As far as the origin of language is concerned, Abrahamic traditions agree on the fact that language is a gift of God to humanity. To exemplify, the Holy Bible in Genesis 2:20 (King James’ Version) states that: “[20] And Adam gave names to all cattle, and to the fowl of the air, and to every beast of the field; but for Adam there was not found an help meet for him.” Identically, the Holy Qur’an in Surah Al-Baqara (The Cow) voices the following verse: “And He taught Adam the names of all things; then He placed them before the angels, and said: ‘Tell me the names of these if ye are right’?” Both of these divine expressions indicate clearly that mankind was created from the beginning with an innate capacity to use language. Therefore, a theist from any level of society does not have any doubts about the origin of human language; for him the explanation is both simple and persuasive.

However, for those who do not subscribe to such a faith tradition, it is rather nerve-racking to come up with a unanimous answer as to the emergence of language since there are so many competing and contradictory theories and hypotheses. Efforts to explain the origins of language usually sound dubious and are collected under two main hypotheses in linguistics that are based upon human invention and necessity. According to the “pooh-pooh hypothesis,” the first words originated from involuntary exclamations expressing a human’s pleasure, dislike, pain, hunger and so on, which later on led to the expression of more complicated feelings and ideas. Given this, the first human words would have been involuntary “Aa!”  “ouch,” “ha-ha-ha,” etc., which were used to name the actions that resulted in these sounds. Yet, the problem with this thesis is that emotional exclamations not only constitute only a small part of any human language but also that they are highly language specific. Apart from sneezes, tears, and laughter, exclamations show variations among languages. For instance, English people say “ouch,” Russians “ol,” and native Indians “eee” to indicate sudden ache or discomfort. That is, their forms mostly hinge on a specific language that already exists rather than preceding language.

The second is Charles Darwin’s own “ta-ta hypothesis” (which he himself finds rather erroneous) about the origin of language. For him, human speech might have come from a kind of mouth pantomime according to which speech organs were used to imitate different forms of hand signs. That is to say, human language originated from body movements which were soon imitated by speech organs; therefore the first-ever words used to be lip icons of hand movements. However, here again we notice inconsistency because the meaning of human gestures vary from culture to culture, such as the “thumbs-up/thumbs-down” once used by Romans to decide upon the life of a defeated gladiator. While for Western people the “thumps-up” gesture implies a positive remark expressing mainly a task well done, it surprisingly has negative implications in Greece, Russia, Italy, Latin America and West Africa where it instead stands for the middle finger.

These are only two amid various other inconsistent hypotheses (which include the “ding-dong”, “bow-wow”, warning, “yo-he-ho”, and lying hypothesis) offered as an explanation for the origin of language. What is interesting is that in the late 19th century, the Linguistic Society in London and Paris forbade any commentary and debate on the emergence of human language for valuable time was wasted to find a sane thesis.

This reminds me of letters from the Islamic scholar Said Nursi in which he states that just showing the evidence is sufficient to prove the presence of anything; otherwise you have to inquire of the entire world so as to show its non-presence. In Islamic law, two witnesses are enough to resolve any skeptical case; this may be a lawsuit, a dispute, doubt or disagreement between people. For example, if two people testify that they have seen the crescent, which is the harbinger of the holy month Ramadan in Islam, there is no need to ask other people for verification of the same sight. Even if thousands of people oppose the sighting, it is worthless and does not change the truth. Perhaps, what Abrahamic traditions are teaching us on language is the only source to verify its origin.

Global Climate Report. NOAA National Centers for Environmental Information (http://www.ncdc.noaa.gov). July 2019.

It’s summer, and it is hot out there; but if it feels like record-breaking temperatures are becoming more common globally, they are. The National Oceanic and Atmospheric Administration and European Copernicus Climate Change Service announced that July 2019 was the hottest month across the globe ever measured since measurements began, in 1880. Global temperatures averaged 16.73°C in July, which is 0.95 °C higher than the 20th-century average of 15.78°C . Average Antarctic sea-ice coverage was 8.5% below the 1981-2010 average. And sea ice coverage was 10.5% below the overall average, which is based on records beginning in 1979. The scientists also released geographical data, showing that the regions where temperatures varied furthest from averages, were Alaska, Central Europe, Northern and Southwestern parts of Asia, and certain regions in Africa and Australia. These findings corroborate scientific predictions regarding the effects of man-made climate change. Human activities, primarily from burning fossil fuels, emit carbon dioxide and other greenhouse gases that trap heat in the atmosphere. Increasing greenhouse gas emissions are associated with warmer global surface temperatures. The planet’s 10 hottest years on record have all fallen in the past two decades. Scientists and policymakers around the globe are also feeling this heat.

Unless significant measures to curb greenhouse gas emissions are adopted, scientists expect temperature records to keep falling. Scientists say global temperatures could increase by at least 3°C this century, which will create conditions on Earth that have not been seen in more than 2 million years. Given the notable trends in higher temperatures and natural disasters, we might be pushing the climate system toward states that we haven’t seen in our societal experience – and even in our species’ experience.

