A small-scale blueprint of the universe, the human body is a miraculous work of art that manifests the beautiful divine names and attributes of God Almighty. A human body is made up of a set of hierarchically organized components: an organ system, organs, tissues, cells, organelles, macromolecules, molecules, atoms, neutrons, protons, electrons, and subatomic particles. In this biological organization, it is striking to observe a proportionately allocated space between components on each level for their efficient functioning. The size of human body would be reduced if these spaces between organs, tissues, cells, and atoms could be removed, and the entire human body would not be bigger than a small ball.

The structure of an atom explains a lot concerning the real size of our body, which is filled with space. An atom is comprised of protons and neutrons in its nucleus, around which electrons continuously orbit. The mass of neutrons is almost equal to the mass of protons. Electrons, however, are 1,837 times smaller in mass than neutrons and protons. That is, almost 99.95% of the atom’s mass is in its nucleus. The mass of electrons is almost non-existent compared to the nucleus.

Both the universe and our body are filled with more hydrogen than any other atom. In each one billion atom in our body, six hundred thirty million are hydrogen atoms. In a hydrogen atom, electrons rotate only 0.53 nm (one billionth of a meter) away from the nucleus, which makes the atom’s volume to be around 6.10^-28m³, whereas the volume of the proton is 7.10^-45m³, i.e., the nucleus is only as big as one hundred quadrillionth (100.10¹⁵) of the atom’s total volume. In other words, while the nucleus comprises almost the entire mass of the atom, its volume is of no considerable size. The density of protons in the nucleus is 2,3.10¹⁷ kg/m^{3 (where does the period go here??)}, which means that there is around a hundred trillion tons of matter in only one cubic meter. If we could gather all neutrons and protons in one spot, a man who is 69 kg would be only 3.10^-7 mm³ in volume. That is, the volume the total substance of our body takes up is around one ten millionth of a cubic millimeter. The human body, which is constructed of atoms with electrons rotating on an orbit quite far away from the nucleus, is in a way no different than an “inflated space.” For a comparison, the space between the earth and the sun can be filled with as many as 107 suns, whereas 450 thousand protons are needed to fill up the distance between the proton and electron in a hydrogen atom.

The subatomic world is even more amazing. In subatomic particles are found six types of quarks. A quark is considered a fundamental constituent of matter. Combinations of quarks in different shapes and numbers result in subatomic particles, the further combinations of which produce atoms, molecules, and so on. Quarks are considered to be without mass; that is to say, they are nothing else but energy. Humans have mass, but this mass consists of quarks that are without mass.

This incredibly vast space between atoms that make up matter teaches us that our true value does not lie in our physical structure, but in the artworks of no comparison designed by the Divine as manifestations of His most beautiful names. Thus, we, who are so little in material substance, should seek other gateways in the depth of our souls and attain some value with proximity to the Divine.

We may never have revolted against God Almighty in our entire life; yet still our material minority should free us from all kinds of pride and conceit. Our physical structure is very much like the number “zero,” for 0 is also nothing, and it is drawn by inflating.

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.

Spending so much time in the library for a particular book further amazed me about the answer I was searching for in my research. I am trying to understand how our genome is organized and how it functions. In order to make myself clear, let me first try to explain what the genome is. I bet you will be amazed by the impressive genome organization and its flawless function, too.

The genome can be thought of as a library. Each book in the “genome library” is what we call a “gene”. Every gene is different in size and the information they contain, just like the books in the library. Like the different sections in the library, our genes are also compartmentalized into different chromosomes. We have 23 pairs of chromosomes. One pair contains the information from our father and the other one from our mother. Therefore, unlike libraries, where you may find more than one copy of a book, our genome has two copies of each gene (except the genes on the X and Y chromosomes which carry only one set of genes).

Every cell in our body carries its own library: the genome. Our genome is the smallest library in terms of physical volume, yet contains relatively the largest amount of information. In our body, which contains roughly 100 trillion cells, we carry 100 trillion of these libraries. Here comes the amazing part; each of these libraries contains 3 billion letters of information. If this information were to be printed, it would take 1000 books of 200 pages each. The information in our genome is coded by a 4 letter alphabet; Adenine (A), Guanine (G), Cytosine (C) and Tymine (T). These four letters (A,G,C,T), called deoxyribonucleic acids, are the building blocks of every DNA strand on earth. The collective amount of these letters in any organism constitutes of its genome. We, as humans, have about 3 billion of these letters in our genome, which is encapsulated in the nucleus of every cell in our body. The total length of our genome is 2 meters long. This 2 meter long stretch of DNA (3 billion letters of information) is highly compacted and packaged in the nucleus, which is only 2 micrometer in diameter, an amazing 1,000,000 fold compaction!

How is our genome, which is 2 meters long, compacted so much that it fits in a nucleus only 2 micrometer in size? In the nucleus, DNA is wrapped around a group of 8 proteins called histones. This combination of DNA and histone proteins forms a special structure called “beads on the string”. Each bead is called “nucleosome” (Figure 1).

Multiple nucleosomes are then coiled together and stacked on top of each other. This organisation further packs the DNA up into a thicker fiber called “chromatin”. This chromatin fiber further condenses by forming tight loops. The structure which we call a “chromosome” is actually the most compact form of the chromatin fiber, which is only visible under the microscope during cell division. This remarkable chromatin organization allows a 2 meter long DNA to fit into the nucleus of each cell, an object so small that 10,000 of these nuclei can fit on the tip of a needle!

