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	<title>traits &#8211; Fountain Magazine</title>
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		<title>Science Square (Issue 92)</title>
		<link>https://fountainmagazine.com/all-issues/2013/issue-92-march-april-2013/science-square-issue-92/</link>
		
		<dc:creator><![CDATA[The Fountain]]></dc:creator>
		<pubDate>Fri, 01 Mar 2013 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 92 (March - April 2013)]]></category>
		<category><![CDATA[aggression]]></category>
		<category><![CDATA[aggressive]]></category>
		<category><![CDATA[billion]]></category>
		<category><![CDATA[cancer]]></category>
		<category><![CDATA[cells]]></category>
		<category><![CDATA[correlation]]></category>
		<category><![CDATA[cosmological]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[Double Helix]]></category>
		<category><![CDATA[facial]]></category>
		<category><![CDATA[guanine]]></category>
		<category><![CDATA[light]]></category>
		<category><![CDATA[physical]]></category>
		<category><![CDATA[principle]]></category>
		<category><![CDATA[researchers]]></category>
		<category><![CDATA[Science Square]]></category>
		<category><![CDATA[shape]]></category>
		<category><![CDATA[skull]]></category>
		<category><![CDATA[structure]]></category>
		<category><![CDATA[structures]]></category>
		<category><![CDATA[study]]></category>
		<category><![CDATA[traits]]></category>
		<category><![CDATA[universe]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2013/issue-92-march-april-2013/science-square-issue-92/</guid>

					<description><![CDATA[Facing Aggression Gómez-Valdés et al. Lack of Support for the Association between Facial Shape and Aggression: A Reappraisal Based on a Worldwide Population Genetics Perspective. PLoS ONE, 2013; 8 (1) It is a common misconception that some people are profiled to be angry or aggressive because of their physical appearances, particularly their craniofacial shapes. In [&#8230;]]]></description>
										<content:encoded><![CDATA[<h3><b>Facing Aggression</b></h3>
<p><em>Gómez-Valdés et al. Lack of Support for the Association between Facial Shape and Aggression: A Reappraisal Based on a Worldwide Population Genetics Perspective. PLoS ONE, 2013; 8 (1)</em></p>
<p>It is a common misconception that some people are profiled to be angry or aggressive because of their physical appearances, particularly their craniofacial shapes. In addition, there have been some studies suggesting that men with certain facial traits (round-shaped faces) are more likely to develop aggressive and unethical behavior. A new study using a sample of around 5000 individuals from 94 different countries has found no correlation between facial shape and aggressive/criminal behaviors. Researchers analyzed fWHRs (facial width-to-height ratio) and 2D/3D craniofacial landmark coordinates to estimate any possible correlation between skull shape and aggressive behaviors in men. First, they utilized the famous skull collection in Hallstatt/Austria to investigate any potential correlation between skull features and life history parameters of individuals, such as their overall fitness. Second, they analyzed the male prisoners convicted of crimes like inter-personal aggression (homicide, robbery etc.) from Mexico City Federal Penitentiary to see whether there is any relation between skull shape traits and aggressive crimes. Analyses of both databases have found no significant correlation between skull shape traits either with the fitness of males or with their aggressiveness. This study has very important social and political implications in today’s societies, as we unfortunately see many ethnical, racial and even physical prejudices. This comprehensive study has undoubtedly showed once more that physical traits cannot be a reliable predictor of complex human behaviors, which are mostly shaped by external factors such as education and socio-cultural practices.</p>
<h3><b>Biggest Structure in the Universe Discovered</b></h3>
<p><em>Clowe et al. A structure in the early Universe at z ∼ 1.3 that exceeds the homogeneity scale of the R-W concordance cosmology. Monthly Notices of the Royal Astronomical Society, January 11, 2013 </em></p>
<p>Throughout history, mankind has been trying to answer the questions of “how big” or “how far,” when looking into the vast expanse of the universe. As new technologies are developed, bigger discoveries and consequently bigger numbers are brought to light. An international team of astronomers recently discovered a collection of 73 quasars which form a single structure; the largest structure ever observed in the entire universe. A quasar, short for quasi-stellar object, is the luminous center of a galaxy that surrounds a super massive black hole. The distance of these newly large quasar groups to the earth is about 9 billion light years (1 light year is approximately 9.5 trillion kilometers). The size of these structures is simply mind-blowing. Even if we have a spacecraft that travels at the speed of light, it would still take about 4 billion years to cross. If we put this overwhelming size into perspective, the Milky