Cultural differences have a potential to trigger conflicts at all levels, and the response each society gives to these conflicts depend on what they hold most dear as a foundational norm: independent existence of individuals or social interdependence. This calls for awareness in differences and discussion to benefit from cultural diversity.

Michael was having a problem with his neighbor next door. He decided to seek advice from his coworkers on the issue. Paul suggested that he express the problem openly right away, and, if that wouldn’t help, to take the neighbor to the court. Akihiro, on the other hand, warned him not to get too serious, and recommended him to write a letter which talks about their good memories in the past and how pleasant their neighborhood was. The backup plan in this case would be to invite a mutually respected neighbor of theirs to mediate the situation.

Of course, Michael has many other options to address the given problem. Yet, it is interesting to note the differences between the suggestions of the two coworkers. One party is focused on the issue per se and pursues a direct approach; whereas the other is concerned about the relationship and follows indirect/accommodating means to handle the situation. This article is intended to provide a better understanding of these two main approaches in conflicting situations. Since the responses to unease are generally situational, we may not judge whether any of the resolution efforts are good or bad, but rather, look closely on their rationale respectively.

Cultures differ on various aspects of life. Naturally, the approach of their members to conflict will also vary depending on the value they place on issues of interest and dominant cultural characteristics. A close examination of these features in a given society will give an idea on how its members would respond to conflicting situations in general. Given the growing interconnectedness of societies today, such knowledge of cultural tendencies might help in the development of strategies for conflict resolution and prevention.

Societies that promote independent existence of individuals are referred to as individualistic, and those which assume a great deal of social interdependence are grouped as collectivistic cultures.¹ Prior to discussing responses to conflict in these two types of cultures, it may be better to highlight some examples of their interpretations which will provide hints about their foundational norms.

He who hesitates is lost. (American expression)

Strike while the iron is hot. (American expression)

More haste, less speed. (Chinese expression)

A deliberate inaction is better than a blind action. (Chinese expression)

Different cultures may have different viewpoints about the same issue. This affects the responses of their members and the methods they favor in various situations. Existing theories in social sciences, which generally reflect social values of individualism and autonomy, may be inadequate in societies that do not share the same values and foundational norms, and vice versa. Such a cross-cultural analysis requires an understanding of the prevalent cultural values and norms in a given society.¹ These shared values, through which cultures develop and continue, are communicated in a variety of ways. One technique that commonly appears is the use of proverbs or sayings, and such quotes throughout the commentary will provide a general idea about some differing characteristics of these two cultural approaches.

Rather than criticizing or promoting any specific cultural aspect, this piece aims to discuss another dimension of multicultural approach to serve to break the stereotyped images (if any) about different cultures, and to help accept everybody as they are in a world of cultural diversity. Once we have a broad picture, we will further look into how interpersonal conflict is handled, and conclude with some overarching suggestions to foster mutual understanding in cases of unease.

Two’s company, but three’s a crowd. (American expression)

If you congregate, you live. If you scatter, you die. (Korean proverb)

One who leaves the herd, gets snatched by the wolf. (Turkish proverb)

One palm makes no applause. (Chinese proverb)

Two widely held worldviews have become evident in the cross-cultural literature as variables on which most cultures vary: individualism which objectifies the self, and collectivism which submerges the self to emphasize the group. A middle course in the de bate between those who claim the primacy of society and those who emphasize the primal significance of the individual would state that there is no society without an individual; and also that no individual can survive without society.² These concepts do not necessarily form opposite poles and may coexist due to the enormous intercultural mix, yet one approach may still have dominance to the other in a given culture.³

“The freedom to be an individual is the essence of America.” (Marilyn vos Savant)

“It is hard to be an individual in Japan.” (Haruki Murakami)

In individualistic societies, a person is an autonomous entity defined by a somewhat distinctive set of attributes, qualities, or processes; and these internal attributes determine the behavior. Yet, in collectivistic societies, a person is an interdependent entity who is part of the encompassing social relationships. This is not to say that a person in such a society lacks unique attributes, but rather that these are not primary forces that guide the behavior. In such societies, behavior is a consequence of being responsive to others and origins of behaviors are relationships and social harmony.³

He who converses not knows nothing. (English proverb)

He, who knows, does not speak. He, who speaks, does not know. (Lao Tzu)

In Western cultures, a highly verbal individual is perceived more positively, whereas in Eastern cultures perceptions for highly verbal individuals may not be that positive. Traditionally, communication apprehension has been attributed to a weak sense of identity and is viewed as a deficiency; but on the contrary, this reticence may be due to politeness or a tendency to preserve harmony in collectivistic cultures, depending on the social context.

Stand up for your own rights. (American expression)

Unless you blow your own horn, who will? (American expression)

Once you preach, the point is gone. (Zen phrase)

Mature rice plants bow down lower. (Korean expression)

According to individualistic point of view, communicators can get things done by being assertive. On the other hand, from the collectivistic standpoint, people are expected to preserve group identity and may be discouraged from asserting themselves as individuals. Therefore, it will not be a true assumption to attribute this lack of assertiveness to some negative traits such as low self-esteem, shyness, disinterest, or ignorance.³

Cultural dimensions of conflict resolution

“The practice of peace and reconciliation is one of the most vital and artistic of human actions.” (Nhat Hanh)

Keeping all the above examples in mind, now let’s briefly compare and contrast responses to conflict in individualistic and collectivistic societies:

Since individuals’ self-articulated interests are of utmost importance, individualistic perspective frames conflict as the divergence of interests or issues, which limits the focus of solution efforts solely to reconciling the differences in interests between parties. Yet in collectivistic cultures, social harmony is a critical aspiration and community involvement is likely even in interpersonal matters. Then, a deeper and wider analysis that will address the concerns of both types of approaches should better view conflict as a situation and place the situation to the heart of any resolution endeavor.¹

“He who wants to persuade should put his trust not in the right argument, but in the right word. The power of sound has always been greater than the power of sense.” (Joseph Conrad)

The one who raises his/her voice has already lost. (Japanese proverb)

Members of individualistic cultures tend to prefer direct/dominating/prompt communication styles, since they deem open discussion as the best way to deal with their interpersonal problems. On the other hand, individuals in interdependent societies are less likely to “express negative emotions (such as anger) to confront each other, and to use verbal aggressiveness and open discussion in conflict situations. They may avoid reactions to their relational problems that can potentially cause further conflict”. Among them, the stress is not so much upon the individual and his/her interests, but on the maintenance of the collectivity and the continuation of harmonious relationships; conflict is viewed as damaging to social fabric and relational harmony, so it should be avoided as much as possible. This naturally leads to the adoption of high compromising and avoiding behaviors and a relatively low preference for competing and assertive postures which emphasize the value they place on maintaining social harmony rather than personal interests in conflict interactions.³

“Peace is not absence of conflict; it is the ability to handle conflict by peaceful means.” (Ronald Reagan)

There is a natural tendency to avoid conflicts as much as possible. While it is a major strategy to preserve harmonious relationships in Eastern cultures, Western societies may view accommodation efforts as giving up critical values and personal rights. Furthermore, according to the Western approach, people will prefer to avoid conflict only if their stake in an issue is not high enough to get involved, whereas collectivist cultures actually utilize it as a social remedy.³

In collectivistic societies, “understanding is seen not as the result of putting meaning into words, but rather as the greater understanding of shared perspective, expectations, and intimacy”, and avoidance is utilized as a strategy to handle the conflict. Besides expressing the discomfort indirectly/nonverbally in a polite and educating way, non-confrontational communication modes in problematic situations include, but are not limited to: “(a) the use of management to prevent a conflict before it happens, (b) expression of conflict emotions like anger or frustration by non-communication, such as ignorance or silence, (c) pretense of being harmonious in peoples’ presence, even though parties are actually avoiding each other, (d) management of conflict using a third party, (e) tendency of directing accusations against oneself.”³

Cultural differences in third party intervention

“The Believers are but brothers; so make peace and reconciliation between your brothers… ”⁴

How, when, and why a third party interferes has been the central focus of conflict resolution studies. Models on interpersonal conflict that assume a great deal of individual autonomy and privacy in interpersonal matters hardly speak about engaging one’s social network into a conflict, however interpersonal conflict intervention in a collectivistic setting will not take place only between contending individuals and the intervener, but is likely to engage other entities (e.g. extended family members) almost in any given conflict. This involvement of others, with the purpose of securing, improving or sustaining a resolution, can be added strength for conflict intervention and resolution.¹

“Washing one’s hands of the conflict between the powerful and the powerless means to side with the powerful, not to be neutral.” (Paulo Freire)

Western literature on interpersonal conflict intervention generally undermines the adjustment of the involvement style depending on the stage of the disagreement. However in collectivistic societies, “third parties are expected to function in a reconciliatory mode, unless clear injustice or deviance takes place. In this case, third parties should get actively involved in restoring justice and eliminating deviance before returning to the reconciliatory role.” Consultation may be utilized “when relationship issues (perception and attitudes) are not suitable for mediation, and to help parties clarify their underlying needs (security, or identity for example) and interests tied to such needs. Mediation, on the other hand, aims at negotiating certain substantive issues, based on a clear understanding of relationship issues and parties’ own needs and interests.”¹