This remarkable genome organization further impresses us when we think about the utilization of this genetic information by over one hundred trillions of cells in our body. These many cells in our body are not all similar to one another. Most of the cells in our body are specialized to carry out specific functions. We have more than 200 different cell types specialized for unique functions. Some cells, like B and T cells in our immune system, are dedicated to fighting against infectious agents, whereas other cells, like neurons, function by transmitting signals between our brain and muscles. Since these cells have different structures and carry out different functions, they require different sets of instructions coded by genes in the genome. There are roughly 20.000 genes in our genome. Importantly, each specialized cell in our body utilizes only a subset of these genes, not all of them, at any given time. In other words, from the library analogy, roughly two third of the books (i.e., genes) are needed for each cell to function. The remaining one third of the genes is not necessary for that particular cell type. For example, the MYOD1 gene encodes a protein required for muscle cell differentiation. Therefore, this gene is absolutely required for muscle cells. However, the same gene is not required for the B or T cells that function in our immune system. While the MYOD1 gene has to be stored in an easy access location (open chromatin) for muscle cells, immune cells do not need this gene, and therefore it is stored in the depository section of the “genome library” (closed chromatin), which is not used very often.

In line with this, each cell has to organize its genome in a special way so that the genes needed for its function should be easily accessible. This remarkable genome packaging and organization allows each cell to easily and very quickly access the required genes for transcription into the proteins. On the other hand, those genes that are not going to be used are stored in relatively inaccessible regions in the genome library. Therefore, the genome is not packaged similarly all along. Certain regions of the genome are “open” and therefore easily accessible (called euchromatin) for transcription, while other regions are kept “closed” by condensed and packed structure (called heterochromatin). Since each cell type requires different set of genes, the genome is also differentially organized between cell types. Genome organization in a muscle cell is remarkably different than genome organization in, let’s say, a skin cell.

After all these explanations, I hear you asking, “How does each cell in our body know how to organize their genome? How does, lets say, a muscle cell decides to become muscle but not a blood cell?” These are exactly the same questions that many scientists are asking nowadays. Since the completion of the Human Genome Project (HGP)1,2, which determined the entire sequence of information of our DNA, scientists have been trying to understand how this amazing alphabet is being used in each and every cell in our body. Francis Collins, one of the great scientists of our time and the current director of National Institute of Health (NIH-USA), is especially noted for his landmark discoveries of diseases associated genes, as well as his leadership in the Human Genome Project. He calls the information coded in our DNA the “Language of God” in his recent book.3 Recent technological advancements allow scientists to better study the structure and function of this language and get better clues about the organization of this genomic library.

Whether we believe that this genomic information is “the language of God” or not, we are closer than ever to understanding the codes of this amazing language. New technological advancements allow us to get better insights about the organization and utilization of this information. The more we learn about it, the more we are amazed about not only its flawless packaging but also its differential utilization in each cell. At any time and in any tissue, trillions of cells are using different sections of the genome library to get the necessary instructions decoded from “the Language of God” and continue their journey in our bodies without any conscious decision making on our part.

Ahmet Mir Fazil holds Ph.D. degree in molecular Biology. He is a research scientist in Boston.

References

1. International Human Genome Sequencing Consortium (2001). “Initial sequencing

and analysis of the human genome.” Nature 409 (6822): 860–921.

2. Venter, JC, et al. (2001). “The sequence of the human genome.” Science 291

(5507): 1304–1351.

3. Francis S. Collins. 2006. The Language of God: A Scientist Presents Evidence for Belief. Free Press.

We can use electron or tunnel microscopes to extend our observations. Moreover, we discover that the great forces which help to keep together all the parts, from the biggest to the smallest, are active all the time just in order to make the wall stand still. This tells us that the wall has been built according to pre-determined calculations and geometry. So we can extrapolate this and imagine the creation of matter first as a sub-atomic particle, after that as a nucleus,¹ an atom and a molecule and continuing on. This situation clearly shows that at first matter (a kind of raw material) was created in a way that we cannot explain with causes. This matter was then subjected to construction by the Divine Knowledge, Will, and Power in the framework of the relationship of cause and effect in the universe. Today, we know that, starting from the molecule and going into more detail, that in the atomic system there is the atomic nucleus, and in the nucleus there are nucleons (protons and neutrons) and quarks in each nucleon; these tiny particles are kept together by very high forces (strong nuclear force). In other words, as the sizes of things get smaller in this physical world-from the galactic scale to the subatomic scale-the force required to keep things together becomes greater, in inverse proportion to the size. There are four kinds of forces known in the physical world: gravity, weak nuclear force, strong nuclear force and electromagnetic force. Gravity is the weakest of these forces, while strong nuclear force is the strongest. Gravity, the natural force by which all objects are attracted to each other, operates between immense objects like stars, medium-scaled things like planets and small things like apples. Gravity is 1,040 times weaker than the strong nuclear force that is used to keep the sub-atomic particles, such as the proton and quark in the nucleus, together. It is still a matter of debate in quantum physics if sub-atomic particles (those that are smaller than the electron) have a physical entity that we call a “body,” even though their existence has been proven and they have been named.

Can sub-atomic particles give information about the actual nature of matter?

Sub-atomic particles

It has been determined in research that has been carried out since the 1930s, as a result of collisions in particle accelerators, that the quark is the smallest particle. Another, theoretical, way to obtain the quark would be to heat matter to a trillion degrees Celsius and, break the matter down as much as possible. But in today’s conditions this is not possible. Therefore, the theory of Big Bang first came about as an idea that said: “There must have been extremely hot temperatures, or more accurately, there must have been very great and sudden explosions that caused these hot temperatures during the first creation of matter.” This idea has been widely accepted among physicists. At the end of the 20th century, it was realized that the same situation is valid for anti-matter. It was also obvious that matter and the organization and continuity of its mirror image, anti-matter, cannot be explained by mere coincidence.