Way—earth’s home galaxy—is only about 100,000 light-years wide and our neighbor galaxy Andromeda is only 2.5 million light-years away from the Milky Way. So these quasars are 1600 times larger than the distance from the Milky Way to Andromeda. This discovery seriously challenges the size calculations based on the widely accepted Cosmological Principle which assumes that the universe is essentially homogeneous when viewed at a sufficiently large scale. Cosmological Principle predicts that there should not be any structure in the universe larger than 1.2 billion light-years. A four billion light-years wide structure would obviously be an outlier when compared to other structures in the universe and it might contradict with the homogeneity of the universe. However, scientists think that such contradiction would not necessarily falsify the Cosmological Principle originally established by Albert Einstein. It might only change the assumptions of the theory that define at which scale the universe can sufficiently be viewed.</p>
<h3><b>More Twists on Double Helix</b></h3>
<p><em>Biffi et al. Quantitative visualization of DNA G-quadruplex structures in human cells. Nature Chemistry, 20 January 2013.</em></p>
<p>About 60 years ago, on April 25th 1953, James Watson and Francis Crick published a one-page paper where they described the “double helix” structure of the DNA, the molecule that carries genetic information from parent to offspring. This discovery not only revolutionized the biological sciences and medicine but also dramatically changed the way we perceive life, nature and most importantly ourselves. Yet, new findings on DNA structure keep surprising us. Scientists from Cambridge University discovered the first quadruple helix—a four-stranded DNA structure in human cells which they named “G-quadruplex.” These structures were previously observed in test tubes but they were never found in cells. The building blocks of DNA molecules consist of four different bases: Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). G-quadruplexes (G stands for Guanine) are formed by four guanine bases that forms a square DNA helix. Researchers found that these structures are enriched in rapidly-dividing cancer cells, specifically at the ends of chromosomes called telomeres. When researchers targeted and trapped these quadruple DNA structures with synthetic molecules, they found that DNA replication slows down and cell division is blocked. Researchers suspect that these quadruple DNA structures in telomeres of cancer cells could explain why cancer cells rapidly proliferate and divide. It is still not clear whether G-quadruplexes exist in healthy cells but targeting these structures in cancerous cells with pharmacology seems to be a promising method to stop the spread of cancer.</p>
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		<item>
		<title>Moderation as a Way to Address Prejudice</title>
		<link>https://fountainmagazine.com/all-issues/2013/issue-91-january-february-2013/moderation-as-a-way-to-address-prejudice/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Tue, 01 Jan 2013 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 91 (January - February 2013)]]></category>
		<category><![CDATA[albert]]></category>
		<category><![CDATA[aspects]]></category>
		<category><![CDATA[availability]]></category>
		<category><![CDATA[dialogue]]></category>
		<category><![CDATA[external]]></category>
		<category><![CDATA[extreme]]></category>
		<category><![CDATA[group]]></category>
		<category><![CDATA[heuristics]]></category>
		<category><![CDATA[individual]]></category>
		<category><![CDATA[individuals]]></category>
		<category><![CDATA[information]]></category>
		<category><![CDATA[judgment]]></category>
		<category><![CDATA[labeling]]></category>
		<category><![CDATA[moderation]]></category>
		<category><![CDATA[people]]></category>
		<category><![CDATA[person]]></category>
		<category><![CDATA[prejudice]]></category>
		<category><![CDATA[prejudicial]]></category>
		<category><![CDATA[Prejudicial thinking]]></category>
		<category><![CDATA[thinking]]></category>
		<category><![CDATA[traits]]></category>
		<category><![CDATA[white]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2013/issue-91-january-february-2013/moderation-as-a-way-to-address-prejudice/</guid>

					<description><![CDATA[Of all the faculties and senses that man is endowed with, moderation is one of the most essential virtues. Moderation concerns all people within society, and can become an unattainable virtue unless all members of society have gained a sufficient level of straightforwardness in their thoughts and actions. That straightness of conduct can only be [&#8230;]]]></description>
										<content:encoded><![CDATA[<blockquote>
<p>Of all the faculties and senses that man is endowed with, moderation is one of the most essential virtues. Moderation concerns all people within society, and can become an unattainable virtue unless all members of society have gained a sufficient level of straightforwardness in their thoughts and actions. That straightness of conduct can only be sustained if a sufficient number of people in that society understand, desire and practice the virtue of moderation.</p>