Adhering to the common good while not favoring any of the parties has good intentions, yet the mediator may face difficulties in modern diverse societies, where notions of common good may be too diverse and vague; focus being on the individual. Material resources are often the codes used, thus legal procedures are vital parts of the resolution in these societies, and mediators are expected to be professionals who are knowledgeable of legal procedures. Thus, actions in a resolution process are task-oriented. Conversely in collectivistic societies, where the main focus is on social harmony and social norms/values form the basis of a solution, mediators are generally seniors (in terms of age or hierarchy) who are knowledgeable of cultural norms. Some codes mainly used by interveners in these cultures include honor, dignity, unity, future of the next generations, religious values, and tradition of forgiveness.^1,5

Speaking of religion and its role in conflict, one’s voluntary sacrifice from his/her rights in some conflicting situations, repelling evil with what is better,⁶ and forgiveness has been encouraged for thousands of years by major world religions.⁷ “Adherents of these religions have claimed that forgiveness yields numerous emotional and spiritual benefits, and can dramatically transform one’s life.”⁸ Hence, it may be useful to explore their resources, which are rich with conflict intervention principles, values and models, in a way that would prepare them for contemporary practice. For instance, it is stated that reconciling a dispute between two parties is a charity,9 and that “kind words and forgiving of faults are better than charity followed by injury.”¹⁰

The most beneficial approach for the involved parties in a conflict situation would be an attempt to address fully the concerns of both parties and to find mutually satisfactory solutions to the cause of the conflict. This collaborative approach is of utmost importance and most viable, particularly when the issues are critical and maintaining an ongoing relationship is important. For an effective assistance, third parties involved in mediation processes should carefully study the needs and values of contending parties and have cultural awareness in order to provide mutually satisfactory resolution options regardless of the society they operate.

Considering that disagreements could be resolved much easily when parties are aware of corresponding needs/values and interests/concerns, getting to know one another would be an important basis for any resolution endeavor. Therefore, the more we exchange ideas without prejudice, the more we’ll understand each other. Although some disagreements yield positive outcomes and new ideas, intense conflicts generally drain energy and resources. Hence, it is heartening to observe that peace studies such as conflict resolution are blossoming, despite some scholars expecting a “clash of civilizations” and some claiming that we are at the “end of history.” Contrary to the arguments that define life as a series of struggles for limited resources, this relatively new field of social sciences will help humanity make the best out of its potential and reach a better state of living. Comprehensive resolutions which are globally applicable to disagreements in-between individuals, organizations, or nations overall, call for good deeds, positive motives, and pure intentions without self-interest. Tolerance, forgiveness, altruism, compassion, submission to ethical/moral codes, fairness, openness of hearts and minds, and welcoming people as they encompass some of the universal means to cure conflicts at various levels.

References

1. Abdalla, Amr. 2000. “Principles of Islamic Interpersonal Conflict Intervention: A Search within Islam and Western Literature.” Journal of Law & Religion 15, no. 1. 151-184.

2. Nasr, Seyyed H. 2002. The Heart of Islam: Enduring Values for Humanity. San Francisco: HarperCollins.

3. Kim, Min-Sun. 2002. Non-Western Perspectives on Human Communication: Implications for Theory and Practice. Thousand Oaks, Cal.: Sage Publications.

4. Qur’an, 49:10.

5. Abu-Nimer, Mohammed. 1996. “Conflict Resolution in an Islamic Context: Some Conceptual Questions.” Peace and Change 21, no. 1. 22-40.

6. Qur’an, 41:34.

7. For some of the Qur’anic verses on interpersonal forgiveness and reconciliation not mentioned in the text, the reader may refer to 2:280; 3:134, 4:128, 135, 149; 24:22; 25:63; and 42:37, 40, 43.

8. McCullough, Michael E., Kenneth I. Pargament, and Carl E. Thoresen. 2000. Forgiveness: Theory, Research, and Practice. New York: The Guilford Press.

9. Bukhari, Sulh, 11; Muslim, Zakat, 52.

10. Qur’an, 2:263.

Factors underlying variable DNA methylation in a human community cohort. L.L. Lam et al. PNAS October 16, 2012 vol. 109

The effect of environment on genes can be very profound. Our surroundings may not directly change our DNA sequence but it can surely dictate how our genes are transcribed. Epigenetics studies heritable changes in gene expression caused by non-genetic mechanisms, i.e. mechanisms other than the changes in the DNA sequence itself. DNA methylation is one of the major epigenetic modifications to regulate the gene expression. The addition of methyl groups on DNA sequence acts like a dimmer on a light bulb switch, which will turn certain genes on or off. A recent study showed that a person’s early life experiences shape their DNA methylation patterns. The research team discovered that childhood poverty (not socioeconomic status as an adult) is highly correlated to distinct methylation marks left on genes. Although children in rich and poor households have identical sets of genes, the degree of adversity or stress at home determines which combinations of those genes are activated or silenced through differential DNA methylation. One can imagine that such epigenetic changes might cause some alterations in the gene expression program of blind people to certain environmental signals or make them even more sensitive. Perhaps such changes could make some people more adaptive to harsher life conditions, hence enhance their survival. These findings suggest that environmental conditions early in life shape our epigenomes permanently thereby influence our life experiences, health and probably many other things that we are not yet aware of.

An alien planet next door

An Earth-mass planet orbiting α Centauri B. X.Dumusque et al. Published online 17 October 2012, Nature

Astronomers have just discovered an earth-size alien planet right next to our solar system. A new earthlike planet, named Alpha Centauri, is just 4.4 light-years away. That’s 40 trillion km away from earth! Although this rocky planet’s mass is similar to Earth’s, it orbits much closer (25 times closer than the Earth) to host star Alpha Centauri B. As a result, a year lasts 3236 days and the surface temperature of the planet reaches around to 1200 °C, which makes the planet incapable of supporting any life form we know. However, solar systems with a rocky world are usually predicted to have multiple planets. One possibility is that that Alpha Centauri A, the bigger sibling of Alpha Centauri B, might host some yet to be discovered unknown planets with more habitable zones. Although this recent discovery has sparked people’s dreams to travel to another star system outside of our planetary system, such an exploration mission unfortunately seems impractical in the near future. Even a cell phone-sized probe that is accelerated to 10% of the speed of light would need to travel non-stop for 40 years to reach the target. So, what is the next best thing to do? Will it be taking photos or dropping probes on the planet’s surface to study a potentially modified atmosphere? It seems like while astronomers work hard on the identification and characterization of this new star system, scientists should focus on developing super-fast propulsion systems, which will perhaps include new concepts like nuclear rockets and antimatter fusion drives.

Bad memories, substitute or suppress

Opposing Mechanisms Support the Voluntary Forgetting of Unwanted Memories
Benolt RG et al., Neuron, Volume 76, Issue 2, 450-460, 18 October 2012

For the nervous system, forgetting a memory is almost as complicated as creating one. A recent study probed the mechanism of how the brain allows us to voluntarily forget unwanted memories. Researchers utilized functional magnetic resonance imaging (fMRI) to examine the brain activity of participants who had learned associations between pairs of words and subsequently attempted to forget these memories by either blocking them out or recalling substitute memories. The fMRI results showed that two separate forgetting strategies looked equally effective yet they seemed to use different neuronal circuits in different parts of the brain. For memory suppression, dorsolateral prefrontal cortex inhibits neural activity in the hippocampus which is a critical region for recalling past memories. On the other hand, memory substitution specifically activates caudal prefrontal cortex and midventrolateral prefrontal cortex that are known to bring specific memories into awareness in the presence of distracting memories. These findings can help us to better understand the mechanisms of memory disorders such as posttraumatic stress disorder, and may ultimately help to develop effective treatments. At a more personal level, this study may direct us to explore how we deal with our unpleasant or unwanted memories. We might be surprised to realize that one approach might be working much better for us than another one. In other words, neuronal wiring in our brain might simply favor one approach over another.

Every blessing of God is an opportunity given to human beings that calls for a corresponding responsibility.

Health is a blessing that should be used to fast, to pray, and to strive on God’s path so that one can express gratitude for this blessing. If a person gives this gratitude, God will return that body in the next world for eternity and without flaw, and with all its potential revealed.

Intelligence is one of God’s favors. If the horizon of one’s mind has been enlightened by the lights of revelation, and he is therefore distanced from inappropriate things and makes decisions according to the true path, intelligence is a source of inspiration. If he uses the blessing of his mind appropriately and introduces Truth to those who have strayed, he is giving the mind its due. On the contrary, if he only uses intelligence for worldly or evil tasks, he is being ungrateful for that blessing.

Power of expression is one of the greatest blessings that God has given humanity—so much so, that the name of the Qur’anic chapter where this is explained is called Rahman (Mercy). Al-Rahman is one of the Exalted Names of God. Some of the manifestations of God’s Mercy are giving means of subsistence in a broad circle to everyone even if they are not believers, and nourishing creation with various blessings, including human’s power of expression. This ability makes them eligible to be an addressee to God. They may understand God’s words and at the same time express their thoughts to Him. God says, “Come, pray to Me and bow in My presence.” Then they can say, “praise be to God” and with faithful and obedient devotion they can stand in God’s presence. In one sense, this is understanding God and speaking with Him. One of the Successors (the generation after the Companions of the Prophet) said, “If a person who reads the Qur’an says that he spoke with God, it would not be a lie.” Therefore one who says, “praise be to God” can be considered to have spoken with God.

