]]]></description>
										<content:encoded><![CDATA[<p><em>Artificial Intelligence is a promising approach to automating process planning. Expert Systems or Intelligent Knowledge Based Systems are able to automate the reasoning activities to capture logic, experience-based reasoning and knowledge in a computer environment. </em></p>
<h3><b>CAD/ CAM IN AUTOMATION</b></h3>
<p>The developments of manufacturing can be categorized in two stages, namely the <b><em>mechanization stage</em></b> and the <b>automation stage. </b> In the early stage of manufacturing, tools and processes were mechanized. All of the various manufacturing processes were divided into categories such as casting, forging, turning, milling, drilling and cutting, with workers specialized in one of these areas. Specialization resulted in the separation of design from manufacturing. One person would design a product while other specialists would manufacture it. Design and manufacturing communicated through drawings. The mechanization stage was able to accomplish mass turnover and speed in production. However, it lacked flexibility and integration.</p>
<p>The next stage in the development of manufacturing is automation. In 1975, mass production was automated through the use of transfer lines. In 1976, batch production was automated through Flexible Manufacturing Systems (FMS). In 1979, design and draughting through CAD (Computer Aided Design) started to be used widely. The integration of these started in 1985. The goal of this stage is to have completely automated manufacturing plant operating with only a minimum of human involvement. Progress is being made in this regard, but total integration has not yet been achieved. The totally automated factory will be capable of mass turnover and speed in production, will be flexible and completely integrated.</p>
<p>The most important development regarding automation in manufacturing has been the computer. It provided developments in manufacturing control, material handling, planning and in other activities. The use of computers in manufacturing control improved NC (Numerical Control) technology such as computer aided NC code generation. It is now possible with some CAD/CAM (Computer Aided Design/Computer Aided Manufacture) systems to generate NC tape directly from the designed part stored within the CAD data base. Computers have greatly enhanced automated manufacturing. NC machine tools have been replaced by CNC (Computer Numerical Control) machine tools: almost every machining process can now be efficiently automated with a significant degree of accuracy, reliability and repeatability.</p>
<p>Computer Aided Design (CAD) can be defined as the use of computers to assist in the design process including calculation, analysis, modelling, draughting and testing. Initially, CAD systems were primarily used for draughting. Nowadays it also includes Finite Element Modelling (FEM), geometric modelling and kinematic analysis. (FEM is widely used for the analysis of many engineering problems, namely static, dynamic and thermal stress analysis of various structures including vibration analysis. Geometric modelling is concerned with the mathematical representation of objects in a computer.)</p>
<p>The development of NC machine tools was the beginning of CAM systems. CAM can be defined as the use of computers to enhance or assist in any manufacturing process. CAM comprises a large number of functions such as Computer Numerical Control (CNC), Direct Numerical Control (DNC), Flexible Manufacturing System (FMS), Automated Guided Vehicle (AGV), automated material handling, inspection and computer controlled assembly systems. CNC is an NC system that uses a dedicated computer to perform NC functions. DNC can be defined as a manufacturing system where a number of machine tools are controlled by a central computer simultaneously. The part programme is transmitted to the machine tool directly from the computer. An FMS is a programmable manufacturing system capable of producing a variety of products automatically and it is composed of CNC machine tools, automated material handling systems, robots and a computer system to control them. An Automated Guided Vehicle (AGV) is a robot-like vehicle that is used to carry objects from one place to another and can be programmed to trace a path.</p>
<h3><b>INTEGRATION OF CAD/CAM</b></h3>
<p>Due to development in computer technology, numerically controlled equipment, robots and computer controlled automation in CAD and CAM systems, many manual skills have been automated resulting in reduction of lead times, improvements in production, increase in manufacturing accuracy and flexibility. However, the full integration of CAD and CAM systems in industry has not yet been achieved and they have been developed separately (see Davies et al., 1988; Irani et al., 1990; Joseph and Davies 1990).</p>
<p>It is acknowledged that significant benefits can be obtained when CAD is integrated with CAM within a single company. For this reason the integration of CAD and CAM systems has become an important goal in factory automation (see Semakula and Gill, 1989; Sing et al., 1990). Computer Integrated Manufacturing (CIM) is the term used to denote the complete integration of all aspects of CAD and CAM systems.</p>
<p>CAD and CAM systems have not been totally integrated due to the difficulties in automating intermediate functions (see Joseph and Davies, 1990; Joseph et al., 1990). In order to achieve the goal of full integration of CAD and CAM two major obstacles should be addressed, namely complete CAD and CAPP/CAM interface and a fully automated, flexible CAPP system. (CAPP stands for Computer Aided Process Planning.)</p>
<p>CAPP is an important activity which bridges CAD to CAM (Figure 1) and translates the design information into manufacturing instructions to produce mechanical components (see, most recently Desai and Pande, 1991; Cho et al., 1991). The task of process planning in industry is usually performed by an experienced process planner manually employing his or her expertise and knowledge about machining operations. The quality of the plan developed depends on the experience and preferences of the planner whose highly skilled expertise is difficult to replace (Bandyopathyoy et al., 1981; Joseph and Davies, 1991).</p>