Studies on matter and anti-matter

Matter can be defined as the intensified condition of energy and which can be converted to energy again (E=mc²). The reactions of fission and fusion² mean the transformation of the one-thousandth or one-ten thousandth of a mass into energy (the rest is transformed into other masses). However it is possible for matter to combine with anti-matter and be transformed into energy with 100% efficiency. So what is anti-matter? In 1931, Paul Dirac started to make predictions about the existence of a strange group of particles that he called anti-matter, as a result of theoretical studies.³ After Carl Anderson of the California Technology Institute carried out studies that supported Dirac’s ideas began to attract attention. But not liking publicity and being a retiring type, Dirac did not encourage the media to become interested in this subject-he had earlier turned down the Nobel Prize. Today, Dirac’s name is known only by those who are expert in the subject, but anti-matter is one of the deepest secrets of modern physics. It is not difficult to understand anti-matter, in spite of the fact that it is often presented as a very complicated subject. In some cases, the particles of anti-matter are the same as those of matter-for example, mass. In anti-matter the situation of properties such as electrical charge,⁴ magnetic moment,⁵ and spin,⁶ which are related to the main particles, is the opposite of the main particles of matter. The greatest difference is that the electrical charges are opposite. The nucleus of anti-matter is negative, not positive. In its orbit there are positrons with positive charges, not negative. The existence of anti-matter has been proven with particle accelerators.

Physicists have been able to obtain very small amounts of anti-matter by breaking down the sub-atomic particles with a speed close to that of the speed of light in CERN (European Organization for Nuclear Research, Geneva) and in the Fermi Laboratories (USA). Just as the system of matter was created from very small sub-atomic particles, anti matter was also created from very small anti-matter particles. The only difference between them is that their charges are opposite. As soon as the very small and very fast main particles of both matter and anti-matter come into existence, they cannot survive long and immediately become energy (in one-billionth of a second) and disappear with the ambiguous physical aspects; this is because they are not suitable structurally or functionally for the conditions of the universe, which has already cooled. In order to determine this, particles without mass or those with very small masses which were obtained after collisions in the particle accelerators were kept in very special conditions; the lightest matter in the universe, that is hydrogen, and the anti-matter of hydrogen (anti-hydrogen atoms) were synthesized (a hydrogen atom is the proton itself). However, all these processes are very expensive. The life of nine anti-hydrogen atoms that were produced in CERN in 1995 was just 40 nanoseconds (one forty-billionth of a second). One million anti-hydrogen atoms were produced in the same laboratories. Their total weight was just one quadrillionth of a kilogram (Weed, 2003). As of 2005, the yearly global production of anti-hydrogen atoms was approximately one hundred billionth of a kilogram and it costs one quadrillion dollars to produce on ounce (28.3 grams) (Berman, 2005). In almost all Big Bang models, it is estimated that equal amounts of matter and anti-matter were created in the time-space universe that existed 14 billion years ago. Taking into account the scale of the universe, the fact that everything was created in pairs seems logical. But apart from the anti-matter that “appears and disappears” in particle accelerators, there is no trace or mark of this. All the anti-matter that is thought to have been created with matter at the beginning seems to have disappeared in less than a second, even if the universe came into being with the Big Bang or something else. So where has all this anti-matter gone and how did it happen? The studies to understand this continue. One of them is related to the radioactive beta decay of weak nuclear force, which is accepted as one of the four fundamental forces. During this decay, a neutron in the atomic nucleus becomes a proton, but the time in which it does this is unpredictable. Meanwhile, an electron and a particle called the anti-neutrino⁷ are emitted from the neutron. In some rare isotopes, we see double beta decay. In this process, both neutrons in the nucleus decay at the same time, which means that they are converted to protons, with two electrons and two anti-neutrinos are emitted at the same time. Physicists have been experimentally observing double beta decay for more than 20 years. However, Hans Klapdor-Kleingrothaus and his colleagues from the Max Planck Nuclear Physics Institute (Heidelberg) say that they have been observing a different version of double beta decay and claim that no anti-neutrino appears in this experiment. This process was predicted by the Italian physicist Ettore Majorana in 1937, but he found it impossible to prove it. The Heidelberg team now says that they have succeeded this. The important thing about the matter and anti-matter relationship is this: if one or two anti-neutrinos are emitted from the nucleus during a normal beta or double beta decay, this means that there is a neutrino in each neutron. On the other hand, in double beta decay, in which no anti-neutrino is emitted, an anti-neutrino appears as a result of the decay of the neutron and is absorbed by another neutron without being able to be emitted; this is contrary to well-known laws. Did the Divine Power hide anti-matter in this way? If the results are correct, double-beta decay that does not emit anti-neutrino apparently indicates that the neutrino, which is hidden in the structure of the neutron, has a different place among the fundamental particles of matter.

Physicists state that the interactions and decay of matter and anti-matter are dependent on special laws, such as the preservation of energy and the number of leptons.⁸ These laws say that the duration of the exchange of matter and anti-matter is equal to time dating back to the beginning of the universe (the Big-Bang). When we look at the emission of a neutron, we can see that anti-neutrinos indicate the same number of neutrons that at the beginning each absorbed a neutrino. The results attained by the team in Heidelberg may help us to explain why the universe is full of matter and not anti-matter and why there is no visible anti-matter.

Why matter and anti-matter?