</blockquote>
<p>John B. Watson and his colleague conducted an experiment if an emotion could be generalized from one subject to another subject similar to the first. He targeted a baby, called Little Albert, who had no fear of small furry animals like white rats at that time. To carry out their hypothesis, Watson and colleague presented a white rat for Little Albert to play with. But after a while, the researchers made a very loud disturbing noise whenever Little Albert attempted at reaching for the white rat. After several times the researchers paired the loud noise with Little Albert’s attempts at reaching that white rat, a time came to the point where Little Albert was scared of the animal on its own—without the loud sound. From that on, Little Albert generalized his fear to anything furry, including non-white rabbits and dogs. (Watson &amp; Rayner, 1920)</p>
<p><span id="more-1453"></span></p>
<p>From early years of childhood, we have directly and indirectly learnt how an excess and shortage of anything could be undesirable. No matter who an individual is or where he or she comes from, that individual knows that eating too much can cause a bloated feeling, eating too less can harm health, talking too much could hurt others, and so does not talking at all. Moderation is such a universal virtue that every individual from every religion, ethnicity, and background knows that a life lived in moderation always reaps the most benefits.</p>
<p>Not just on trivial daily matters, moderation can address any issue that has significant relations to human life. Moderation is related to healthy lifestyles, satisfactory life outcomes, healthy relationships, and many more. But one aspect of humankind that is faced everyday—yet it seems to be ignored most of the time—is the mindset, way of thinking, or the cognition. We can have times when there is a “shortage” of the mindset, but more problematic is the instances when some individuals choose to adopt an extreme way of thinking.</p>
<p>Consider the case of Little Albert above, because of one tragedy Little Albert generalized his feelings and fear that anything furry was scary. Probably because that white furry rat seemed to produce such a loud scary noise, Little Albert thought, “so, anything furry MUST be scary too…” This is one example where way of thinking can be extreme. Moderation does not seek to moderate this extreme way of thinking, rather it seeks to moderate way of thinking generally so it is not as extreme.</p>
<h3>How moderation is related to prejudice</h3>
<p>As mentioned above, moderation can address many issues, and this includes prejudice. Prejudice is defined as the way we see others—the social orientation that is based on a membership of a particular group (Brown, 2010). To understand prejudice, one has to note that prejudice comes from a generalized attribution or characterization (or what is commonly known as a stereotype). Prejudice is the emotional aspect of stereotypical thinking. Like Little Albert, the infant generalized his prejudice to anything furry, and although Albert’s reaction to those furry objects was dramatic, our modern prejudicial reaction is usually more subtle and hidden.</p>
<p>In relation to the issue of prejudice, moderation is synonymized to being fair-minded—a way of thinking that employs the middle point between two extremes. Prejudice is, in its basic form, a way of thinking that is located in one extreme. The extremity comes from the aspect of generalization of prejudicial mindset in its beholder’s way of thinking. But where do these thoughts come from? People’s tendency to generalize their observation of a trait of a person to his or her group members always comes from the external sources.</p>
<p>One study supported the notion that people obtain prejudicial thinking from external sources (Aboud, 1976). The research method involved asking participants to seek information on three fictitious groups. Prior to seeking information, the participants were shown statistics of certain traits related to these groups. This was done to “set” the minds of the participants on the traits that were more likely to be shown by the members of these groups. Consequently, when seeking information on the groups after shown the statistics of the groups, the participants were more likely to “confirm” what they had been told from the statistics, allowing a generalization to occur in their mindset.</p>
<h3>Availability heuristics and their role in prejudicial thinking</h3>
<p>Why do humans generalize more than they should, or at all? Perhaps it is because of the information they can readily and superficially obtain from the target of their prejudicial thinking. Stereotypes are always something people can see directly, such as weight, skin color, and intelligence shown through behavior and many other characteristics. These sets of readily available information seem to be more important because there is one type of heuristics, availability heuristics that is present in the human mind to help them judge on frequency or probability (Tversky &amp; Kahneman, 1973).</p>