<p>Several CAPP systems have been developed. However, the computer can only assist the planner generate process plans. Fully automated CAPP does not exist and its benefits in the real industrial environment are still to be seen (see, e.g. Chang. 1990; Domazet and Manic, 1990). The complexity of decision making in process planning is a barrier to automating process planning. Many of the tasks carried out by the planner require expert knowledge, experience and intelligent reasoning (see Rustom and Mileham, 1989; Stewart et al., 1989). Other major impediments to the implementation of fully automated CAPP are related to the capturing of planning logic and heuristic knowledge. Industrial robots are programmed by a human programmer. But how does a bee know how to built a honeycomb and make honey?</p>
<p> </p>
<p>Algorithmic programming techniques are considered unsuitable to automate process planning because process planning problems are usually solved heuristically, that is, on the basis of human ability to use reason and learn from experience (see Tonshotf et al., 1987; Dumazet, 1992). Manufacturing processes change over time on the factory floor. Algorithmic programs are not flexible enough to accommodate modifications since any alteration in the programme affects the whole structure of the software (Changer et al., 1991). Artificial Intelligence (AI) is a promising approach to automate process planning. Expert Systems or Intelligent Knowledge Based Systems are able to automating the reasoning activities to capture logic, experience-based reasoning and knowledge in a computer environment. An Expert System represents and stores the domain-specific knowledge in a special manner so that it is possible to add, delete or modify the knowledge within the database without any alteration in the program.</p>
<p>In short, the main goal for the industry of tomorrow is to integrate all the activities on the factory floor, i.e. to have automation from design to final manufacturing, (Nordland, 1988).</p>
<p>Assuming that we had a chance to visit such a factory of the future totally integrated, automated, unmanned except by robots, we would be aware that the automation is achieved and controlled by a computer programme which processes data, solves the problems that arise and gives the commands necessary to run the factory.</p>
<p>It is obvious that every such programme requires a programmer. Nobody would claim that the machinery, robots. etc. have themselves decided to develop the complicated software to control the system on the factory floor: it is easy to see that machines and mechanical parts do not have the ability, intelligence and knowledge even to wonder at their own structure.</p>
<p>Even if we do not see the programmer we can infer that one exists who is expert in the particular field and who programmed the automatic systems to do particular things. Similarly, we can liken the earth to an automated factory where animals and plants are like robots or automatic systems that perform some intelligent actions. If, within this factory a bee, for example, is not attributed to a Creator Who tells it how to make its honeycomb and honey then it must be that bees themselves know the necessary chemistry and geometry to do so. But we know that a bee is so unintelligent that when it is trapped indoors it tries to get out through a closed window. Even where there is an open window nearby it does not think of using the open window, but only finds it randomly. Therefore, we may not suppose that bees are intelligent and skilled enough to make honeycombs and honey. Even we, humans, who are the most intelligent creatures on earth, are not able to make proper hexagon-shaped honeycombs without using tools or a die. So we cannot expect a bee to do so all by itself without using a tool.</p>
<p>Every fruit tree is a fruit factory. A vegetable plant is a vegetable factory. They produce fruits and vegetables, respectively. If they are not attributed to a Creator then it must be that they are creating fruits and vegetables by themselves. We know that trees and vegetables are not intelligent enough and lack the knowledge of biology or chemistry to combine the necessary minerals or molecules to create the fruits and vegetables that fulfil our needs. They are not even aware of what we need. Examples can be extended to other creatures in the earth. Vegetables and animals perform some intelligent actions and yet they are not intelligent. Although we do not see the Creator of this factory, the activities around us show that there is One, Who is All-Wise, creates and controls the actions within this factory-like earth. </p>
<h3><em><b>REFERENCES</b></em></h3>
<ul>
<li>ClANG, T.C. (1990) ‘Expert Process Planning for Manufacturing’, Addison-Wesley Publishing Company, USA.</li>
<li>CHANG, T.C.,Wysk, R.A. and Wang, H.P. (1991) Computer Aided Manufacturing, Prentice Hall, USA.</li>
<li>CHO, K.K., Lee, S.H. and Ahn, J.H., (1991) ‘Development of Integrated Process Planning and Monitoring System for Turning Operation’, Annals of the CIRP, 40/1, pp.423-7.</li>
<li>DESAI. VS. and Pande, S.S., (1991) ‘GFM. An Interactive Feature Modeller for CAPP or Rotational Components’, Computer Aided Engineering Journal, pp. 217-21.</li>
<li>IRANI, R,K., Saxena, M. and Finnigan, P.M., (1990) ‘Boundary Based Feature Modelling Utility’, Proceedings of the ASME International Computers in Engineering Conference, 1, pp. 45-51, Boston.</li>
<li>JOSEPH, A.T. and Davies, B.J., (1990) ‘Knowledge Based Process Planning System for Turned Components’, The International Journal of Advanced Manufacturing Technology, 5, pp.52-65.</li>
<li>JOSEPH, A.T. and Davies, B.J., (1991) ‘Elictation of Process Planning Knowledge in a Manufacturing Environment’. The International Journal of Advanced Manufacturing Technology. 6, pp.16-34.</li>
<li>NORDLAND, G.L., (1988) ‘Integrating CAPP Into Factory Management Systems’, CAPP From Design to Production, ed. Joseph Tulkoff, SME, pp. 134-136.</li>
<li>RUSTOM, E.A. and Mileham, A.R., (1989) ‘The Development of a Generative Computer Aided Process Planning System for Prismatic Parts’, Advances in Manufacturing Technology 4. Proceedings of the 5th National Conference on Production Research, Huddersfield Polytechnic, pp. 259-63.</li>
<li>SINGH, R., Sittas, E., Mullineux. G. and Medland, A.J., (1990) ‘Intelligent Communications Between CAD and Manufacturing Activities’, Proceedings of the 28th International MATADOR Conference, pp. 305-1 2.</li>
<li>STEWART, C.D., Wallace, W. and Boswell. C., (1989) ‘The Development of a Knowledge-Based Process Planning System’, Advances in Manufacturing Technology 4, Proceedings of the 5th National Conference on Production Research, Huddersfield Polytechnic, pp. 265-68. </li>
</ul>
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