The prayers that believers recite every day actually reflect a conversation with God:

You are the Most Beneficent and the Most Compassionate: You first gave me consciousness and then the ability to express this consciousness. This is a manifestation of Your Mercy.

You are the Master of the Day of Judgment: I am preparing for that day within the framework of Your commands.

I serve only You and I seek help only from You: I do so in order not to be smashed under the weight of servanthood.

Most people probably never really ponder the prayers in this way, but if they were to reflect, the prayers allow them to rise to a very honorable station.

If a person went and spoke with a head of state, he would talk about it everywhere; he would find an opportunity in every environment to mention that conversation. Therefore, if a person views talking with a head of state as this important and mentions it everywhere, then he should think deeply about what it means to have the privilege of addressing God.

A sacred saying from the Prophet (hadith qudsi) is stated as follows:

“I share the recitation with my servant in prayer; half belongs to Me and half to him and what My servant wants will be given to him. When the servant says, ‘Praise be to God, the Cherisher and Sustainer of the worlds,’ Exalted and Glorious God says, ‘My servant praised Me!’ When he says, ‘Most Glorious, Most Merciful,’ God says, ‘My servant glorified Me.’

“When he says, ‘Master of the Day of Judgment,’ God says, ‘My servant exalted Me.’ When he says, ‘You do we worship and Your aid we seek,’ God commends him: ‘This is a pledge between Me and My servant. I gave him what he wanted.’

When the servant says, ‘Show us the straight way, the way of those on whom You have bestowed Your grace, Those whose portion is not wrath, and who go not astray,’ God says, ‘This belongs to My servant and he has been given what he wants.’”

In recitation, the chapter al-Fatiha is divided between the servant and God—some is spoken by the servant, and some is answered by God. In a sense, this is nothing other than a conversation with God. Consequently, the power of expression is a great blessing from God, and its greatest right is to praise God, who honored human beings with the power of expression.

Like a town crier, we must speak of our Lord, who gave us the capability of expression, everywhere we go. If you give a crier a little money, he will promote his wares from morning till evening in the marketplace. Salesmen do the same thing; they go to houses, fawn on people and try to sell their goods. In the end, what they will sell is one or two pots and pans. In the same way, Heaven will be given to us for doing very easy tasks. We are in a position to be made worthy of seeing God’s Beauty by using, in the best way, the power of expression bestowed upon us by God. Even if no one remained on earth to hear us, then we have the responsibility to climb the mountains to the skies and live for the excitement of talking of God to the jinn and demons. As a friend of truth said, even if one is imprisoned and there is no one around, then he should try and teach the demons about God to fulfill his responsibility.

The subject is the importance of a person returning a favor given by God by making the best use of the ability bestowed. Only by means of this kind of reciprocation can gratitude for that blessing be fully shown. God will continue bestowing that blessing here and in the next world. If a person only gives the right of property, but does not give the right of his mind, health, or power of expression, then he still will have been ungrateful. If a person cannot speak, he has a pen. If he does not give the due of the pen, then he will have shown ingratitude before God. If one who has strong mental abilities does not use them for God, then he will have been unjust. Whatever God has given a person should be used on the path of God to teach others about Him.

If a person does not give gratitude for his other blessings, but only gives financial aid when his financial situation is favorable, then at least he has performed a large part of his responsibility. If he gives help beyond the alms tax, financial aid is a serious sacrifice, and voluntary acts and altruism within this framework is great, because it is the virtue of giving for God’s sake. In fact, our Prophet said, “Generosity is like a tree. Its roots are in Heaven and its branches have hung down to this world. Whoever lives under that tree and behaves generously, sooner or later he will hold on to one of the branches and rise to Heaven where the tree’s roots are.” It can be understood from this that a generous person, even if he is a sinner—God willing—will eventually enter Heaven. If a sinner does not deny God, and he is generous, it is said that he will enter Heaven. Saying, “A stingy person is closer to Hell,” our Master used an expression of warning for miserliness. We can infer that since generosity is one of God’s attributes, He will not put a person with that attribute into Hell.

Attributes are very important; people must give what is due to the attributes God blessed them with. In this way, one’s work should be arranged according to God’s blessings. Worldly tasks should not be forgotten and neglected. Regardless of where he is, a believer should always be at the forefront of those living in his own time. Doing this, he will always be avant-garde—but while doing this, he should put his life in order and never neglect God’s rights. In short, a believer should use all the abilities God has bestowed upon him, and use them in such a way that he has given those blessings their due.

A particularly interesting class of all these non-coding RNAs comprises riboswitches. Riboswitches are structured mRNA elements that regulate gene expression upon binding of a specific small metabolite. These biosensors were first discovered in 2002 in bacteria. Later, it was shown that plants, green algae and fungi also posses riboswitches. Although, only one type of riboswitch is found in plants and none has beeen detected in mammals yet, metabolite-sensing riboswitches are commonly used for the regulation of fundamental biochemical pathways in bacteria. Riboswitches help cells monitor the environmental conditions and determine if a compound is present at sufficient levels or not. Based on this decision, production, degradation or transport of the related metabolite is either turned on or off.

Architecture of a Riboswitch

A standard riboswitch is divided into two parts: a ligand-binding domain and a gene expression domain (Figure 1). Small molecular metabolites bind to the ligand-binding domain, which is called aptamer, of riboswitches with astonishing specificity. For instance, purine riboswitches differentiate guanine from adenine by at least 10,000-fold based on the identity of a single pyrimidine (thymine or cytosine) that binds to the ligand (1). When a ligand binds to aptamer, conformational changes of the RNA’s structure occur at the gene expression domain. Eventually, this leads to the modulation of gene expression. Some of the riboswitch mechanisms to regulate the expression of genes include formation of stem-loops, lollipop-like RNA structures, which lead to the blocking of transcription or translation, which are the processes where proteins are synthesized using the mature mRNA, self cleavage or mRNA destabilization (Figure 2).

Classes of Riboswitches

The numerous distinct classes of riboswitches discovered so far are differentiated by their ligands and remarkably, the same class of riboswitches can control gene expression through different mechanisms in various organisms. For example, a riboswitch that recognizes and binds thiamin pyrophosphate (TPP), a derivative of vitamin B1, is called as TPP riboswitch (2). In plant cells, when TPP levels are high, excess TPP binds to a TPP riboswitch located in one of the TPP biosynthesis genes. As a result of TPP binding, conformation of that RNA segment changes, which leads to the formation of an unstable mRNA product which degrades quickly. Although, a very little amount of stable mRNA is also produced, it is not enough for the protein synthesis of an important component of TPP biosynthesis. Therefore, TPP biosynthesis can not be completed and consequently TPP levels drop in the cell. On the other hand, when TPP levels are low in plants, more stable mRNA is formed because there is not enough TPP that can bind to the riboswitch and cause structural changes which will result in the formation of unstable mRNA. The stable mRNA produced in the absence of excess TPP is used for the protein biosynthesis of TPP metabolism successfully and thus TPP levels increase in the cell. Unlike plants in bacteria, when TPP concentration is high, riboswitches down-regulate expression of thiamin biosynthesis genes by either blocking the formation of any type of mRNA (both stable and unstable) or preventing the mRNA process rather than destabilizing the mRNA. Some of the other riboswitches that bind vitamin derived compounds are adenosylcobalamin, the coenzyme form of vitamin B12, and flavin mononucleotide, a biomolecule produced from vitamin B2, riboswitches. There are also riboswitches that can bind to amino acids such as lysine riboswitch. The cyclic diguanylate (c-di-GMP) riboswitch is the first known example of an RNA that binds a second messenger, which carries signals from receptors on the cell surface to target molecules inside the cell (3). Purine riboswitches selectively recognize guanine or adenine and regulate purine biosynthesis and transport, which is important for DNA/RNA synthesis. Another interesting type of riboswitch is the glmS riboswitch. It modulates gene expression by undergoing self-cleavage when there is a sufficient concentration of glucosamine-6-phosphate, an important amino sugar. The spectrum of ligands that can be recognized by riboswitches also includes a metal ion, as well. Mg(2+) riboswitches control Mg(2+) transportation when cells are grown in high Mg(2+) environments. In brief, the growing list of studies on riboswitches shows how novel mechanisms are which they use to regulate the gene expression of many fundamental metabolic pathways.

Applications for Riboswitches as drug targets and chemosensors

Riboswitches are powerful and essential components in all three domains of life which are bacteria, archaea (a group of single-celled microorganisms) and eukaryotes ( organisms whose cells contain complex structures inside membranes such as plants and fungi) functioning as intracellular biosensors and regulators. They regulate gene expression in a highly efficient, precise and fast way. Therefore, they can be engineered for various applications.

First of all, riboswitches are excellent candidates as drug targets since they control many important bacterial and fungal genes. Chemical analogs that mimic the actual ligands of the riboswitches can be designed to silence or regulate the expression of defective genes responsible for disease development or even kill certain bacterial pathogens by turning off the genes that are involved in fundamental metabolic pathways. A great example of this strategy is presented by the Breaker laboratory at Yale University. The Breaker group chose guanine-binding riboswitches as targets for the development of novel antibacterial compounds. They have designed several guanine analogues and tested their ability to be bound by the riboswitch and repress bacterial growth (4). They have been able to inhibit the bacterial growth by inducing guanine riboswitch action. Their approach could be used to discover new antibacterial compounds that specifically target other riboswitch classes.