It is difficult to store anti-matter in great quantity and it is also dangerous and costly; if anti-matter comes into contact with matter, both disappear and release a great deal of energy. Dirac thought that anti-matter masses could be hidden in remote places of the universe. At this time this was a reasonable hypothesis, as a galaxy created out of anti-matter could not have been differentiated from a normal galaxy. Spectroscopic analyses at that time did not reveal any differences. But today it has been claimed that anti-matter is infrequently found in outer-space. The contact between electrons and positrons produces gamma rays with an energy equivalent to 511,000 electron volts. If anti-matter were galaxies to exist, they would interact with the usual particles that swim through intergalactic space and would cause gamma ray circles around existing galaxies. These kinds of circles were looked for, but nothing was found. We live in a new universe of matter (Berman, 2005). Marc Lachièze-Rey, the French astrophysicist, says that, “If there were any antimatter asteroids in our galaxy, they would emit x-rays that we would be able to detect as soon as it disappears with its material,” (Poirier & Greffoz, 2001). The current explanation of the physicists about the domination of matter over anti-matter in the universe has the laws of physics arranged in favor of matter. When a team from the Stanford Linear Accelerator Center (2004) determined a minor but distinctive difference in the behaviors of some matter and anti-matter particles, this explanation was supported. This result implied an arrangement in which the material side overpowered the laws of physics. In terms of the causes operated being dependent on these laws, a universe that includes so much anti-matter would be very dangerous; when matter and anti-matter contact, the result is the transformation of matter into energy (E= mc²). It means a release of energy 143 times greater than a hydrogen bomb. If a marble that weighs an ounce collides with an equivalent anti-marble, 50 billion times a trillion erg of energy is released as a result of this reaction; this is enough to light all the electric bulbs in the US for a day. (Berman, 2005). In fact matter and anti-mater are similar to one another. Nobody has been able to explain why matter is dominant over antimatter instead of the other way round. Today, theoretical and experimental physicists predict that the half of the universe has been lost and the last time that it was seen was at the time of the creation of the universe. Matter and its opposite-charged anti-matter demonstrate that there was a certain predestination at the beginning of Creation, to be more exact before the Creation, in terms of knowledge, power and creating. This means that matter and anti-matter cannot exist by themselves. All the causes from the beginning were gathered to reveal a “universe of matter” (not a “universe of anti-matter”) that we can spiritually and intellectually comprehend. Anti-matter and matter demonstrate that they were created with a knowledge, will and power that existed before the creation. Otherwise, how could the first subatomic particles like hadrons, then the protons and the neutrons, then the atomic nucleus, after that the atomic system and the molecules in the sea of quarks, which are thought to be the most transparent, the most scattered, but at the same time the most fluid state (this is what can be predicted by looking at the results of particle collision experiments) of matter that appeared as the result of the Big Bang and under very great temperatures (trillions of degrees Celsius), have been formed? How could the laws that operate as the causes of this universe, a realm of symmetrical matter and antimatter, and then the structures and functions that became dominant have been formed? Could the sea of quarks (maybe the ether), which is the basis of matter, have been transformed by itself into organizations of new matter in the shape of nucleus, atomic system, and molecule only as a result of a decrease in temperature?⁹ Even if the temperature decreased, the sea of quarks could have remained the same, considering its structure. The cause and effect relationship-which we explain with the present physical laws-about temperature changes or about different states of matter may not have existed. Could the quarks have established this law? If the existence of matter and space¹⁰ occurred as a result of the Big Bang and a heat of trillions of degrees Celsius; how, when, for what reason and in which physical realm did this accumulation of energy happen? If there was no physical realm before the explosion, does physics stem from the metaphysics? Yes! The universe was created from nothing. Even if we search for the answer to this question in terms of the exact sciences, we again arrive at the same answer. The universe was created! These questions are not being asked for the first time. However the “hand of science” cannot grasp metaphysics (or pre-physics). Another interesting point here is this: the events on the large scale of the galaxy or even of the universe are trying to be understood by studies on a small scale (such as with sub-atomic particles) and by collisions in accelerators. We can say that small particles contain the index of the entire universe. Moreover, the studied particles do not individually exist. They were in the conditions of the high temperature. We can also say that, if we go in depth in sub-atomic particle studies, the existence of the particles that have very small mass (one quadrillionth of a kilogram) or those with no mass, are very rapid and have a very short life; this makes us think that matter can be created out of nothing at any moment and can be transformed into larger particles that have a greater mass. Most importantly, if we had not seen the activities in the sub-atomic realm we would not be able to understand that God’s Knowledge, Will and Power have penetrated everywhere at all times. If the sub-atomic realm had been static and inactive, God forbid, we would think that this realm was left to its own devices or that the Divine Power could not reach here. If God had not created such small, quick particles that can come into existence at any moment and be transformed into something else, we would not be able to comprehend the greatness of His Power and the intricacy of His Knowledge and Calculation.

References

• Berman, B., “What’s the Antimatter?” Discover, Vol 26, No 10, October, 2005.
• Weed, W.S., “Startrek,” Discover, Vol 24, No 8, August, 2003.
• Poirier, H. & Greffoz, V., “Asteroïdes: La menace se précise,” Science & Vie, No 1006, July, Paris, 2001.