Manipulation of brain circuits using smartphone-controlled device

Qazi R et al. Wireless optofluidic brain probes for chronic neuropharmacology and photostimulation. Nature Biomedical Engineering, August 2019.

Scientists recently designed a device that can regulate brain circuits using a tiny brain implant controlled by a smartphone. This bluetooth-enabled device utilizes replaceable lego-like drug cartridges to target neurons with drugs and light. Existing methods to deliver drugs and light to the brain typically involve metal tubes and optical fibers. These tools are rigid and can substantially damage the brain’s soft tissue over time. Moreover, this bulky equipment often limits the patient’s movement because of the wired connections, making them unfit for long-term use. To achieve chronic remote-controlled drug delivery without exhaustion and evaporation of drugs, scientists invented a neural device with a replaceable drug cartridge, which could allow neuroscientists to study the same brain networks for several months without depleting the drug supply. These “plug-n-play” drug cartridges were integrated into a brain implant for mice with a soft and ultrathin probe (about the thickness of a human hair), which consisted of microfluidic channels and tiny LEDs (smaller than a grain of salt), for unlimited drug doses and light delivery. The implant is regulated via a smartphone, allowing researchers to trigger precise combinations and sequences of drug and light delivery. In animal models, these stimuli can be triggered with the target outside of the laboratory, allowing researchers to wirelessly instill changes in the animal’s brain while in its natural habitat. Using these neural devices, researchers are now able to perform fully automated animal studies where the behavior of one animal could positively or negatively affect behavior in other animals by conditional triggering of light and/or drug delivery. This device will allow researchers to better dissect the neural circuit basis of behavior and how specific neuromodulators in the brain tune behavior in various ways. In addition, the device can be utilized in complex pharmacological studies to develop potentially new therapeutics for pain, addiction, and emotional disorders.

The secret weapon of E.Coli 

Melson E. at al. The sRNA DicF integrates oxygen sensing to enhance enterohemorrhagic Escherichia colivirulence via distinctive RNA control mechanisms. Proceedings of the National Academy of Sciences, June 2019.

Scientists have revealed how E. coli (Escherichia coli) bacteria seeks out the most oxygen-free parts of your colon to cause the worst infection possible. E. coli normally live in the intestines of healthy people and animals. Most varieties of E. coli are harmless or cause relatively brief diarrhea. But a few particularly nasty strains can cause cramps, diarrhea, vomiting – even kidney failure and death. Children are particularly at risk. A new study uncovers how this foodborne pathogen knows where and when to begin colonizing the colon on its way to making you sick. Bacterial pathogens typically colonize a specific tissue or organ in the host. Therefore, as part of their infection strategies, bacterial pathogens precisely time deployment of proteins and toxins to these specific colonization niches in the human host. This allows the pathogens to save energy and avoid detection by our immune systems and ultimately cause disease. The researchers in this study identified how E.Coli detects low oxygen levels in the large intestine and then produces proteins that allow it to attach to host cells and establish infection. Oxygen actually diffuses from the intestinal tissue into the gut, and there are comparably higher levels in the small intestine than the large. Remarkably, E. coli specifically waits until it has reached the-low oxygen large intestine before striking. E. coli controls this process via a small form of RNA that activates particular genes when oxygen levels are low. This is the point when the infection really gets established and the bacteria are able to begin to manufacture harmful Shiga toxins. The researchers predict that other bacterial pathogens, such as Shigella and Salmonella, likely utilize a similar control mechanism. Researchers suggest that if we can find a way to block oxygen sensing, we may be able to prevent the infection by allowing E. coli to pass harmlessly through the body.

One of the signs of anarchy in a region could be the marching of an army to get a particular situation under control and, if it is indispensible, destroy or suppress anarchists. Similarly, the first response of the body to such uncontrolled growth is the destruction of tumor cells by activating inner mechanisms that lead to cellular suicide (apoptosis). Anarchy is by definition not to accept any border and authority, causing disorder or upheaval. According to twentieth century thinker Nursi, anarchy cuts and throws away norms and laws that organize social life, one by one, thus destroying the order and leading to mischief and rebellion. In addition, anarchism does not consider the rights of any. Analogously, one by one, cancer breaks genetic rules that organizes cell proliferation and eliminates pathways that suppress tumor formation. Thus, it eradicates the order and triggers chaos and malignancy. Again, cancer works against the life of the body without considering the rights of other cells.

Another characteristic of anarchism could be the elimination of its leaders. Thus, once you get rid of the key players, anarchy may not resurface. Likewise, you can use a strategy in certain cancer types where you can specifically target cancer stem cells. As a result, cancer growth could be suspended and it may bring an opportunity to shrink tumor through chemotherapeutical approaches. One such example is the targeting of CD24, a putative cancer stem cell antigen expressed by a minority of adenocarcinoma cells. This cell-based cancer immunotherapy method uses genetically engineered cancer killing T cells, which are directed towards cancerous tissues using chimeric antigen receptors. This is similar to the taking over of trained Special Forces when anarchy becomes malicious and unceasing. Both natural and genetically engineered cancer killer T cells in our body resemble trained Special Forces that patients need to fight against cancer.