In addition to being drug targets, riboswitches can open new frontiers in bioremediation, bionanotechnology, and synthetic biology. In 2007 Shana Topp and Justin P. Gallivan from Emory University demonstrated that Escherichia coli can be reprogrammed to detect, follow, and precisely localize to a completely new chemical signal by using a synthetic riboswitch (5). They suggest that the bacteria with synthetic or mutated riboswitches could be used to follow and degrade pollutants in soil or target small-molecule signals of disease. Overall, their work to equip the bacteria which can autonomously follow chemical signals, degrade, synthesize or release compounds can help scientists invent new technologies in bioremediation, drug transport, and synthetic biology.

Furthermore, riboswitches are ideal candidates for use in analytical devices and techniques. Their binding features make them suitable in all specific analytical applications in which selective recognition is required. Therefore, these powerful molecular tools can be utilized in analytical chemistry, molecular biology and biosensor technology (6).

As a result, living systems utilize riboswitches to detect the concentrations of small-molecule metabolites and to modulate the expression of related genes via numerous elegant mechanisms. The use of genetic engineering of riboswitches holds enormous potential for inventing new applications to sense and destroy pathogens, deliver drugs, perform bioremediation, detect chemicals and many others that might have significant impacts on our lives. It is also remarkable that only a couple of decades ago most of the non-coding RNAs were assumed to be useless, and are called junks since they do not provide any information for protein synthesis. Yet riboswitches by themselves are enough to prove that God has created everything with a purpose. He is All-Wise and he does nothing in vain. Riboswitches are not useless at all. They are such complex, and perfectly working systems that they can serve humanity as well-designed on/off switches in numerous applications.

Safiye Arslan is a research fellow in the area of biological chemistry and lives in Nevada.

References

1. Gilbert SD, Reyes FE, Edwards AL, Batey RT. 2009. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. Structure 17, 857-868

2. Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR. 2007. Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19, 3437-3450.

3. Kulshina N, Baird NJ, Ferré-D’Amaré AR. 2009. Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch. Nature Structural & Molecular Biology 16, 1212-1217.

4. Kim JN, Blount KF, Puskarz I, Lim J, Link KH, Breaker RR. 2009. Design and antimicrobial action of purine analogues that bind Guanine riboswitches. ACS Chemical Biology 4, 915-927.

5. Topp S, Gallivan JP. 2007. Guiding bacteria with small molecules and RNA. Journal of the American Chemical Society 129, 6807-6811.

6. Mairal T, Ozalp VC, Lozano Sanchez P, Mir M, Katakis I, O’Sullivan CK. 2008. Aptamers: molecular tools for analytical applications. Analytical and Bioanalytical Chemistry 390, 989-1007.

Original Article: Akashi M. et al., PNAS 107, 15643 (2010).

Feeling sleepy during the day after a long flight? Internal body clock genes are to blame. Circadian (Latin: “around” “the day”) rhythm genes take part in a time dependent cycling of an organism to carry out daily physiological processes. These signals include very basic needs such as feeling sleepy at nighttime and waking up during the day and repeats about every 24 hours. Malfunctioning circadian rhythm genes are implicated in several sleep disorders. According to a recent study done by Makoto Akashi and his colleagues at Yamaguchi University in Japan, hair follicle cells were found to closely follow the gene expression pattern of the internal circadian rhythm of the human body. Gene expression patterns can be extracted from hair follicles from pulled hair. Studying the circadian rhythm genes and expression profiles has been quite an inconvenience for researchers up until now. This study provides a new alternative method for tapping into this machinery. Don’t be surprised if you are asked for a couple of hairs pulled from your scalp if you go to a doctor complaining about your sleep disorder in the future. This method could have implications in the field of diagnostic medicine as a less invasive method for diagnosing problems since it allows us to conveniently gain access to the gene expression profiles of a person. We are not at a stage where we can control our sleep cycle at our convenience, but this is a step towards facilitating our understanding of this mechanism.

2- Western diet disturbs our bacterial guests

Original Article: De Filippo C. et al., PNAS 107, 14691 (2010).

Did you know that there are 100 trillions of microbes living happily ever after in your gut? This is about 10 times as many cells as make up the whole human body. But, no need to panic, because the sole purpose of their presence is to serve us by aiding in our daily digestion, metabolism and improving our immune system overall. A recent study shows that our friendly inhabitants are drastically affected by the human diet. A research group at Meyer Children Hospital in Italy analyzed and compared the fecal microbiota of children from Europe to that of children from rural African village of Burkino Faso (BF). When they examined the diets of each group closely, they saw that the BF diet is rich in cereals, vegetables and legumes, whereas the European diet is usually rich in animal protein, sugar, starch, and fat. Thus, children from Africa typically have a high-fiber diet and the children from Europe have a low-fiber diet. Next, researchers characterized the gut microbiotas of each group from fecal samples. The results revealed that gut microbiota was drastically different between these groups. Interestingly, BF children had several types of bacteria that seem to produce substantial amounts of short chain fatty acids (SCFAs) as a result of fiber-rich diet. The high levels of SCFAs are known to result in high energy levels and an increased anti-inflammatory capacity. The fact that African populations have almost no non-infectious colonic diseases may be attributed to the enriched diversity of gut microbiota due to the high-fiber diet of African children. This study once again emphasizes the importance of a fiber rich diet and it becomes clear that the adoption of such a diet and refraining from fast food culture would be beneficial to all of us.

3- Eat more, enjoy less

Original Article: Stice E. et al., The Journal of Neuroscience 30, 13105 (2010).

Why do obese people tend to overeat? A new study suggests a vicious cycle stemming from an obese individual’s desire to compensate for reduced pleasure from food. Degree of pleasure derived from eating correlates with the amount of released dopamine, which is associated with food intake. The researchers studied 26 overweight and obese volunteers, who were subjected to fMRI brain scans to identify brain regions that became active as they sipped both sugary milkshakes and a flavorless liquid. Every participant was tested twice over a six month period. Participants who gained weight showed significantly less activation in response to the milkshake intake upon a six-month follow-up relative to their baseline scan and relative to participants who did not gain weight. According to these results intake of palatable food results in down regulation of D2 receptors, reduced D2 sensitivity, and decreased reward sensitivity, implying that overeating may contribute to reduced striatal responsivity. These results will likely be important in developing programs to prevent and treat obesity, and also help us understand why obesity typically shows a chronic course and is resistant to treatment. Here is another reason to eat less: to get more pleasure from the food we eat.

4- Tough Malagasy spiders

Original Article: Agnarsson I. et al., PLoS one 5, e11234 (2010).

There are 40,000 kinds of spiders. They have little bodies, but the webs that they knit with their long thin legs using the silk from their tiny bodies are examples of great talent. Among the 200,000 types of silk which spiders produce, each have different combinations of properties, such as stickiness, durability or thickness, etc. A recently discovered spider found in Madagascar has an even more amazing talent. This kind of spider with its 3–5 cm long body size can make a web that can cross a river 2.5 meters wide with the ends of the nets attached to trees on either bank of a riverside. These nets have been found to be the strongest biological material ever known. After careful measurement, it was discovered that these webs are 10 times stronger (350 MJ/m3) than Kevlar, which is the material used in bulletproof vest, and some threads become even more durable (520 MJ/m3), which means that this spider beats even the most talented scientists and engineers with its skinny small legs and tiny little brain by developing material which is more than ten times tougher. It is believed that these spiders need to have strong nets in order to bare the extreme weather conditions above the river and catch the bugs flying over the river. There are still investigations that have yet to be done in order to find out further properties of such webs. “Verily in these things there are signs for those who consider.”

Moving on from that relation, I would like to open a small window onto the meaning of literature as I understand it. However, I must first beg that my readers pardon my humble statements on a subject that is in fact beyond my ability, and that they judge this essay not on how it stands, but for the good intentions with which it was written. I should confess that just as I and people like me with narrow horizons cannot judge matters even in our own field properly, so too is it very difficult for us to express other matters very clearly, even when we may have judged them correctly. And I think this is generally true of all who tackle this topic. For instance, after Imam Shafii had personally corrected his book Kitab al-Umm, and afterwards still others had repeatedly corrected it, he found that certain points still bothered him. He raised his hands to God and admitted that no book can be faultless, except for divine revelations.

Even the enchanting states inspired by the most magnificent pieces of writing, the greatest works of art, the most eloquent words, and the most dazzling conceptions which are not based on divine speech and are not illumined with the shining of His light have a completely relative beauty. And even if they hold any value in terms of being a reflection or an echo of the beauties He possesses, they can hold absolutely no individual value of their own.

Nevertheless, this reality should never dishearten us or paralyze our determination to work. We should always think, speak, plan, try to realize what we have planned, and while doing all this, we should never forget that we can occasionally make mistakes, that very often we can fall into error. This is natural; as soon as we recognize them, we will correct them, try to compensate for our shortcomings and stick to seeking the best possible alternative. Our decisions may not always be accurate, but we will try to fulfill what divine wisdom requires of us by implementing our human capacity for understanding and judgment (ijtihad).