<p>To understand heuristics, consider the two images below that we come across very often. How do you know which gender is which symbol? The existence of heuristics allows us to manage this world in a more simplified and helpful way. Society uses symbols that represent certain group of people to give certain information. No matter where we are, our brain is integrated with the understanding that “skirts” are something only women would wear—it is how, by using that heuristic, we know that the first symbol tells us that it is a women’s place, or belongs to women, or can only be used by women—depending on where we see the symbol.</p>
<p>Heuristics are tools to help people make a cognitive decision on something such as deciding who someone is, if he or she is a righteous person, or what leads to a particular event, or how a certain event happens. Availability heuristics is the tool used to make a judgment when it comes to the frequency of probability that something occurs to that particular target. For example, one may judge the traits of people in community A, after seeing the behavior of a few members of community A. Availability heuristics help people simplify judgment to the most simplified information they can get in mind, and that information can come from various sources, such as a personal experience like the one in the Little Albert case, and others like the statistics given in the study described above.</p>
<p>Availability heuristics can be useful in some situations, such as estimating voting behavior in an election period, or predicting divorce cases for a particular year, but sometimes it has a negative consequence. Prejudice partly comes from the use of availability heuristics and blind “compliance” to such judgment. In this case, availability heuristics are a form of excess of the use of limited information offered to the human mind prior to judgment because blind belief to such heuristics can lead them to generalize. This is an extreme way of thinking that would go against the very nature of moderation itself.</p>
<h3>Labeling and availability heuristics</h3>
<p>Availability heuristics can be so powerful that sometimes people do not even realize that it is affecting their way of thinking. This is due to the excess use of labeling to simplify and categorize objects. Labeling affects human judgment and interpretation toward something or someone (Jussim, Nelson, Manis, &amp; Soffin, 1995). Labeling is one of the sources of availability heuristics because labeling comes from the traits of physical attributes that people see from the individuals that they label. For example, individuals are labeled as doctors after they are seen wearing a white coat with a stethoscope around their neck, or a man is labeled as dangerous when walking in the dark with a hooded jumper on. Once labeling happens, individuals who conform to the traits and physical attributes that resemble the labels are stereotyped and these stereotypes become the readily available information to serve as a tool to form availability heuristics.</p>
<p>Labeling is not all inaccurate, but the negative consequence of labeling happens because people are too focused on the external traits of a target of the label. People seem to readily judge that a person in a white coat is a doctor, or that a man who has a hood on while walking in the dark is dangerous. These are all the external qualities of the person in a white coat and the man with a hood that people focus on to make a judgment, and eventually they have prejudicial thinking against these targets.</p>
<p>When discussing the topic of faith, Benjamin Franklin said, “Faith is confirmed by the heart, confessed by the tongue, and acted upon by the body.” This definition of faith is in parallel with the definition given by various religions. It emphasizes the importance of both external (confessing and acting upon) and internal aspects (believing) of spirituality. One cannot have one aspect without the other. Moderation involves professing your faith internally, such as believing and keeping your motivation, and externally, such as taking care of your appearance in line with your faith, and being concerned about what you say and do. This means that you do not just focus on either one aspect alone, but prove your stand by maintaining your faith, internally and externally.</p>
<p>In relation to prejudice, labeling happens due to focusing more on the external aspects of traits, like the group members’ appearance, behavior, and even intelligence (as it can be seen from their way of thinking and speaking). But we often neglect to remember that there are interior aspects of those individuals—the aspects that are dismissed from the factors of being labeled. These interior aspects can be different across individuals, thus labels alone could not make an entirely accurate judgment on an individual.</p>
<h3>Conceptual frameworks of the relationship between moderation and prejudice</h3>