Notes

1. This before and after relationship is valid; Our Creator, Who created the time, is not bound by time.
2. The slow chain reaction fission (the division of atomic nucleus) is the working principle in nuclear plants and it is the working principle of atomic bomb as a rapid chain reaction.
3. In 1928, Paul Dirac also predicted the existence of the positron, the anti-particle of the electron. This prediction was proven by physicist Carl Anderson at California Technology Institute in 1932.
4. The electrical charge is the application of the force of a matter on another matter, and the unit is the coulomb (C). A body is charged with electricity as a result of friction, induction, or chemical change. The charge itself shows an electron unit on the body (negative charge) or loss of electron (positive charge). The static electricity that we see when putting on an acrylic sweater or combing our hair is the result of the loss or gain of an electron from surface atoms. A charge flow, such as the passing of electrons from a copper wire, is electrical current and its unit is the ampere (A).
5. Magnetic momentum is the effect that happens dependent on the length and force of the magnet.
6. Spin is the natural angular momentum of a sub-atomic particle, such as a proton or neutron, of an atomic nucleus, an atom or a molecule; spin continues to exist even if the particle becomes inactive. A particle, in a certain state of energy, has a spin peculiar to itself as well as having an electrical charge and mass.
7. The neutrino is one of the three uncharged main particles (and one of the three uncharged anti-particles) belonged to leptons and it has a very small mass (almost zero). The three types are electron neutrino, muon neutrino and tau neutrino. The anti-particle of an electron neutrino is the anti-neutrino that is emitted during the beta decay of a nucleus.
8. Being one of the fundamental particle types that are not affected by strong nuclear forces, leptons correspond to the electron, muon, tau and the neutrinos of these three particles and also to the six anti-particles of these. In July 2000, direct proof of the tau lepton was obtained in the Fermi Laboratories. The muon, on the other hand, is a fundamental particle similar to the electron except for its mass. It is 207 times greater in mass than the electron. Its half-life is two millionthof a second. It is transformed into electrons and neutrinos at the end of this period of time. Although it is thought that the muon is a meson in origin, it has not been classified as a lepton yet. Meson is an unstable sub-atomic particle group consisting of a quark and anti-quark. Its existence was determined by cosmic radiation and it is emitted by a nucleus that has been exposed to the bombardment of very high-energy particles. The sub-class of hadrons, mesons, includes kaons and pions. Their existence was predicted by the Japanese physicist Hideki Yukawa in 1935.
9. It seems that the existence of matter and anti-matter causes the high temperature present at the beginning to drop and the combination of the sub-atomic particles (nuclear synthesis). The encounter of matter and anti-matter causes high energy. Therefore, we can understand that a very large explosion (the Big Bang) and very high temperatures were the conditions at the beginning of time.
10. Today physicists accept that matter was created out of nothing and in the space in which it was embedded.

A group of scientists attempted to do just this; they used focused electron rays as their writing implement, rather than a pencil. Some researchers at Liverpool University developed a power source that can draw a line of light no thicker than the width of two atoms. This line is so narrow that if millions of them were to come together they would still fit inside the line drawn by the thinnest pencil lead. Drawing such lines would certainly not be something one could do by hand. The smallest vibration would cause the lines to converge. The only way to successfully do this is to send the electron rays by computer.

If we think that nearly 4 trillion atoms can fit on the head of a pin, which is accepted as being equal to one millimeter square, then we can understand how small atoms are. If we arrange the atoms as squares consisting of 100 atoms each, with 10 atoms at every edge, this means that we can get 40 billion of these squares on the head of a pin. We then put one letter into every one of those squares, with some squares being used as blank spaces between the words. If we think that on average there are six letters in a word, we can use 4.7 billion words to fill only 28 billion of our squares. There are nearly 50 million words in the Encyclopedia Britannica. Previously, it was thought that it would not be possible to fit the encyclopedia on the head of a pin, but now we can see that only one percent of the pinhead would be used up. Even if every letter were written ten times larger, it would still fit on the head of the pin. What a huge area a pinhead is! To see if their theory would work the researchers at Liverpool University placed one page of the encyclopedia on the pinhead.

One may wonder what use writing an encyclopedia on a pinhead could possibly be. We wouldn’t be able to read it, so is it not just a futile exercise? In the future, this technology may lead to some new developments, but for now, we can give an example about how this technology could be used by looking at the works of art created by the Divine Power. One of the wonderful examples of “books” in which atoms are used as letters is in the cell of a chromosome. God Almighty writes with His Pen of Power the coded programs and characteristics for living beings in the DNA molecules. The Human Genome Project has made it possible for us to read the genes in chromosomes; each of these can be compared to a library or a data bank. This development has shed a great deal of light on the biological secrets and features of the human being, which can be considered to be a “minor universe.”

How can so much knowledge fit into the DNA? DNA molecules are found in the chromosomes, which are packaged in the form of chromatin in the nucleus of a cell. If a DNA molecule was unfolded and each piece was to be laid side by side, it would measure up to 6 meters. In order to understand how many atoms can be found on such a long DNA, the following example may be of some assistance: if we place 75 million hydrogen atoms next to one another we make a hydrogen chain that is 1 cm. long. As each chromosome is 6 meters, and there are 46 chromosomes in a cell, the total length of the chromosomes in just one cell is approximately 300 meters. Now, if we remember the two-atom wide line drawn by the researchers at Liverpool University with the electron rays, (i.e., a million times thinner than the line drawn by a pencil), then we can imagine how small the DNA chain is in its folded state. In fact, this means to compress human being called micro cosmos as chromosome in 1/100.000 or 1/1.000.000 of one cm. Of course, this miraculous task is not the work of lifeless and unconscious beings called atoms or the result of confused coincidences, but must be the work of God, Whose every job is miraculous and Whose knowledge and power is eternal.

The Qur’an on an atom

Now, can the Qur’an be written on an atom? Since atoms are too small to be seen with the naked eye, let’s think of an apple that is the size of the earth; thus we will better be able to see the atoms, and the subject will be more easily understood.Like everything, an apple is also made of atoms. In such a huge apple, an atom is the size of a football. But still we cannot see the nucleus of the atom, including the neutron and proton. The space between the nucleus and the electron is a vast distance in the scale we are using. The radius of this distance is a ratio of 1/100,000 for the electron to the atom. If we imagine this electron to be in the size of a marble with a radius of 1 cm, this means that the nucleus is 1,000 meters away from the marble. When we enlarge the nucleus to the size of a football, the smallest atom (e.g. the hydrogen atom) is a sphere with a 2,000 meter radius. Then, how many Qur’an copies can we write using electrons, which are as big as marbles, or neutrons and protons which are 1,836 times larger than electrons, as letters. The Qur’an can be written 10 times, maybe even a 100 times on such a huge surface. One of the important things to note in these examples is that atom are almost entirely hollow. If we try to fill atom with nuclei, we need as many nuclei as 1015. If we write the Qur’an not only on the surface of the atom, but also on the inside and the cavities of that huge sphere, then thousands of Qur’an copies, each of which has 300,620 letters, can be written using atom nuclei as letters.