So these humble contemplations must be seen in the same way. Speech was born with humanity, developed with humanity, and it constitutes a very significant depth of being human. So speech reached its contemporary level of maturity through history after having been repeatedly distilled through countless filters of thought and fashioned by masters of words, and then became what we now call literature. In this respect, it can be argued that the present moment of literature is brighter than its past, thus it can also be said that so too its future will be brighter than the present, or at least it should be so. As Said Nursi explains, human beings will eventually turn completely toward knowledge (ilm) so that they will derive their power from knowledge. As a result the ultimate say will pass into the hands of knowledge. At the stage when knowledge shows such a level of development, the command of language and eloquence, reaching its peak, will outweigh all other values. Possibly, in such a period, in order to make others accept their ideas, people will use language as a weapon, try to penetrate hearts through their facility with language and conquer souls with the charm of literature.

The reality of knowledge and speech manifested only concisely in Adam and it reached its most brilliant form with the Final Prophet, yielded its awaited fruit, and became fully realized in the Qur’an. Now, if the world is going to last any longer, in the years ahead, while knowledge reaches its peak, language too will rise to the rank of the interpreter of knowledge in almost all circles, accompanied by the most powerful of orators and richest of speeches voicing the truth.

The power of expression, which is always nourished and develops in the bosom of need and necessity, will flourish in this environment for one last time, make its voice heard as powerfully as it can. If you will, you could also say this will be the reliving of the Age of the Qur’an in its most mature state, an Age of the Qur’an where love of truth and love of knowledge, where zeal to understand and passion to explain, where human values and their appreciation will live alongside one another. Incidentally, I would like to underline one point: future architects of thought and masters of language should do whatever they can to protect and honor the power of expression, for it has fallen into the incapable hands of people like us. They should untie its tongue, so that it can voice our own world of thoughts. Otherwise, it is obvious that we will keep on hearing the cawing of crows where we expect to hear the singing of nightingales; we will not be able to be free of the distress of thorns on the way to roses.

The power of speech and refinement of eloquence have always developed, found its proper consistency, and come to maturity in the realm of literature and under the tutelage of literary thought. However, it is also very important what we understand-or we are supposed to understand-when literary thought or literature is mentioned.

Human beings have always expressed their feelings, thoughts, and the inspirations of their heart through cinema, theatre, and symbolic painting, along with oral or written literature. When the subject extends beyond spoken or written language, naturally gesture, facial expression, sounds and other means replace words and sentences. Even so, they have never been able to truly substitute for speech and writing. The most reliable way for a people to preserve their literature and make it flourish in its own framework and fertile ground is to put it into a written form. This turns it into a common source to which individuals may refer to at any time. It allows it to become as widely accessible as possible, paving the way for it to become the national style of an entire society, the nation’s shared property. It thus becomes a field of exposition for future generations, an exhibition ground of verbal excellence, and a trust to the common conscience, guarded by national memory and perpetuating its own origin.

In this respect, we have always sought literature in the magical world of written or spoken words and always realized our acquaintance and encounters with it among the pages of books and magazines. Whatever style is adopted in recounting a given subject – whether the work produced is approached with an artistic concern or expressed in a plain style, whether a small, select audience is targeted or large crowds are addressed – when literature is mentioned, what comes first to mind is the written word.

It does not make any difference whether the subject of a piece of literature is religion, an idea, philosophy, or doctrine; literature is one of the most important ways that humans can transfer the accumulation of knowledge they have gained through history from one generation to another. Through it they can sense all the depths and richness of yesterday in the present. They see the past and present as two dimensions of reality, and savor the future in its relative depth.

Furthermore, believers should firstly be faithful to their heritage and refer to it frequently, as much as they embrace universal human values. They should emphasize the essence of their common conscience and take it as an essential constituent. They should use this heritage as the canvas for the embroidery in which they depict their literary feelings and understanding of art, so that they do not destroy the spirit of their own literature, and are not constrained solely to foreign borrowings. If they use their own sources and weave their own cultural values on their own loom, there does not seem to be an obstacle to their progress, and they can walk to universality carrying the interpretations of their own time.

Believers should place the main sources of belief, cultural heritage and memory of universal values, in the center of their lives. Thus after having secured themselves from deviation, believers should strive to establish connections with the outside world; remaining indifferent to others’ values restricts what is normally broad and universal, is an obstruction to growth, causing agony for the living, and falling from the degree of being envied to a state of envying others; the condition of Third-world countries today presents so many living examples of that.

These countries always go through a period of standstill in their literature, sometimes due to customs, sometimes because of the influence of local understandings, and sometimes due to a fear of self-alienation-which can be empathized to a certain extent. Approaching literature liberally to a large degree ceased due to excessive reactions; some very important sources of inspiration were dried up, and efforts to enrich literature were perceived as fantasy and subsequently dismissed. Moreover, the field of literature was further narrowed at certain times by favoring a region or dialect at the expense of other varieties of the language; the branches with potential to develop were cut off and the roots were removed by prohibiting the field of literature from being ploughed. Thus, in such countries, the development of a language that may have been more representative of the wider society was prevented, and instead a dialect on the margins has been preferred over others, and as a result their literature was reduced to the voice of a small minority rather than becoming a respectable representative of literature in the world. This can also be called surrendering to oblivion.

In fact, what becomes dormant, stops growing, and what is not open to developing withers. Whatever is static then topples over. And that which does not give fruit dies. This is not limited to literature; it is true for almost every subject, from religion to thought, from art to philosophy.

Nevertheless, literature does not simply mean playing on words with written or spoken language skills and producing phrases people will like; it means making the art of expression lovable with the dimensions of eloquence and clarity. It is the water and air of feeding, adorning, and enriching daily language with the cleanest, purest, most lovable, and lasting material, and it is a treasure which increases with use.

A writer of verse or prose who pens his or her thoughts with literary considerations always relies upon a purpose and overtone; using a rich vocabulary, harmonious statements, and a grand style, writers activate words, long and short, aiming for excellence of expression. While moving toward this aim, writers place all the words or sentences they have picked and fitted in their places in such a way that they all sound out like notes serving to support the general theme of the tune they play. As these sounds and notes voice their intended ideal, they continue to play in the background, reflecting the author’s mode of thinking, general tendencies and mood.

In a lyric verse, produced by a master of expression the words, feel as if they are filled with that person’s excitement. The words, sentences, or lines, springing from a literary heart kindled with epic feelings, ring in our ears like the march of a glorious army. All the words in a masterfully written drama resonate in the depths of our soul and almost bring to life the story therein. A literary person is able to think very differently and reach different judgments; writers always pursue quality and strive to leave future generations a legacy they will gladly inherit and respect.

Actually, like literary language, daily language also has its own kind of beauty, ease, allure, and naturalness that entices pure pleasure. However, literary language is poetic, musical, and constructs a pleasing whole in harmony with the meanings it holds. It is superior in linguistic utilization, taste, and refinement in the way that demonstrates coherence within the text as a whole and cohesion between words and sentences. Let alone feeling and savoring these, it is sometimes very difficult for people who lack the aptitude to even understand them.

All that notwithstanding, it is not correct to regard literary style as the language of an upper class or an aristocratic group. On the contrary, even if they cannot penetrate as far as the secondary meanings and connotations suggested by the composition, people of every level should somehow be able to understand, and they should be able to benefit from that source, even if only in a limited way. Thus, in time they will be elevated to a level where they can express their feelings and thoughts more comfortably and gain greater language skills through the expansion of their knowledge. In the meantime, they will consolidate what they already know of language, enrich it by making suitable contributions as far as they can, and add new depths to their horizons of thought.

No matter at what level, the language almost all of us speak today, which has quietly settled in our memories through generations, is to a great extent the fruit of master poets’ and writers’ concerted efforts that have been adopted by our souls. With the sensitivity of a goldsmith, these masters of expression presented us with the beautiful jewels of expression and necklaces of words that they prepared; thanks to their legacy, we express ourselves through this rich resource to the best of our abilities. Even though not everybody understands the magnificent works they produced and the aesthetic depth in the spirit of those works, all of us have always appreciated them and felt eager for more. For such a level of appreciation one does not need to know the writer’s artistic anxiety, power to construct, mental strain, success in planning, nor his or her true value to the extent a skilful goldsmith knows the precious stones.

People have always held the literary artists in high regard, certainly with exceptions. They have applauded these people’s efforts, appreciated their labor, and frequently expressed this appreciation by imitating them. Then what falls to literary people is that they put their language skills and artistic talents at the service of the right, good, and beautiful, instead of hurting the souls of the masses-who can be regarded as their apprentices-by describing what is corrupt, or contaminating people’s pure thoughts with dirty images, and condemning them to the slavery of materialism with descriptions of carnal desires. According to Bediüzzaman Said Nursi, people of letters need to have high morals and act within the universal codes of conduct prescribed in divine scriptures. He also reminds us of the divine source where the “power of expression” originates from and advises us to duly respect this capacity, which is regarded as an important depth of our humanity.