Cancer treatments

Cancer is nowadays mainly treated with chemotherapy, radiotherapy and surgery, and to some extent with immunotherapy. The many purposes of chemotherapy include relieving or preventing the suffering of the patient, prolonging the life span, and if possible, completely curing the cancer along with surgery or radiotherapy regimens. Chemotherapy mainly uses cytotoxic drugs that kill cells by attacking one of the main properties of cancer cells—rapid division. Unfortunately, since cancer cells are not the only rapidly dividing cells in the body, chemotherapeutic agents also harm healthy cells. Another fall back of chemotherapy drugs is the lack of specificity that does not provide a therapy against a specific cancer type and their efficacy vary from patient to patient. In these cases, the indispensable path is synergistic use of radiotherapy with chemotherapy.

As its name implies, radiotherapy involves the use of ionizing radiation to kill cancer. It relies on the destruction of dividing cells by introducing DNA damage, which leads to induction of cellular death through apoptosis. Radiotherapy is therapeutically useful in cancers that are localized to one part of the body. It is also useful to prevent tumor relapse after surgical removal such as in breast cancer. However, radiation, which radiotherapy depends on, is itself the potential cause of cancer and leads to various side effects.

Citizens of the body need justice

Chemotherapy or radiotherapy, which harms both healthy and cancerous cells, recalls the practice of absolute justice versus relative justice. Absolute justice requires protection of every individual while punishing the criminals. On the other hand, relative justice is the justice where the rights of one person are ignored for the betterment of the whole. Absolute justice is always the best practice if it can be properly established. However, relative justice may be sought if absolute justice is absolutely out of reach. Current chemotherapy and radiotherapy treatments are like the practice of relative justice, which harms both cancerous and healthy cells. Of course, these treatments are considered as the last resort for many cancer patients but this analogy regarding absolute justice toward cells in the body urges us to seek for cancer therapies that follow absolute justice. In other worlds, we need to practice an approach that is more specific toward cancer cells. This could be, as we mentioned above, the use of cancer immunotherapy where cytotoxic T cells are directed towards cancer cells through genetic engineering by introducing chimeric antigen receptors (CARs). CARs should be able to recognize unique or relatively specific antigens located on the surface of cancer cells to execute them.

Cancer killing T-cells: Equipped with chimeric antigen receptors

There are three main approaches in cancer immunotherapy including immunization, use of antibodies and cellular immunotherapy. Immunization by administering a cancer vaccine prepares the patient’s own immune cells to recognize tumor cells as targets to be destroyed. The use of therapeutic antibodies specific to cancer cells recruits immune cells in the patient to abolish tumors. Cellular immunotherapy, on the other hand, uses patients’ own immune cells like the natural killer cells, cytotoxic T cells and so on. Basically, those cells could be stimulated in patients with the administration of interleukins or they could be isolated from the patients’ blood and cultured in the laboratory and following expansion and in vitro training, then transfused back to the patient to fight against cancer.

Cytotoxic T cells are unique immune cells that recognize target cells via T cell receptors. Over the past decade, scientist engineered T cell receptors and developed chimeric antigen receptors that specifically recognize target antigens. This recognition lead to signaling pathways that resulted in apoptosis of tumor cell through the production of granzymes, perforins and cytokines such as IFN-γ, and TNF-α (Figure 1). There are a number of success stories using CAR+ T cells for cancer immunotherapy used in patients. Encouraging results were obtained with CARs targeting lymphoma (by targeting CD19 antigen), coleractal Cancer (by targeting CEA antigen), and melanoma (by targeting melanocyte-specific markers MART1, MELOE-1 and gp100).

Universal chimeric antigen receptors

Two recent studies published by two different groups increased the hopes in the battle with cancer. They developed novel and universal CAR technologies that combines cell based immunotherapy and use of therapeutic monoclonal antibodies. This new approach relies on the recognition of specific molecules such as FITC and Biotin by corresponding Anti-FITC and Anti-Biotin (Avidin) CARs. The decent thing about these specific molecules is that you can attach them to any antibody, ligand, or aptamer known to target specific tumor antigens (Figure 2). One of the universal chimeric antigen receptor, for instance, uses FITC, a fluorescent molecule widely used in flow cytometric assays. Since it is easy to label antibodies, this provides wide range of antibodies to target cancer cells. In addition, scientists using this approach could target more than one tumor antigen or could use another antibody that targets different antigen even if cancer relapses. Moreover, since antibodies used to activate CAR+ T cells will degrade and their bioavailability will decrease in the body by time, there will be no need to kill injected T cells with suicide mechanisms. Once FITC labeled antibodies are stopped from being given to patients, CAR+ T cells will stop attacking cells and cease-fire since their guns (CARs) cannot recognize tumors or anything nonspecific. This approach is highly encouraging and has brought with it great hopes in the treatment of cancer.