<p>As discussed, prejudice comes from many factors that are not in line with the concept of moderation and this can be prevented by allowing the right way of thinking to be our habit. Moderation is a middle pathway to prevent prejudice. One way to do so is by understanding that while the outside of a person can tell something about him or her, the inside parts can be important too. Figure 1 illustrates the conceptual framework on how moderation can address prejudicial thinking.</p>
<p>Figure 1 shows a continuum of the way of thinking with moderation in the middle and “indifference” and “prejudicial thinking” on each extreme end. Prejudicial thinking, in one extreme, focuses only on the external aspects of a group of people, by which the aspects are used to make a judgment if the group is “good” or “bad.” These judgments are then used to make a generalization. On the other hand, indifference is shown when people have a neutral attitude; too much of it that they do not care about what is happening around them.</p>
<p>Moderation is located in the middle. It is neither prejudicial nor indifferent. People with a moderate way of thinking consider both the external and internal qualities of individuals to make a fair judgment. Each judgment is different across individuals because he or she knows that even if an individual belongs to a certain group, that individual does not have to be the same as the other members of that group. People with a moderate way of thinking know that tolerance needs to be exercised whenever needed, without any unfairness to any individuals who belong to a certain group of people.</p>
<h3><b>Conclusion and a suggestion</b></h3>
<p>When making a judgment or decision on a target’s attribution, it is important to examine the extent to which heuristics or the person’s dependence on readily available information—also known as availability heuristics—affects their judgment. Heuristics can be useful to help people organize, manage, and simplify their thoughts, but it should be supervised so that it is only used in moderate levels. Whenever one feels the need to make a quick judgment, he or she should break it by “educating” the self. Educating the self in its simplest form can be to ask, “What if I am judged that way? Would I like it?” By educating yourself, you make a psychological and mental reminder that to quickly judge means to unfairly treat that individual, which is something you would not want happen to you.</p>
<p>Another way to hinder the potential formation of prejudice is to empathize. By putting yourself in the target’s own shoes, you will be able to see how unfair stereotypes can be to a particular individual. Self-serving bias is a social cognitive error in which you are more likely to view positive events as a result of your own doing and negative events as the consequence of an external factor (Miller &amp; Ross, 1975). This is viewed by psychologists as an error in thinking about other people, but interestingly, this can actually help in reducing prejudice. Prejudice can occur because you fail to attribute a person’s behavior or trait fairly, because he or she is simply another person you cannot relate to. Therefore, by empathizing with a person, you would more likely start to view that behavior through your own lens. By doing that, “self-serving bias” can begin and that is equipped with the ability to also consider your own internal attributes. Therefore, there will be a balance between focusing on internal aspects because it is you, and focusing on external aspects, because it is others.</p>
<p>Moderation is indeed a virtue that can help us develop and grow as a well-adjusting human being. By employing moderation in every aspect of our lives, we can see that moderation can address almost any issue, including prejudice. Moderation is the middle and the most proper pathway of thinking.</p>
<p><em>Taufik Mohammad, PhD, is a senior lecturer in Universiti Sains Malaysia.</em></p>
<h3><b>References</b></h3>
<ul>
<li>Aboud, F. E. 1976. The effect of stereotype generalization on information seeking. Canadian Journal of Behavioral Science , 8, 178-188.</li>
<li>Brown, R. 2010. Prejudice: Its social psychology. Oxford: John Wiley &amp; Sons Ltd.</li>
<li>Jussim, L., Nelson, T. E., Manis, M., &amp; Soffin, S. 1995. Prejudice, stereotypes, and labeling effects: Sources of bias in person perception. Journal of Personality and Social Psychology, 68, 228-246.</li>
<li>Miller, D. T., &amp; Ross, M. 1975. Self-serving biases in the attribution of causality: Fact or fiction? Psychological Bulletin, 82, 213-225.</li>
<li>Tversky, A., &amp; Kahneman, D. 1973. Availability: A heuristic for judging frequency and probability. Cognitive Psychology, 4, 207-232.</li>
<li>Watson, J. B., &amp; Rayner, R. 1920. Conditioned emotional reactions. Journal</li>
</ul>
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		<title>Can Genes Alone Explain Everything?</title>
		<link>https://fountainmagazine.com/all-issues/2008/issue-66-november-december-2008/can-genes-alone-explain-everything/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Sat, 01 Nov 2008 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 66 (November - December 2008)]]></category>
		<category><![CDATA[biological]]></category>
		<category><![CDATA[complex]]></category>
		<category><![CDATA[effects]]></category>