Literary styles of expression are different than other styles. For example, in scientific writing or speech it is essential to have a sound pattern of reasoning, a systematic thought, well-versed statements, and no mental, logical, and emotional gaps should be left unfilled. Oratory style emphasizes proofs and arguments, maintaining interest and enthusiasm, making occasional repetitions, supporting the narration with paraphrases when necessary, using colorful expression, and enlivening the speech by inspirational shifts without detracting from the main axis. On the other hand, literary style requires a variety of linguistic arts, such as vividness of expression, accuracy of language, beauty of presentation, richness of imagination, the utilization of metaphors, parables, idioms, figures of speech, and allusions-as long as it does not reach the point of excess. Because excess will spoil-as in everything else-the naturalness of language and muddy the heavenly spring of expression, people of sound taste will mostly find it strange. As Said Nursi also expressed, the wording should be as ornate as the nature of the meaning allows. Form should follow content, and while it is being crafted, permission for literary license should be requested from the meaning in order to avoid excess. The brightness and resplendence of style should be given proper due, but the aim and intended meaning should never be neglected. The imagination should be given room to maneuver, but not at the cost of the Truth.

The complex nature of genetics and its wide implications for all living organisms from viruses to humans provide raw materials for creative imaginations. In the present scenario, many consider it vital to comprehend all the genetic information necessary to support life on this universe. One of the common constraints on the understanding of genetics is the assumption that genes are the sole causes of all activities of living organisms and can explain all aspects of biological life on earth. For example, some believe the behavior and development of an organism can be predicted, if its genetic information is known-this belief is called “genetic determinism.” However, it is true that neither all aspects of inheritance are in all cases well explained, nor that the mere effect of genes on complex traits is well interpreted. The boundaries of the effects of genes on physical existence, development, survival, and the behavior of organisms are not always simple and straightforward. The capacity of humans for genetic manipulation-at least as it is commonly assumed or claimed-is limited in several ways and some of the basic causes of such barriers have yet to be explained. The focus of this article is to point out the limitations on attempts to appoint genes as the driving force of life.

The Central Dogma

Genes are small fragments of genomic DNA, encoding mRNAs which are later translated into proteins that participate in different biological metabolisms, hence conferring different traits on an organism. The biological functions and transmission patterns of genes over generations were being investigated well before the discovery of DNA as hereditary material and date back to the recognition of Mendel’s laws in the early twentieth century. Genetic information is coded in the form of a short string of DNA called a gene, which is employed in the expression of a trait(s) or mechanism(s) through synthesizing a chain of amino acids called proteins. These proteins either can be stored in different body parts or serve as enzymes in various biochemical reactions such as fighting infections. This flow of genetic information from gene–mRNA–protein synthesis is called the “Central Dogma” in biological sciences. In this biological doctrine, a very solid and predictable mechanism is assumed. Prior to the release of the human genome sequence information, the number of genes in the human genome was estimated as ~100,000. However, this estimate was far more than the actual number of genes (~35,000), which led us to question the validity of the “Central Dogma” as an explanation of the complexity of human beings. Out of these ~35,000, only 300 genes are unique to the human species.¹ This is another blow to the authenticity of the original central dogma theory. Are those 300 genes the foundation of all humankind and do they distinguish us from the rest of the mammals? Reducing humankind to its biology and explaining it based on genes has been questioned extensively and could be the subject of another discussion. But even considering such a view valid for purely practical purposes, the big gap between humans and other mammals cannot be due to the existence of this small number of genes.

Recent scientific discoveries have revealed a key point about the structure of genes-that each gene has a set of sub-segments called exons. Each exon can make a new protein. Hence, the gene can be the template for more than one protein. In the presence of other genes and proteins, the code of a particular gene can yield different kinds of proteins under variable circumstances. The flow of information can be both ways, and hence there are no predetermined factors controlling the flow of information. That means, we might know the information on what genes are present, and we can even decode it to know what is in there, but we cannot be sure what result (proteins in this context) will come out at the end when it is in the context of real life.

From physical characteristics to their genetics

Working back from a particular trait and trying to infer the genes that are involved in expression of such trait is a different approach to reveal the role of genes but surely it is not an easy task. Traits that are expressed by a single gene or a small number of genes are known as Mendelian/qualitative traits and their pattern of inheritance is simple and detection of the gene(s) is straightforward. Some of the disease resistance in plants and blood groups in humans are classic examples of Mendelian traits. The main distinction between such traits and the quantitative ones is their discreteness. For example a human being can have only one of four blood types: A, B, AB or O, and each of these groups is solid and no other blood types exist in between. In this type of trait, the role of a particular gene(s) is usually predictable and the pattern of transmissions over generations both for the future and the past can be inferred.

However, only a small percentage of traits is qualitative and expresses Mendelian inheritance. Most traits, such as intelligence, skin color in humans, height of an organism, seed yield of a grain, and diseases that have genetic causes like cancer, are quantitative traits and complex in nature. The ultimate phenotype (what we can see or measure from a trait) emerges from the joint effect of many genes as well as interaction with the particular environment in which the individual develops. The number of genes that is involved in the expression of a particular trait can be hundreds or even more. An objective assessment of each trait and quantification (called the phenotype) is impractical in most cases and could lead to another discussion. But assuming that we can measure a trait feasibly, the inference of genetic bases could still be controversial. Considerable efforts have been devoted to unveiling the effect of genes in the expression of complex traits whose inheritance pattern deviates from Mendelian inheritance. A special genetic technique, known as genetic mapping, is used to identify multiple genes that underlie a complex trait and this has practical applications for crop improvement. In humans, efforts are directed toward the detection of genes which predispose to complex inherited diseases. In this type of situation, the effects of genes on a trait are additive and can only explain a certain amount of change in the trait that we are interested in. Detection of all genes involved in the expression of a quantitative trait is practically impossible. The environment is an important factor with a pivotal role in the expression of such traits. The term “environment” is not restricted to what is present within the cell or surrounding the cell or individual. It rather refers to larger scale effects in the process of biological life that cannot be explained by genetics and the term can be used interchangeably with non-genetic effects.

One of the most striking examples of the role of genes on the expression of the phenotype is the presence of differences between identical twins. Despite the fact that they have completely identical sets of genes, studies have shown that twins can indicate different degrees of psychiatric diseases such as bipolar disorder.² Similar phenomena may be observed in crop species. In crop breeding programs different varieties are usually tested in different environments. In most cases varieties rank differently based on their performance in different environments.³

Genetic background

Genes that do not code any information for the trait of interest can also be a part of the process of expression of the trait. In other words, certain genes can be employed to stop or alter the function of a particular gene. Modifying the utility of a gene can also be done by a series of complicated reactions within each organism through mechanisms known as epigenetics. This type of alteration in gene function is also observed empirically during the process of transferring genes between different organisms through genetic engineering.⁴ Most transferred genes are silenced (turned off) by different mechanisms in a new organism regardless of patterns of inheritance. This is particularly interesting because it clearly indicates that the existence of a particular gene in the body does not necessarily guarantee that it will be functional. Even if it is functional in one individual, it might be silent in others. Even if a gene is functioning in all the individuals carrying it, the degree of expression may be variable.

The end of genetic determinism

With the discovery of the code of genes, we now know more about the biology of living organisms than ever before, as new genetic tools have enabled us to better understand what kind of information is stored in each gene.

Most of the traits of living organisms are affected by the existence of many genes as well as non-genetic effects (denoted as environment in genetics). Although Mendelian traits can be predictable to some degree, yet we can not completely infer all the genes that are employed in the expression of a complex trait, nor the amount of contribution from each single gene and portion attributed by non-genetic factors. So we cannot determine the presence of genes by simply observing the phenotype or expression of a trait.

Considering each individual gene separately will allow us to understand its possible functions more clearly and accurately. Nevertheless, the knowledge of possible functions and structure is not enough to predetermine if the information coded in the gene will be used by the organism, and, even if it will be used, how much of that information will be processed is uncertain. Whether the information that is processed will be observed or not is another ambiguity.

Assuming that we can and will know all components of life by having the knowledge of genes is known as genetic determinism. In some cases, genes are described as independent entities that drive living organisms and manage life because of the assumption that their presence will be enough to predetermine all the biology and the behavior of an organism.

Simply, in order for a gene to be an independent agent by itself, it needs to have the knowledge of all other genes as well as all the non-genetic factors for expression of a simple trait. In reality, genes contain a very limited amount of knowledge which makes them no more than tools or parts of living organisms that are employed in the existence of life on earth. Biological life itself is incredibly complex and its sustainability requires a more comprehensive knowledge that is beyond our current understanding based on the genetic code.

Seyyidhan Mirza is a PhD candidate of Plant Breeding, Genetics, and Genomics. He can be contacted at seyyidmirza@gmail.com.