Anarchy, spirituality, and prayer therapy

Hunger, poverty, social inequality and economical issues could be asserted as the basis of anarchy within a society. However, according to Nursi, the real basis of anarchy is spiritual weakness and poverty. Similarly, the basis for cancer could possibly be the lack of appropriate spiritual diet that may eventually make a person fall spiritually and physically weak. For example, fasting is a physical and spiritual fast prescribed in monotheistic religions which increases spirituality and has been shown to be synergistically effective in chemotherapy with cancer treatments. It has been observed and scientifically recorded that patients with strong beliefs and continuous prayers and spiritual support overcome diseases much faster than those without. This raises certain questions regarding our spiritual makeup and many other dynamics involved in being sick and getting well. So, are we getting ill because some evil spirits are manipulating our biological condition by settling in the tumors and propagating cellular anarchy? Is radiation, which leads to cellular mutations, a result of spirits that are created of “scorching fire” (The Qur’an 15:27)? Is cancer a result of such manipulations and should we seek cure for it not only through biological medicine but also through spiritual healing?

Various scientifically proven causes are known to increase the likelihood of cancer, which includes, but is not limited to, smoking, viral infections, radiation, and pollutants that lead to internal genetic faults within cells. Considering the fact that there are many cases in which patients have been reported to have recovered from their illnesses by reciting prayers, then such cases are worth examining to find out whether and to what degree non-material factors are involved as causes for our illnesses. Studying these cases may offer science new opportunities to be able to remove the present obstructions and make greater advances in the medical field by perhaps developing cancer therapies that combine prayer therapy and cancer immunotherapy using genetically engineered T cells during the treatment of patients.

Ali Fethi Toprak is a PhD candidate at University of Texas Southwestern Medical Center.

References

Döğen, Şaban. 2005. “Bediüzzaman and Anarchy.” Köprü Dergisi, No 89.

Nursi, Bediüzzaman Said. Işarâtü’l-I’caz. Şahdamar Yayınları.

Chmielewski et al. 2012. “CAR’s made it to the pancreas.” OncoImmunology 1:8, 1387–1389.

Tamada et al. 2012. “Redirecting Gene-Modified T Cells toward Various Cancer Types Using Tagged Antibodies.” Clin Cancer Res.

Urbanska et al. 2012. “A universal strategy for adoptive immunotherapy of cancer through use of a novel T cell antigen receptor.” Cancer Res.

Gülen. M. Fethullah. “Cinler, Hastalıklara Sebep Olabilir mi?” Retrieved from http://tr.fgulen.com/content/view/708/3/ on 12/24/12.

Bukhari, i’tikâf 8, 11, 12; Muslim, Salam, 24; Ibn Maja, Siyam 65; Abu Dawud, Sawm 79; Adab 81; Muslim and related hadith narrated by Abu Hurayrah, Bukhari 7.582.

¹ See Yücel, Salih. 2010. Prayer and Healing in Islam, NJ: Tughra Books.

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.

Decisions within the cell: mathematical and algorithmic character

In order to enable Escherichia coli bacteria to use lactose (disaccharide), the genetic information of the enzymes that have role in transporting the lactose into the cell and converting it into glucose is coded in the bacteria’s genome. The binding and decoding structure which enables the genes to be transcribed at the right time in the appropriate amount is called the operon. The operons are model mechanisms which work on the synthesis or destruction of every chemical molecule (metabolite). One of these, lactose operon, is a good example that demonstrates how the decoding information contained in DNA is regulated and controlled in the bacteria. E. Coli is equipped with a system that distinguishes lactose and glucose when they are combined and this system functions perfectly. Primarily, all of the existing glucose is consumed before the start of the production of those enzymes that splits lactose into glucose and galactose. It has been discovered that this operation in the bacteria is followed by an interaction between DNA sequences located on the upper part of the lactose gene and various molecules. The DNA sequences on the upper part of the gene are the signals that format DNA for transcription. These signals cause the decoding of the genes that interact with the transcription factors. While some of the signals in the relevant region of the genes are common in most genes, some others are specific.

The most basic interaction system of the genome-proteome (all proteins in cell) is the suppression of the lactose operon that is observed in E. Coli. This process depends on DNA-protein interactions which are based on a mutual relationship and it requires the existence of repeated DNA sequences. Tetramer lac1 protein control the lac operon binds to four repeating binding regions on the DNA. Since one dimer can be connected to one operator sequence, two dimers are connected to two operator region units, and as a result the result is a loop formation in the DNA structure. Consequently, because of the access of RNA polymerase to the promoter region, the pre-coding process of genes is hindered. If the hindering protein is in the form of a monomer, the operator displays a weak interaction with half of the sequence. In the dimer form there is a stable binding. For this reason, many procedures in the cell occur by working together and making a union of molecules. Since the loop shape of DNA stabilizes the structure, it prevents the RNA polymerase from being connected to the promoter region. In order to eliminate the blockage on the lac operon, the mutual relationship must be prevented by stimulatory molecules, such as lactose.