		<category><![CDATA[expression]]></category>
		<category><![CDATA[gene]]></category>
		<category><![CDATA[genes]]></category>
		<category><![CDATA[genetic]]></category>
		<category><![CDATA[genetics]]></category>
		<category><![CDATA[human]]></category>
		<category><![CDATA[humans]]></category>
		<category><![CDATA[information]]></category>
		<category><![CDATA[inheritance]]></category>
		<category><![CDATA[knowledge]]></category>
		<category><![CDATA[life]]></category>
		<category><![CDATA[living]]></category>
		<category><![CDATA[organism]]></category>
		<category><![CDATA[organisms]]></category>
		<category><![CDATA[proteins]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[The Central Dogma]]></category>
		<category><![CDATA[trait]]></category>
		<category><![CDATA[traits]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2008/issue-66-november-december-2008/can-genes-alone-explain-everything/</guid>

					<description><![CDATA[Genetics is probably one of the fastest developing contemporary sciences with an incredibly large accumulation of knowledge. This knowledge of genetics has been extensively utilized in a broad spectrum of areas including unveiling the genetic secrets of different traits. This has paved ways to improving human health and sustaining agriculture, and preserving biological diversity on [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>Genetics is probably one of the fastest developing contemporary sciences with an incredibly large accumulation of knowledge. This knowledge of genetics has been extensively utilized in a broad spectrum of areas including unveiling the genetic secrets of different traits. This has paved ways to improving human health and sustaining agriculture, and preserving biological diversity on this planet. In addition to its practical implications, genetics is a major issue for philosophy, ethics, ecology, and economy. Genetics has also been readily incorporated into the public perspective through different means of mass communications, that is, electronic and print media.</p>
<p><span id="more-964"></span></p>
<p>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.</p>
<h3><b>The Central Dogma</b></h3>
<p>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.<a><b><sup>1</sup></b></a> 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.</p>
<p>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.</p>
<h3><b>From physical characteristics to their genetics </b></h3>
<p>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.</p>
<p>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.</p>
<p>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.<a><b><sup>2</sup></b></a> 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.<a><b><sup>3</sup></b></a></p>
<h3><b>Genetic background</b></h3>
<p>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.<a><b><sup>4</sup></b></a> 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.</p>
<h3><b>The end of genetic determinism </b></h3>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p>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.</p>
<p><em>Seyyidhan Mirza is a PhD candidate of Plant Breeding, Genetics, and Genomics. He can be contacted at seyyidmirza@gmail.com.</em></p>
<h3><b>Notes</b></h3>
<ol>
<li>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</li>
<li>Cardno, A. G., Rijsdijk, F. V., Sham, P. C., Murray, R. M. &amp; McGuffin, P. “A Twin Study of Genetic Relationships Between Psychotic Symptoms.” 2002. Am. J. Psychiatry 159, 539-545</li>
<li>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</li>
<li>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</li>
</ol>
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		<title>The Question of Lifestyle in Interfaith Relationships</title>
		<link>https://fountainmagazine.com/all-issues/2004/issue-47-july-september-2004/the-question-of-lifestyle-in-interfaith-relationships/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Thu, 01 Jul 2004 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 47 (July - September 2004)]]></category>
		<category><![CDATA[christian]]></category>
		<category><![CDATA[christians]]></category>
		<category><![CDATA[conflict]]></category>
		<category><![CDATA[context]]></category>
		<category><![CDATA[country]]></category>
		<category><![CDATA[dialogue]]></category>
		<category><![CDATA[dress]]></category>
		<category><![CDATA[foreign]]></category>
		<category><![CDATA[group]]></category>
		<category><![CDATA[impact]]></category>
		<category><![CDATA[lifestyle]]></category>
		<category><![CDATA[lifestyles]]></category>
		<category><![CDATA[media]]></category>
		<category><![CDATA[muslims]]></category>
		<category><![CDATA[people]]></category>
		<category><![CDATA[question]]></category>
		<category><![CDATA[traits]]></category>
		<category><![CDATA[values]]></category>
		<category><![CDATA[world]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/2004/issue-47-july-september-2004/the-question-of-lifestyle-in-interfaith-relationships/</guid>