Notes

1. Siepel A., M. Diekhans, B. Brejová, L. Langton, M. Stevens, C. L.G. Comstock, C. Davis, B. Ewing, S. Oommen, C. Lau, H. Yu, J. Li, B. A. Roe, P. Green, D. S. Gerhard, G. Temple, D. Haussler, and M. R. Brent. 2007. “Targeted discovery of novel human exons by comparative genomics.” Genome Research. Cold Spring Harbor Laboratory Press; ISSN 1088-9051/07; www.genome.org
2. Cardno, A. G., Rijsdijk, F. V., Sham, P. C., Murray, R. M. & McGuffin, P. “A Twin Study of Genetic Relationships Between Psychotic Symptoms.” 2002. Am. J. Psychiatry 159, 539-545
3. Epinat-Le Signor, C., S. Dousse, J. Lorgeou, J.B. Denis, R. Bonhomme, P. Carolo, and A. Charcosset. 2001. “Interpretation of genotype x environment interactions for early maize hybrids over 12 years.” Crop Sci. 41:663–669
4. Kooter, J.M., Matzke, M.A., and Meyer, P. 1999. “Listening to the silent genes: Transgene silencing, gene regulation and pathogen control.” Trends Plant Sci. 4: 340–347

With all respect for its grandeur, I have to confess my inability and insufficiency to elaborate on the depth of meaning and richness of expression and style of the Qur’an. A considerable number of studies have been dedicated to the Qur’an, and many more studies will be carried out on this topic. There is no doubt that all these studies have presented valuable content for any seeking person to grasp the gist of what the Qur’an stands for and to believe in its message, and they mirror the order of Islam in its true essence. However, it would not be right for anyone to claim that they have come up with a perfect interpretation of the endless content of this expository atlas of humankind, the universe and the truth of Divinity. The Qur’an can be interpreted only to the extent that a heavenly and Divine word can be interpreted by human perception. Thus, although it does not seem to be possible to spell out this huge atlas within the measures of an article, we cannot stay indifferent to or neglect studying the Qur’an with the excuse that our interpretations are deficient or the power of our discourse is inadequate. Everyone has the right to study the Qur’an, more than that, it is a duty upon those equipped with necessary, accurate knowledge. We should work harder to better understand the Qur’an, while the learned should wield all their perceptiveness and sensations toward understanding it and conveying its message, allowing a wider audience to learn more from it.

The Qur’an is a miracle of eloquence honored with the merit of being the voice of all ages. It is the most luminous expression of the Divine Speech, around whose light the angels hover like moths. If we take into consideration its Source and purpose of revelation, its first representative(s) and the impact it leaves on hearts, then we must realize that it is not a book to put to one side. When the Qur’an speaks, angels fall deep into a silent vigilance, spirit beings fall prostrate, and the jinn, enchanted with its voice, set out to the deserts to meet it.

The Qur’an is the expression and explanation of God’s laws of creation or “nature,” and the strongest and immutable source of religious rules and pillars. The Qur’an is the indisputable Book that includes the most reliable criteria for studying existence (the whole universe and humankind), thus for all individual, familial, social, or ethical problems we must seek wisdom and illumination from the Qur’an; it cries out that its source is the all-encompassing Knowledge of the One Who knows everything with their causes and results. The Qur’an has captivated everyone to whom its voice has reached-provided they were not prejudiced-with its holistic perspective, comprehensive discourse and style, the vastness of its content and meaning, its delicate expressions, its magical expounding in proportion to the different levels of knowledge and understanding, and its capacity to penetrate souls. Neither its friends nor its foes have been able to come up with something in a similar style or an utterance that is equal in grandiosity, the former motivated for imitation, the latter in fury to choke off its voice, despite their efforts for almost fourteen centuries, even when they use the same material and concentrate on the same issues. Their works have never been able to overcome artificiality, they have never been appreciated by masters of literary skills, and they have never evoked any lasting or effective influence.

The Superiority of the Qur’an

The Qur’an has such a musical harmony and delicate correlations between the topics it deals with, be they interrelated or apparently unrelated with each other, so that one is able to realize, with only the slightest effort of comprehensive thinking, that many apparently unrelated topics have points of junction. The mastership of discourse belongs to the Qur’an, which no literary personality can challenge, and enables those of its audience who are unprejudiced and can judge with some reason to obtain some things from it, introducing them to deeper contemplation beyond their horizons of thought. If once they can judge fairly and let their souls delve into this heavenly waterfall of expression, all other speech-like voices will immediately turn into nothing but rumblings.

Above all, the Qur’an has come from an all-encompassing Knowledge; it contains and explains the meaning and content of human and non-human existence, of humankind, nature, and all the worlds; it is both their language and interpreter of their purpose of creation. It speaks to multifarious dimensions of its audience all at the same time: while addressing the mind, it does not neglect to speak to the heart in its own language; when it calls out to the consciousness, it does not push emotions aside; while conversing with the faculties of reasoning and logic, it does not leave the soul without any favor. All faculties and senses, external and internal, benefit from the Qur’an, which gives each its share without giving rise to any deprivation and contradiction. They all receive their share from this heavenly table, each to the extent of its capacity, and enjoy a most harmonious composition.

All Divine Scriptures, especially before human interpolations were mixed with the original texts, possessed the same holistic approach and all-embracing quality; nevertheless the superiority and widest comprehension of the Qur’an are evident in proportion to the profundity of the spirit of the Prophet Muhammad, upon him be peace and blessings. It is by no means possible to show any other heavenly or man-made book which excels it with its content and extensiveness. It is by no means an exaggeration to claim its uniqueness in dealing with humanity, the universe and Divinity in the most comprehensive, as well as the most exquisite fashion, while interpreting them in the best forms of synthesis and analysis in its own way.

Topics in the Qur’an

All of the topics that the Qur’an deals with are the most valuable treasures of the truths pertaining to Divinity and the realm of creation. Some of these truths are decisive or explicit in meaning and content, and others are concise, metaphorical, and allegorical, the explanation of which has been entrusted to the one who brought the Qur’an, upon him be peace and blessings, and the scholars favored with inspiration. The Qur’an never complicates any of the matters it presents or analyzes. It presents topics concerned with the essentials of faith, worship, and morality, and basic principles of individual and social life clearly and succinctly; while for matters requiring comprehensive thinking, reflection, and careful consideration, it demands deeper examination and scrutiny, and suggests turning to God, without approving of burdening oneself with grave matters that one cannot shoulder. Like a magical chandelier which continuously shines brighter, it is a means for brand new discoveries at diverse wavelengths as hearts and minds go deeper in thought, thus offering Divine gifts of all kinds to our internal and external senses. With its blessings and inspirations augmenting in excess, and light rain becoming a deluge, and with its endless beauty and glittering lights, the Qur’an showers banquets one within another to those who ponder and study it.

True understanding of existence and what lies beyond the sensed dimension of the cosmos, and also humankind with its spiritual depths is possible only through the Qur’an. They discover in its bright realm straight thinking and real sources of reflection, and are thereby saved from the vicious circles of deception and misjudgments based on probabilities. There is no other source of knowledge that is not mistaken or not entrusted to uncertainty or doubt other than this miraculous Speech from God, the All-Knowing of the Unseen. The Qur’an explains and presents everything explicitly, plainly, and correctly. It enables us to understand that it is we who make errors in evaluating the issues, giving rise to contradictory judgments and in filling in the gaps entrusted to reflection. Understanding and interpreting the Qur’an correctly is not only a duty upon us, but also a requirement of our fidelity to it. The fulfillment of this duty and fidelity is closely related with the erudition of every capable and well-equipped individual and in their living in devotion to God. Such individuals dive into this vast ocean with utmost sincerity and commitment for the good pleasure of God, uncovering the truth so that it flourishes. They proceed toward this infinite horizon with caution, composure, comprehensive thought, and without surrendering to their carnality. The Messenger, who brought the Qur’an from God, is their first and greatest guide; they follow the pious scholars among the earliest generations of Islam in the light of its expressions, which are decisive and explicit in meaning and content. They are less likely to err; their efforts to attain the pleasure of God are rewarded with special treatment. Their interpretations and explanations of the Qur’an are each a hue and adornment of Qur’anic uniqueness.

A sound interpretation

On the other hand, the Qur’an cannot be explained as it deserves in consideration of its position and loftiness with rudimentary Arabic and the limited scope of dictionaries; such an attempt would also be manifest disrespect to this heavenly monument of speech. It should be rendered in other languages as is required. Anything concerning Qur’anic expositions (tafsir) should be very well versed and before they are launched, every tafsir should be tested against the exalted Islamic sciences. What falls to us is not to bring the Divine Word down to our level of perception and expression in its immeasurable immensity and depth, excusing such an act as we have translated it for the benefit of everyone. While it is a duty, an appreciation of, or an act of respect toward the Qur’an for experts to make the Qur’an known to everyone via exposition, interpretation, or a commentary, such an attempt would be paramount to insolence if one did not have a high command of Arabic grammar, the principles of rhetoric or eloquence, knowledge of the study of Qur’anic exposition (tafsir), the methodology of hadith studies (Traditions of Prophet) and Islamic jurisprudence (fiqh). The Qur’an cannot be translated as a novel is; even the translation of a novel calls for an expertise in its own genre. Forging the way toward a sound interpretation of the Qur’an, it would be better to discuss first what a “translation” is, and what tafsir (exposition) and ta”wil (commentary) mean. Translation is the rendering of a text or statement in one language into another language, while preserving the meaning. An accurate translation would be to transfer the exact meaning of every word—if this is ever possible—while preserving the relationships between word combinations. On the other hand, a literal translation of the words only, or an exclusively semantic translation would be a deficient translation. To a certain extent we can also talk about translation software; however, the current technology or even more advanced technology to come is not able to help very much in the translation of substantial literary works. Consider the situation when the text is the Word of God, which addresses all times, conditions, and levels and therefore the exposition of which with all its depths is considerably dependent on time, inspiration, and circumstances. Some works of literature are said to be impossible to accurately render; then it is clear that there is no way that the Holy Qur’an, with its immense profundity, can be expressed by an ordinary translation. Many Muslim scholars, including Bediuzzaman Said Nursi, are of the opinion that it is impossible to translate the Qur’an, due to the aforementioned and many other considerations. Some other scholars, on the other hand, approach the matter cautiously, but more moderately, provided that the prerequisites underscored above have been abided with. The late Hamdi Yazýr, one of the greatest contemporary expounders of the Qur’an, states that the translation must exactly correspond to the original text in terms of explicitness and indications, conciseness and comprehensiveness, generalizations and specifics, restrictedness or exclusiveness and inclusiveness, powerfulness, and appropriateness, and eloquence and style. Therefore, prose or poetry can be translated into another language which is as developed as the original language, with the condition that the translator is well-versed with the subtleties of both languages; however such a translation is hardly possible for a book which addresses the mind and heart, the soul and all the senses together, with all its diverse literary delicacy, and its vigor and exuberance. And what happens if the book to be translated is a work of God that transcends all other books Divine or non-Divine with its dimensions beyond time and space, and speaks to all ages?!…