There is metabolic information in cells that measure and control the physiological condition. The sequences on the regulatory region of the lactose operator and the data concerning the physiological condition of the lactose and glucose metabolisms are analyzed in the cell which perceives the presence and the amount of glucose through the changes in the system that transports the glucose into the cell. The molecule that announces the presence of glucose in E.coli is cyclic-AMP and concentration of this molecule in the cell is inversely proportional to glucose. The level of this signal affects both the coding and regulation of genomic information. The protein that transports glucose into the cell contains a phosphate group; as it transports glucose into the cell, this carrier protein phosphorylates the glucose molecule thereby loosing its phosphate group. As a result, the proportion phosphorylated transport protein and those without phosphate provides information about the glucose level in the cell. The phosphorylated form of the carrier protein activates the adenosine cyclase enzyme. Through this enzyme, ATP is converted into cyclic-AMP. The cyclic-AMP level increases in the cell. Consequently, the situation that concerns the increasing concentration of the phosphorylated transfer protein and the cyclic-AMP is interpreted as non-existence of glucose in the cell. The CRP protein that binds to regulatory region of the lactose can only bind to this region in the presence of cyclic-AMP. The cyclic-AMP-CRP complex which is tied to the promoter region of the lactose gene speeds up the transcription of the lactose operon. Transcription rarely happens when there is no lactose. This is because the lactose repressor protein lacI, hinders the RNA polymerase reaching the lactose promoter region by binding to the operator of regulating region. The cell can sense the existence of lactose in a circuitous manner. Low levels of coded Permease enzyme on the lacY region transfer some lactose into the cell. The coded beta galactosidase on the lac Z region alters them into a sugar called allolactose. The allolactose is bound to the lacI repressor protein and changes its conformation. The allolactose –lacI repressor complex can not bind to the operator region. The promoter region, called LacP, of Lactose operon is set free for transcription. In fact, every one of these molecular interactions is an incident of information being transferred. All these incidents demonstrate that an algorithm (If there is no glucose and only lactose exists, then transcribe the lacZYA enzyme) that is able to distinguish the difference between two sugars exists in bacteria cells and that it functions perfectly.

In short, the signal transfer in lactose operon occurs with the activation of chemical molecules that represent the experimental data pertaining to the physiological environment of the cells. For example, the levels of cyclic-AMP, allolactose and protein phosphorylation indicate the existence of glucose and lactose. The regulating network system, on the other hand, combines many aspects of cell activity (transport, enzymology, energy metabolism) in order to make the transcription decision. Briefly, it is impossible to show that arranging the order of the genome in any cell occurs independently from physiological or biochemical processes.

The principle of “using combinations in the arrangement of specific binding regions” is commonly used in metabolic signal networks that control cell physiology and the differentiation of cell (morphogenesis) that are oriented towards tissue formation. Such an interaction takes place on these network paths between proteins and DNA sequences to ensure that the cell is allowed to process molecular information and to calculate whether it will transcribe a specific genetic sequence. The common binding regions on DNA have vital roles in the coordinated control of various genetic loci, and it is then that the decoding of genes in a harmonious (symphonic) manner becomes possible. Various combinations of these regions are also used in making more complex decisions. As an example, protein-binding regions that are involved in the lowest level of genomic indicators have a role in decoding genes. The proteins that bind to these DNA sequences can become active when they form a group that has an interaction with more than one protein molecule. For instance, each one of the lacO and CRP regions on the lactose operon shows a palindromic sequence structure (the DNA sequence remains the same when the sequence is read from either end). Similarly, the lacP region has two lower regions that are appropriate for the binding of RNA polymerase and are separated from each other by a 16–17 base pair. In all living beings, the proteins and DNA sequences interact with each other. For example, the LacI repressor, which is in charge of controlling the lactose operon,has separate regions for not only binding the DNA region, but also for creating protein-protein binding as well as the binding of allolactose stimulator. The unique combinations of this region on the genome sequence result in a unique protein synthesis.

The genetic engineering procedures in cells

Some of the genetic engineering procedures that take place in the cells are as follows: Recombination systems (mutual material exchange) that are observed in homologous chromosomes (the chromosome pair derived from each parent), recombination specific to a particular region; separation of DNA sequences specific to those regions (fusion of gene pieces, VDJ recombination of genes as appointed in the immune system); the existence of systems that combine end points in non-homologous chromosomes (the binding of broken DNA parts, the formation of new genetic fusion, the formation of sequences that are open to hyper mutations); DNA transposons (DNA sequences that can insert themselves into different DNA sequences or can copy themselves there and leave a copy); the RNA sector that can control the transcription and signals that are responsible for the maturing transcription; the signal sequences that cause the rearrangement of neighboring DNA sequences (such as amplification, deletion, and inversion); and finally, controlling the transcription with micro RNAs.