Amazing similarity

There are a hundred trillion cells in one person, whereas, the science of the human being can be summarized in just one cell. But from the aspect of what is contained in just one cell, the human being is more profound than the greatest written works. If a cell were conscious, most probably it would be just as amazed that it can be the index of humans as we are amazed at the concept that we are the index for the universe.

A human being is 1028 times larger than an atom. The sun is 1028 times larger than a man. This cannot be coincidence; therefore, must there not be some relation between the human, the atom and the sun?

The world is nothing more than one point in the solar system; a person is also like one point in the world. The Owner of the Book of the Universe, when summarizing this Divine Book known as the universe, encapsulated it in the human being, and when summarizing humans He encapsulated them in the tiny book written with the atoms called the genome. It is an interesting fact that the Exalted Creator created the solar system similar to the system in the atom. This indicates that the Creator of the universe is the same as the Creator of human beings. He created spheres like the sun and all other complicated systems and the atom to make us think about His artistry and to astonish us with their beauty.

When speaking of a huge emptiness in between the elementary particles, the French philosopher Jean Guitton (1901–1999) gives the following example:

Think of the proton of the oxygen nucleus as the size of a pinhead; then the rotating electron would draw a circle that traverses the Netherlands, Germany and Spain (assuming that the center of this orbit was France, as Guitton lived there). Therefore, if all the atoms that make up my body were close enough to touch one another, you wouldn’t be able to see me at all. [I] would be a particle of dust, just one thousandth of a millimeter.

If we could enlarge an apple to the size of the world, each atom, proportionally, would be the size of a football. We would then be able to learn everything about the atoms by taking one of those atoms and examining it in our hands, wouldn’t we?

No, we wouldn’t!

It isn’t this easy. Even if an apple were to be the size of the world, it would still be too small to attain enough information about its atoms. If we want to see the nucleus of the atom, we must enlarge it to the size of a town, not a football. Then the nucleus, which is the size of a football, is in the middle, and one of the electrons, orbiting 1 kilometer away, would be no larger than a walnut.

Now let’s apply this example to the hydrogen atom, which is the smallest atom. If the nucleus of a hydrogen atom were enlarged to the size of a football then the atom itself would be a sphere with a diameter of 2 kilometers.

Quantum field

The discovery of the atom is in fact the discovery of empty space. It might sound strange to hear the words “huge” and “emptiness” in the same sentence when talking about the atom.

One night, a pessimist, an optimist, and a physicist were looking at the cloudless sky. The pessimist said, “What a great emptiness,” while the optimist said, “There are countless stars.” The physicist, on the other hand, couldn’t say anything, because he wasn’t sure whether what they had seen was a vast amount of objects or a vast field of emptiness.

The developments in modern physics in recent years have changed concepts such as, “substance,” “particle,” and “vacuum.” Vacuum is usually defined as “the living environment, life breath, or energy” of the universe.

The vast vacuum that physicist sees in the sky is what we call the quantum field

The quantum field is formless and shapeless. It is the field of all forms and the basic essence of the universe. The durable and solid substance that we call a particle is the condensation of this field into small units. The quantum field is the environment of activity, transportation, and communication, all at the same time. It is noteworthy that this approach is very close to the ancient approach that claims that space is full of ether.

Albert Einstein defined matter as the space region in which this field was extremely condensed. According to the understanding of the new physics, both the matter and the field of the matter are the same thing.

According to quantum physics, all matters in space are like islets in an ocean, and are connected to each other through subjacent earths. In the concept of a quantum field, space is a stable integrated whole and unity of waves and these interactions happen in “waves.”

Vacuum is not emptiness

The vacuum was once believed to be a place with nothing inside it. However, the universe has a beginning, and everywhere in this universe was once a single place that later came into existence. Therefore, it is impossible for a place in which “there is nothing” to exist in the universe. In brief, subsequently, there must have been something everywhere that has been created. Just as there is no dry place in the sea, there cannot be any emptiness in this sea of existence that was created out of nothing. Underlining this truth, quantum physics defines the universe as a whole and says there is no emptiness in the absolute sense. In other words, the universe in which there is no “empty” space is a world that has been “called into being.”

If everything around us, even human beings, consists of atoms, most of which are made up of emptiness, and if in fact the actual physical structures that compose our bodies are so few, then why can’t we go through walls or closed doors, like cartoon characters? What makes matter so solid and durable?

In fact it is not easy to answer this question. Electrons are created in small places, like atoms, and have been given phenomenal speed. An electron moves at 1,000 kilometers per second (that means it rotates one million times around the nucleus). As a result of this phenomenal speed, the atom becomes a tough and solid mass. We can compare this to airplane propellers that appear to be a solid and flat surface when spinning.

The amazing electron

The features of electrons, such as being able to pass through two holes in an obstacle at the same time (no other particle can do this) have astonished scientists and brought out a metaphysical dimension that are beyond the wave nature of light. The granular structures of subatomic particles contradict the understanding of matter. According to the findings of quantum mechanics, the particle is in fact nothing but a dynamic effect and movement. The particles can be composed of energy or they can be entirely converted to energy. The classical concept of elementary particle is becoming obsolete in today’s world.