To be understood and to be lived by

The Qur’an is, in the words of Bediuzzaman Said Nursi, a Divine interpretation of the book of existence; it is the voice and breath of the laws of creation, the true interpreter of things and events that bear multifarious meanings, a candid expounder of this world and the world to come, the revealer of the treasure of the Divine Names hidden in the heavens and on the earth, the mysterious key to the mysteries beyond all things, the plain language of the beyond manifested in this world; the sun, the foundation, and the geometry of the spiritual world of Islam, the sacred map that explicitly lays out the worlds of the Hereafter with clearly drawn lines, the voice and clearest interpreter of the Divine Essence, Attributes, and Names, the most reliable teacher of all humanity; the air, the water, and the light of the Islamic world, and the Word of the All-Exalted, All-Majestic Being, Who is the Creator and Lord of all worlds, and His decree and address. This is not to say that the Qur’an cannot be understood; on the contrary and most importantly of all, it was revealed to humanity to be understood and to be lived by. However, its phrases are so deep and have so many meanings, its content is so multi-layered, that even if we can know and understand the meaning of every single word, and sense certain things from word combinations, we will certainly miss many truths that are contained in styles, indications, suggestions, connotations, and purposes, that cannot be fully reflected in any translation. I am of the opinion that every person who approaches the Qur’an with an open mind can perceive all of the above characteristics, and thus appreciate that its sublimity and transcendence cannot be confided to a simple translation. A translation might certainly have some value in proportion to the translator”s learning, knowledge, horizon of perception, and skills; however, it can never convey the Qur’an in all its profundity; therefore no translation, nor no commentary or interpretation can be called the Qur’an itself. A number of books have been written about Qur’anic interpretation and commentary, while objections to the Qur’an and some of its contents have been repeatedly addressed. Many more interpretations and commentaries will continue to be prepared in the future too, just as many new objections will be answered, and this will perhaps continue until the end of time. How many new doubts will be manufactured about the Qur’an; how many more times will minds be exposed to contamination; what new unthinkable plots will Satan, our eternal enemy, play on weak believers; what new scenarios, unheard of until today, will the devils of humankind and jinn put on the stage to tempt humanity; how many more times will they induce suspicion with regards to our values and agitate people? Such animosity has always existed and will continue to exist. Thankfully, hundreds of people with zeal to serve the Religion, will always stand to face them by exploring new depths of that Book of lofty truths and strive to interpret that Eternal Speech, which they hold in the greatest esteem. The mischievous organizations of Satan and his companions will always be challenged by the companions of the Qur’an.

An abridged version of Fethullah Gulen”s introduction to The Qur’an with Annotated Interpretation in Modern English by Ali Ünal.

He is the Lord of the heavens and of the earth, and all that lies between them; He is the Lord of the Lasts. (Saffat, 37.5)

The concept of the Lord of everything is defined in this setting and within the limits of our knowledge. Since the earth, the sky and all else in between have been mentioned, a different reality or a different spatial continuum is not in question. The verse does not end there, however. A new concept is added: ‘He is the Lord of the Lasts.’

So, in addition to the earth, the sky and all in between, we have the concept of ‘Easts’. In Arabic, the plural form is used for three or more things. Therefore, God is the Lord of at least three Fasts, or of many Easts. What kind of scientific concept does this verse introduce? Before seeking an answer to this question, let us call to mind certain facts.

It is a commonplace that we conceive of space in terms of three dimensions. The existence of an object is determined by the space it occupies with respect to the dimensions of length, width and height, in addition to its position.

But is the universe composed of, and space constituted by, these three dimensions alone? Until Einstein’s Special and General Theories of Relativity, scientists believed that the universe consisted of three dimensions. The world-famous physicist, however, determined on the basis of mathematical calculations that there are more than three dimensions and that a fourth, fifth or higher number of dimensions would introduce different concepts of space.

According to Einstein, the fourth dimension is time. Time is not simply a matter of reading a clock, but a dimension of the same order as height, width and length. It is coextensive with the other dimensions. Our visual perception, however, can see in only three dimensions and no more. In fact, some organisms cannot even see the dimension of depth: lizards and snakes see the world in two dimensions, like a photograph or a movie cartoon.

Starting from this milestone of physics, we would have to conceive of spaces other than ours, and in addition to the physical space we observe in the universe at large. In these spaces, velocity is different, time is different, action is different; and so are translation, convergence and regression. This is why the concept of ‘worlds’ introduced by the Qur’an is an expression of such diverse spaces. The world of angelic beings, Heaven, Hell, and the world of spirits all lie in the domain of such spatial continua. Our difficulty in conceiving of them stems from the perceptual deficiencies of our three-dimensional habits.

Having noted this, let us now recall the final part of the verse: ‘He is the Lord of the Easts.

‘East’ is the expression of a direction, a dimension. This expression occurred for the first time in connection with the sun. The word ‘orientation’ or finding one’s bearings implies the Orient or East as the first or primary dimension. Although the expression Lord of the Easts and of the Wests occurs in many verses in the Qur’an, only the Easts are mentioned in this verse. This is why we are dwelling on this point at such length.

The point is that ‘the Easts’ are proclaimed as a set of directions, quite apart from the existents we refer to as the earth and sky. With this verse, God draws our attention to other directions and dimensions, indicating the existence of worlds and spaces composed of dimensions other than the physical world we are familiar with. In a sense, He says I am the Lord of the Easts in order to introduce the notion of infinite dimensions, which contemporary physics is just beginning to discover. But why only the Easts? Because in the definition of dimensions, the first dimension is the East, whereas the West is simply an extension of the Eastern dimension in the opposite direction. We can say that this verse clearly heralds the existence of thousands of spaces and worlds embedded in an infinite-dimensional matrix.

Many other meanings derive from the verse besides the meaning discussed above. I would like to mention two of these.

The meaning ‘births’ can also be derived indirectly from the plural mashariq. In this case the meaning points to a different scientific truth. The East, which is where the sun rises, also symbolizes the direction in which the earth moves around the sun. But, do we have only one East, or only one motion in the universe?

No. While the earth revolves around the sun within the solar system, the sun is also revolving around the Milky Way galaxy together with its family of planets. The Milky Way, in turn, is revolving around the central axis of the supergalaxy or local cluster of galaxies to which we belong. Thus, we may well speak of three different Easts.

This meaning, therefore, is also hidden within the statement ‘Lord of the Easts’ (rabbul-mashariq). The very fact that magharib (Wests) does not succeed mashariq (Easts) in this verse is a confirmation of this. We shall see while interpreting future verses that there are many statements in the Qur’an pointing to the rotation of the earth. For this reason ‘East’ in reference to the earth’s revolution is in the plural, indicating that these rotations occur at many levels.

If we take the verse from the standpoint of a direction on earth, the concept of the East differs for each location on the globe. The east of Turkey is in the east with respect to its western regions, while our east is actually west from the standpoint of Iran, which lies even further east. Therefore, the East concept is different at every point on earth, and these concepts form an ensemble of Easts. This concept geometrically defines the surface of a sphere.

Let us now reread the verse in order to discover another significant scientific observation: He is the Lord of the heavens and of the earth, and all that lies between them; He is the Lord of the Easts (Saffat, 37.5).

The heavens, as we also see from other Qur’anic verses, are very diverse spheres. So what does the expression ‘between the heavens and the earth’ mean? It is known that meteors, stars, even angels and various unknown beings, can be encountered at various levels of the sky. What are ‘those between earth and the sky’? As far as we can tell, they are invisible rays which form the basic building blocks of matter and energy. These rays, earlier lumped together under the generic term ‘cosmic rays’, are differentiated in modern physics within the broad categories of nucleons, haryons, leptons and fermions. These are the subatomic constituents of matter and energy.

With the expression ‘He is the Lord of the heavens and of the earth, and all that lies between them’ God explains that all these energetic particles and rays constitute a vast physical order subject to God’s attribute of Lordship. Modern physics has viewed these incomprehensible energy dissipations and rays with unease, almost seeing them as dangers threatening the destruction of the universe. The Qur’anic verse reveals that, on the contrary, they form a gigantic physical balance under the superintendence of God.