None of the above phenomena which cause in-cell changes are random. Each of the genetic engineering functions is planned in a way that makes specific changes and arrangements. In the processes of insertion, i.e. when a specific amount of DNA is added to a different region of the genome, or deletion, i.e. when a specific amount of DNA is severed, there should be arranging, cutting and coding sequences that will bind the cut part to its new place in an appropriate way. On the genome, special regions that are suitable to mutation are created in order to produce variety and to respond to adaptation. When all these molecular engineering functions are thoroughly analyzed, it can be seen that even the point mutations, which up until now were thought to have happened by chance, are not coincidence; rather, they occur through the divinely designed genetic engineering functions. Most of the mutations that are thought to occur by chance in the cell have been removed by the repair systems and fault correction functions in the cell. Thus, the changeability and variety in DNA sequences are shaped by the power and will of God the Almighty according to a planned, programmed genetic schedule.

The R&D department of the genome

Depending on the stimulation received, God-given genetic engineering functions are arranged in the cells and a decision is made about which parts of the genome should be changed. Some of the changes inside the cell appear on a large scale. Inside the genome, different and far removed regions can be rearranged. The changes are related to one another and are in no way disconnected. One mechanism can produce more than one change. The reconstruction of changes in some organisms is a part of the normal life cycle. In the Cornelius protozoan, the embryonic genome is regularly decomposed to a thousand slices. Then, through processing and rearranging in the cells, a functional genome with a distinct system structure is created.

While the genome is reshaped, there is the production of new different sequences rather than the sequences that they regulate and which have the code for the continuity of existing phenotype features. The organization of the genome along the system base emerges with the functions of the genetic molecules, such as cut-paste-rearrange. For example, in immune system cells, there is a planned disposition to mutation and the specific antibodies are rearranged to recognize an infinite number of different antigens. The life cycles of lymphocytes demonstrates both the control of the DNA rearrangement improvements and the specificity of mutations. It is estimated that the new sequences which do not change the existing structure operate like a research center for the genome.

The God-given genetic engineering systems imposed in the cells, when analyzed from the perspective of the population, are molecular mechanisms that carry out basic changes to ensure adaptation. The duty of reconstructing the genome during adaptation has been assigned to the divine genetic engineering functions imposed in the cell. The divine genetic engineering tools and mechanisms, which are placed in the cell with active nucleic acid elements that carry information, change the genome in parallel to the changes in both the inner and outer environment; this change occurs not only on one point of the genome, but rather on every point of genome. The functions of the DNA elements, which allow for the exchange of genetic information (both horizontally and vertically, in species and between species, between types and classes), are arranged by domestic cell signal transfer and data process networks. The signal network systems that are in charge of rearranging and controlling in-cell procedures not only control when the genome is rearranged, at the same time it decides where these rearrangements take place inside the genome. The selection of the target is planned, it is not random. For instance, R1 and R2 retrotransposons which are established in the DNA region that codes 28S ribosomal RNA have specific recognition regions and the information of endonuclease cutting DNA region on specific points that it had settled down. Eukaryotic cells have more complex decision making systems. The cells continuously create responses in response to DNA damage, cell physiology and outer-cell reproduction factors. One of the critical questions and answers is whether the damage will be repaired or whether programmed death will take place. If the cell avoids giving an answer, then genetic indecisiveness appears and abnormal cell reproduction, i.e., cancer, begins. From this perspective, cancer is a result of pathology in the signal and information process in the cell. The changes in gene expression without any changes in the DNA sequence (epigenetic) as well as the divine genetic engineering functions are clear proof demonstrating that every single action in the cell occurs with a certain aim that is based on knowledge and calculations.

Hamza Aydin holds a PhD in biology.

References

• Shapiro J. A.(2001). “Genome Formatting for Computation and Function: Genome Organization and Reorganization in Evolution: Formatting for Computation and Function.” Presented at the “Contextualizing the Genome” symposium, Ghent University, Belgium, November 25–28, 2001 (Ann. N.Y. Acad. Sci., in press).
• –. (2005). “A 21st century view of evolution: genome system architecture, repetitive DNA, and natural genetic engineering.” Gene 345 (2005) pp. 91–100.
• Shapiro J. A. and Sternberg R V (2005). “Why repetitive DNA is essential to genome function.” Biol. Rev. (2005), 80, pp. 1–24. Cambridge Philosophical Society. DOI: 10.1017/S1464793104006657.

If we try to fill a glass of soda without letting it overflow, we usually notice the bubbles or froth of the drink. As we fill the glass, bubbles form on the surface and these tiny bubbles grow. Reaching a certain size, the bubbles escape from the liquid surface, and vanish into the air. If we put our finger, or a straw into the soda-as most of us did as children- we immediately notice that tiny bubbles of gas form on the object immersed in the glass. Just like in the freezing of water or in the escape of gas from soda, a precise energy exchange occurs at the initial stage of any phase transformation. Completion of any phase transformation – freezing or condensation (clouds transforming to rain)- is impossible without such precise energy exchange. The fact that all these phase transformation occur with precise energy calculations in the best possible temperature ranges to support life is a clear proof that nothing in the universe was created by mere coincidence, and that everything occurs by the command of the Almighty.