Nevertheless, the changes in our perception of matter do not necessarily mean matter is unreal. The truth is that particles of matter do not have a constant reality or an independent essence, in contrast to what has been assumed. Whatever seems to be or is reflected as matter, energy, or value, or whatever we call it, is nothing but the manifestation of the Divine Names of the Creator Who created “nothingness.”

Think of a shadow play. The image that the audiences see on the curtain, which is far from the source of light, is not “real.” The real thing is another object that is in front of the source of light or behind the curtain. What we see is the reflection of the object itself or its movements. If we don’t know how this play has been staged, we may think that the image on the curtain is real. Even though there is an image on the curtain, it does not have its own existence and is not real. In the same way matter exists but its existence and its being in this condition is not something under its control.

Before the realm of the quantum was discovered, Newtonian physics had accepted matter as being solid, durable, and constant. Everything we touch, such as walls, trees, and all the objects we see have the solid and durable condition of matter. But if one looks at an object through an electron microscope, they will see that 99% is vacuum and 1% is light. We can form circle of light if we swing a light source in a dark room. If we add a second, third, and fourth source, and move them so that they can form illuminated spheres, someone who is observing from a distance will perceive a three-dimensional sphere instead of a two-dimensional illuminated circle. Thus, we can understand that by increasing the number of spheres we form a three-dimensional model of matter. According to quantum physics, matter found in the universe is pretty much like this example. In short, matter does not consist of a combination of solid particles. There is almost no difference between the “building stone” of human beings and the image of human on television. And we can say that just as the television broadcast disappears when there is a power cut, it is also possible for this universe, which seems so permanent, to disappear with one command.

A television broadcast is constantly being renewed through the transmission of pictures and sound by means of electronic signals. As in the example above, if our existence is like the image on television, then can we say that the universe is also being renewed every second like a TV broadcast?

None of the objects we see (trees, birds, humans, etc.) take their existence from the concrete reality of the matter that we perceive. Thus, they must receive their existence from the power and the names of the Creator Who creates everything out of nothing and keeps it in perpetual motion. In brief, although created out of nothing, existence is being created all the time.

Metaphors also play an important role in science. Cognitive scientists, who continue to research how language evolved and which tools the mind uses during this process, state that metaphors are widely used tools. Scientists use language, as well as graphs and equations, to explain their models. Therefore metaphors are essential in learning and teaching science. In this article, we will present a few examples of metaphorical thinking in science and how it guides science in new directions that could lead to breakthroughs. We will be concerned mainly with the machine metaphor that affected the way we picture the world.

A short history

Metaphor derives from the Greek verb methaphora (to transport or transfer). George Lakoff, professor of linguistics at the University of California”Berkeley, and philosopher Mark Johnson explain the essence of metaphor as understanding and experiencing one kind of thing in terms of another. We generally use analogies to make less familiar things appear in guises that are more familiar to us. For example, we try to picture time by associating it with a river. Chemists extend their knowledge of a poorly understood compound by finding similarities with familiar compounds. Biologists use biological mechanisms found in organisms to understand similar mechanisms in others. Luigi Galvani associated the transmission of nerve pulses to an electric current.

Metaphor can be defined as the mapping of a source domain onto a target domain. Throughout the history of science, water waves were used prototypically for understanding light waves. People tried to understand light (target domain) in terms of water waves (source domain). This mapping forced scientists to search for a medium”ether”that could propagate light waves, for water waves were propagated in water.

According to the English physicist Norman Campbell, every scientific theory requires the use of models to understand theoretical terms. For example, in order to comprehend the kinetic theory of gas, we must resort to an analogue model gas behaving as if it were composed of point particles randomly moving in a vessel. Metaphorical models help to improve the scientific imagination. But for scientists to take a model seriously, it must be expressible in terms of mathematical equations.

Sometimes, the symbolic representation of a mathematical relation can lead to a metaphor. For example, the space is time metaphor has an interpretation in molecular biology where millions of years (time) are encoded and contained in DNA (space). In addition, metaphors offer insight into mathematical phenomena. The basic example is the number line, which is the result of imagining numbers as points on a line.

The machine metaphor

From the seventeenth to the nineteenth centuries, the dominant metaphor was the machine metaphor: The world is a machine. This connection was made by Galileo (d. 1642), Descartes (d. 1650), Boyle (d. 1691), and Newton (d. 1727). They imagined the universe as a static, predictable machine. This worldview influenced our beliefs and psyche, as well as the way scientists, philosophers, and other intellectuals thought. Scientists started to think of everything in terms of a machine. Muscles were considered to be force-generating machines, nerves to be electronic machines, and photosynthesis to be a solar-powered machine. Lord Kelvin (d. 1907) characterized the universe as a galactic heat engine.

The machine metaphor led to reductionism in philosophy: If we wish to understand how a machine works, we look into its component parts. Descartes’ analytical method of reasoning is based on the assertion that complex phenomena can be understood by reducing them to simple phenomena. Biologists tried to understand living organisms, as well as bodily motions and functions, by reducing them to their constituents. More research was devoted to understanding the nature of genes. Physicist reduced gases’ properties to the motion of atoms or molecules. Locke (d. 1704) attempted to understand society by observing the behavior of individuals.

With the picture of a perfect world-machine, belief in a Creator became a logical necessity, since the machine implies an engineer. Even children know, as a part of their personal experience of reality, that a house implies a builder and a watch a watchmaker. As they study the more intricately complex nature of the human body or the ecology of a forest, it is highly unnatural to tell them to think of all these systems as chance productions of irrational processes.