We know that everything in the universe obeys the minimum energy principle. If we want to freeze water, all we have to do is to cool it to a temperature below 0°C, and the transition from water to ice begins. Water molecules tend to gather together to form clusters. When five to ten of these molecules bond together, however, a difficulty is encountered. The formation of solid-liquid, solid-gas, or liquid-gas interfaces requires a specific amount of energy. In the beginning, the surfaces of these clusters are quite large as compared to their volumes such that the energy they receive to form an interface is much greater than the energy they release; therefore the state of minimum energy is not reached. To explain this to you in another way: let us assume that we manufacture beads for the production of costume jewelry and garments, and the surface of the beads requires treatment. If the beads we manufacture are smaller than the specific size, they will be more expensive to treat, and therefore will not cover the costs, so only producing beads exceeding the specific size will be profitable to the manufacturer. The main aspect here is actually the size of the beads, so if manufacturing beads which exceed the specific size is simpler and more profitable, rejecting the beads smaller than these specifications would be inevitable.

As in this example, because of their high energy value, the molecular clusters formed initially (embryos) return to a liquid form. Then once again the particles begin to bond, but again the result is the same. An embryo must grow to a certain size for its surface area to decrease in comparison to its volume and thus reduce its energy. This is only feasible when many atoms bond, for only when a sufficient number of atoms join together does the embryo transform into a nucleus, and then begin to crystallize and eventually become solid. The process called homogeneous nucleation is only possible under certain conditions: the liquid must be at a temperature of around –40 C^o for both the transition in the balance of energy, and for the water molecules and atoms to become solid and bond to form a nucleus. If we contain pure water totally motionless in the deepfreeze at approximately –8 C^o, we will have supercooled water that has not yet transformed into ice; the temperature between the nucleation and the freezing points, is called supercooling. Supercooling is a metastable condition where liquid or gas remains supercooled without actually becoming frozen, but the slightest intervention or movement can cause the substance to transform into a solid. The tiny bubbles of carbon dioxide in soda is also in a metastable condition, for as soon as the bubbles have the opportunity, they escape from the liquid and vanish into the air. If we immerse a straw or finger into a glass of soda, this forms an added surface, which also facilitates a solid-gas interface, and if we add a teaspoon of sugar to the soda, this induces the drink to froth and bubble at great speed. Water boiled in a saucepan actually nucleates on the wall of the container.

Supercooling is a metastable form of the substance. Every substance or solution has a specific temperature value for cooling. For instance, liquid copper transforms into a solid at 1083 C^o. Homogeneous nucleation requires the bonding of 310 atoms, and supercooling to approximately 236 C^o.

Under normal conditions, substances which have more than one type of molecule undergo phase transformation known as heterogeneous nucleation. In this case, the atoms form primarily on the walls of a container on particles of impurity, or minute solid particles in the liquid, and this significantly reduces the surface energy barrier for nucleation. So for a moment let us return to the bead example. We have discovered that instead of directly manufacturing smaller beads, it would reduce the costs of decorating the surface of the beads to coat and treat larger beads, so the beads are being produced in this way, thus reducing losses.

Supercooling can occur at temperatures even as high as 2–3 C^o, and this is very important. The condensation of water or supercooled water droplets in clouds must reach a specific size and weight in order to fall to the earth as raindrops. Here, the solid microscopic particles combine to form nuclei. Even if the clouds are much lower in temperature, rain cannot form without nuclei. Particles of salt which escape from the sea, sand that rises from the desert, the sulphate released from the ashes of volcanic activity or minute atoms of dimethyl sulphate emitted by certain planktons are driven into the atmosphere by the wind and form nuclei. As the Almighty, the Creator of the universe revealed in Al-Hijr, verse 22 of the Qur’an: “And We send the winds to fertilize, and so We send down water from the sky, and give it to you to drink (and use in other ways)” indicating that one of the duties of the wind is fertilization. Even the particles in smoke released irresponsibly by humans from industrial chimneys, or from car exhausts form nuclei that eventually transform into rain.

During the foundry process, solid substances are added to liquid metals for certain purposes, such as enabling metal to set more rapidly, or increasing the metal’s durability. When liquid metal is cooled, its atoms form nuclei on microscopic solid impurities. These nuclei increase in size and assemble into groups called grains. The irregular zone between these groups is known as the grain boundary. The grain boundary forces the compressed atoms to move and weld, thus increasing the durability of the metal. This method known as infusion or grain contraction ensures an increase in the formation of nuclei, and also in the durability of the metal. Cloud seeding, a topic which mainly comes to light when there is a lack of rain, is actually inducing the clouds to form artificial nuclei that will in turn produce rain.