Theologian William Paley (d. 1805) expressed this creationist view on page 98 of his Natural Theology as: There cannot be a design without a designer; contrivance without a contriver; order without choice; arrangement without a thing capable of arranging … Arrangement, disposition of parts, subserviency of means to an end, relation of instruments to use, imply the presence of intelligence and mind. This Cartesian philosophy connoted the idea that The Hand of God had set the machine in motion at the beginning of creation. As everything had been determined by God already, nothing could be the result of chance. This view is known as determinism.

The computer metaphor

The computer, the current dominant machine, has become the modern era’s dominant metaphor. Visionary physicist Edward Fredkin characterizes the universe as a cosmological computer. The universe appears as a network of a dynamic whole whose parts are essentially interrelated. Modern physicists do not consider the atom a basic building block; rather, it is a web of relations that includes human consciousness in an essential way. Modern biologists describe cells as distributive real-time computers. Making good use of the computer metaphor, they focus more on how neurons work together and how each cell interacts with its environment.

Sociologists study individuals and their social relationships. Psychologists and cognitive scientists use the analogy of a computer to understand the mind. Artificial intelligence is just one consequence of such modeling. The universe is no longer seen as a simple mechanical machine, but as a more complex high-tech computer system.

The computer metaphor supports the view of a dynamic universe more than Newton’s static universe. James Maxwell’s (d. 1879) electrodynamics, the second law of thermodynamics (entropy), and Darwin’s (d. 1882) theory of evolution all involve dynamic concepts. Entropy describes the evolution of inanimate matter and states that inanimate systems tend to go from order to disorder. Entropy is an increase in disorder became a root metaphor at the beginning of the nineteenth century.

Biologists describe evolution as a movement toward increasing order and complexity. Darwinian theory attributes biological complexity to the accumulation of mutations by natural selection. One factor that makes Darwinian theory a naturalistic philosophy more than an empirical science is its claims that all of these dynamic processes are a result of random chance. Natural selection is introduced as the mechanism that minimizes the effect of chance. According to Darwinism, probability governs the universe and there is no need for God.

There are probabilities in the quantum world as well. However, probability and uncertainty show the unpredictability of the outcomes of quantum measurements from a human perspective. This probabilistic vision of universe, contrary to Darwinian theory, deepened the consequences of the machine metaphor: God not only set the machine in motion eons ago, but is still governing the process of creation and changing the probability pattern.

Metaphors and paradigm shifts

According to Thomas Kuhn (d. 1996), metaphorical thinking becomes crucial at periods of scientific revolution and gives way to a paradigm shift. Distant analogies are probably the most useful in times of scientific revolution: Newton’s metaphor of an apple is a moon is of this kind. However, this metaphor became literal after it was understood that the same gravitational force that holds the apple to Earth is the same one that holds the moon in its orbit around Earth.

Kuhn’s paradigm shift and use of metaphors can best be seen in the history of exploring the atom. The atom was conceived first by Democritus (d. c. 370 BCE) as an impenetrable sphere. This analogy was used to explain the behavior of matter until the nineteenth century. Spherical analogy was discarded in favor of Ernest Rutherford’s (d. 1937) analogy between the solar system and the hydrogen atom.

The following interpretations followed the planetary model: The nucleus is more massive than the electron (just as the sun is more massive than the planet), the nucleus attracts the electron, this plus the mass relation causes the electron to revolve around the nucleus, and so on. Object descriptions are disregarded, for there is no attempt to match the nucleus with the sun in color, size, or temperature. Then, the atomic nucleus was analogized to a drop of water instead of to a body like the sun.

Now, in quantum mechanics, every particle is considered to be a probability wave, which is an abstract mathematical quantity. Scientists have not yet been able to put these waves into a metaphorical pictorial model, which makes them difficult to comprehend.

Metaphors in revealed texts

The following Qur’anic verses illustrate the use of metaphors in the Qur’an. Speaking of hypocrites who do not believe in God but nevertheless claim to believe, it states: Their parable is like the parable of one who kindled a fire, but when it had illumined all around him, God took away their light and left them in utter darkness”they do not see. Deaf, dumb (and) blind, so they will not turn back. Or like abundant rain from the cloud in which is utter darkness and thunder and lightning. They put their fingers into their ears because of the thunder peal, for fear of death, and God encompasses the unbelievers. The lightning almost takes away their sight. Whenever it shines on them they walk in it, and when it becomes dark to them they stand still. If God had willed, He would have taken away their hearing and their sight. God has power over all things. O people, serve your Lord, Who created you and those before you so that you may guard (against evil) (2:17-21).

Conclusion

Logic and mathematics are not enough to understand science. We need internal mental pictures to grasp new phenomena. When trying to understand unfamiliar phenomena, the mind thinks of them in metaphorical terms. This not only helps to explore new realms for scientific theories, but also can change the view we hold of the world.

References

• Behe, M. Intelligent Design Theory as a Tool for Analyzing Biomedical Systems. InterVarsity Press, 1999.
• Gentner, D., & Clement, C. (1988). Evidence for relational selectivity in the interpretation of analogy and metaphor. In G. H. Bower (Ed.), The psychology of learning and motivation: Advances in research and theory (Vol. 22, pp. 307-358). New York: Academic Press.
• Hesse, Mary. Models and Analogies in Science. University of Notre Dame Press: 1966.
• Belal A. Baaquie and Lai Choy Heng, Department of Physics, National University of Singapore Method and Anti-Method in the Sciences: Metaphors and Scientific Creativity. http://www.scholars.nus.edu.sg/natureslaw/methodology/anti_method/11.html
• Lakoff, G. and Johnson. Metaphors We Live By. University of Chicago Press, 1995.
• Morris, Henry, ed. Scientific Creationism. 2d ed. Word Publishing: 1974.
• Paley, William. Natural Theology; or, Evidences of the Existence and Attributes of the Deity. Online at: www.hti.umich.edu.