Some creatures on earth protect themselves with mechanisms bestowed by their Creator, and one of these creatures is the wood frog. As the water in its cells begins to freeze, the antigel protein found in its blood surrounds the formation of nuclei, and prevents the nuclei from increasing in size. The frog remains frozen and motionless until the temperature increases. If we touched a wood frog in this condition, its cells too would freeze suddenly, and the frog would die. It is impossible for a frog to know how to cool to the point of freezing, and nucleate. It is also impossible for a frog to adapt to such a mechanism because this would require practice and experience, which would of course be deadly. Therefore, is the frog’s ability to freeze, and its process of nucleation not a clear indication of the providence and blessing of God the Almighty?

Religion and Science: The Institute on Religion in an Age of Science, Inc., will convene on July 29-August 4, 2001. The topic, Human Meaning in a Technological Culture, will explore and evaluate how these powerful [information and biotechnoloy] technologies redefine, for better and for worse, human identity and meaning, as well as ideas about reality and God. www.iras.org.

Call for Papers: The European Society for the Study of Science and Theology (ESSSAT) has issued a call for papers. Details about its conference, to be held during March 19-24, 2002, are now available. www.esssat.org.

The Future of Religion? The World Network of Religious Futurists will meet in Minneapolis, MN, July 29-31, 2001. Attendees are scholars and activists from around the world who study the future of their religious tradition in view of world civilization. www.wfs.org.

Interesting Books: Mariano Artigas, The Mind of the Universe: Understanding Science and Religion; Robert Herrmann (ed.), Expanding Humanity’s Vision of God: New Thoughts on Science and Religion; Arnold Benz, The Future of the Universe: Chance, Chaos, God?; Ted Peters (ed.), Science and Theology: The New

Consonance; Ian Barbour, When Science Meets Religion; Reuven Firestone, Children of Abraham: An Introduction to Judaism for Muslims; Khalid Duran, Children of Abraham: An Introduction to Islam for Jews; Michael Shermer, How We Believe: The Search for God in an Age of Science. www.amazon.com.

African History in for a Rewrite: Professor John Hunwick and Northwestern University have received a $1 million Ford Foundation grant to study sub-Saharan Africa’s written traditions. In 1999, Hunwick discovered 3,000 Arabic manuscripts held by a Timbuktu family since 1592. He hopes to prove sub-Saharan Africans were not illiterate, and therefore uncivilized, before European colonialism. www.chicago-tribune.com.

In Society

Patent Fight Ended: Last year, 2.5 million Africans died from AIDS because they could not afford medicine. Large pharmaceutical companies, citing intellectual property rights, went to court to block South Africa’s efforts to get a WTO wavier to import far cheaper generic drugs on the grounds of national emergency. The companies withdrew their case on April 19, 2001, claiming that harsh international criticism was not a factor. http://dailynews.netscape.com.

Human Trafficking: The recent deaths of 58 out of 60 illegal Chinese immigrants in Europe highlights the problem of human trafficking. The UN estimates that those involved make $8 billion to $12.3 billion annually in profits. www.cnn.com.

Patenting Gene Data: Biotechnology firms are seeking exclusive ownership of the pure scientific formulas that represent genes. Critics claim this would make any recording and storing of formulas illegal without the patent holder’s permission, effectively ending some genetic research. At least 16 such patents are now pending at the Canadian Patent Office, and similar ones in America and elsewhere. Legal scholars and intellectual property experts fear that the free flow of genetic knowledge and innovation is at stake. www.nationalpost.com.

New Data Transmission Record: French and Japanese engineers have squeezed more than 10 trillion bits per second through single optical fibers. This record capacity equals about 150 million simultaneous phone conversations. www.techreview.com.

In Science

Return to Mars: NASA launched its Mars Odyssey orbiter on April 7, 2001. When it lands on Mars during October 2001, it will map the surface’s chemical and mineral makeup, determine Mar’s radiation level and how it might affect future astronauts, locate near-surface water, and map mineral deposits from past water activity. www.nasa/gov.

A Biological First: Biologists have mapped the entire genetic code of Arabidopsis thaliana, a plant belonging to the mustard family. Scientists expect applications in agriculture (the genetic manipulation of rice, wheat, and other crops) and medicine (many medicines come from plants). www.popsi.com.

RNA Chips: RNA switches clustered on a gold-coated silicon surface can identify different strains of E.coli found in bacterial cultures. Scientists hope to develop RNA chips that can reveal the molecular composition of complex mixtures better than current DNA biochips. Future uses are seen in detecting drugs, toxins, metabolites, proteins, and nucleic acids. www.techreview.com.

New Cancer Treatment: Molecularly targeted therapy drugs recognize and attack specific molecules unique to specific cancers. The model drug leading the way is Glivec (STI571), which fights CML, a cancer characterized by excessive white blood cell overproduction. Such drugs are designed by working backward from a known abnormal molecule specific to a certain type of cancer, and thus have a limited use. Glivec is getting a priority FDA review. http://abcnews.go.com.

Virtual Reality Update: Computer scientists affiliated with the National Tele-Immersion Initiative have produced a prototype virtual office. Digital cameras that monitor movements from various angles, head-mounted tracking gear, polarized glasses, and screens mounted at right angles to your desk allow you to see your colleague’s office. All images are life-size and 3D. www.popsci.com.