					<description><![CDATA[A common expression used in “explaining” an apparent animosity among the members of different faiths is to say that “they are opposed to our lifestyle.” While this phrase is used often and carelessly, few people seem to stop and think what it really means and if it is an accurate assessment. Questions such as “Who [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>A common expression used in “explaining” an apparent animosity among the members of different faiths is to say that “they are opposed to our lifestyle.” While this phrase is used often and carelessly, few people seem to stop and think what it really means and if it is an accurate assessment. Questions such as “Who are they?”, “What is our lifestyle?”, “How much do they know about our lifestyle?”, “Does our lifestyle have any impact on them?”, “How different is their lifestyle from ours?”, “Are they opposed to every group of people who practice the same lifestyle?”, and “Are there people who benefit from framing conflicts in this way?” are seldom asked. Consequently, these questions are almost never answered in a systematic, objective way. In this article we will try to explore some of these issues and shed light on some hidden answers in the context of Christian-Muslim relations.</p>
<p><b>Stereotypes and Identities:</b> Who are “They”?</p>
<p>In the context of conflicts that are faith-related or that appear to be faith-related, the term “they” typically represents a media-driven stereotype of a group of persons who seem totally out of “our” world. They speak a different language, they look different, they dress differently, and their values are different. Let’s examine these factors: The fact that some people look or dress differently is not a problem for most. Mexicans speak a different language than Americans. They look and dress differently. The same can be said of Chinese or Japanese. Yet these differences, in and of themselves, do not carry any negative connotations. How about the values? Do Muslims have essentially different values than Christians, Jews and Buddhists? Not really. Indeed, the vast majority of the fundamental values are shared by all these faiths.</p>
<p><b>Defining Lifestyles:</b> What is “Our” Lifestyle and what is “Theirs”?</p>
<p>If we look for common traits of lifestyle of American Christians we realize that most of these traits are shared among Christians in the so-called “Western World”; in fact these can be found, to a great extent, throughout the Christian world. If we go on to compare these traits with those of the Muslim lifestyle, we then realize that Muslims also share these traits. This also answers one of the other questions we asked at the beginning: How much does their lifestyle differ from ours? The answer is, not much; certainly not to the extent that these differences should lead to hatred. Similarly, we should not have any animosity toward other peoples of the world whose lifestyle is different from ours.</p>
<p><b>Communication of Lifestyles:</b> How Much do They Know about Our Lifestyle?</p>
<p>Most Muslims around the world have never met an American Christian in person. Their means of learning about the lifestyle of Americans is through the media. So the question of “how much do they know about our lifestyle?” becomes, rather, how accurately does the media reflect our lifestyle? Most readers might agree that the answer to this question may not be very reassuring.</p>
<p><b>Impact of Lifestyle across the Borders:</b> How Much does Our Lifestyle have an Impact on Them?</p>
<p>For Muslims living in the same society as Christians in the US, this impact may be significant. For most people living outside the US though, the lifestyle of the people in the US has very little impact on them. What does have a great impact is the foreign policies of the government. Therefore, if we assume that there are some people out there who are opposed to the people of this country, then, with this image, foreign policy carries a greater weight. What then needs to be explored is whether the foreign policy of a country reflects the values and choices of the people of that country accurately. Unfortunately, this may not be the case in many situations.</p>
<p><b>Hidden Agendas:</b> Who Benefits from the Lifestyle “Explanation”?</p>
<p>Making the rationale for an attitude that develops into a love/hate relationship between lifestyles helps to achieve group solidarity against another group. By positioning the conflict as a conflict of lifestyles, those who are trying to hide the real reasons behind a conflict or those who benefit from the conflict tell the masses: “It is your problem, they do not like you.” Thus, various entities who cannot act by themselves begin to legitimately act on behalf of the people.</p>
<p><b>Conclusion</b></p>
<p>When we hear the phrase “they do not like our lifestyle” we should be very careful. We should analyze the context and make sure that this is not simply a spurious “explanation” put out by an entity who benefits from conflict or which is trying to hide the real reasons behind conflict.</p>
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		<title>Agrobacterium: A Natural Genetic Engineer of Plants</title>
		<link>https://fountainmagazine.com/all-issues/1993/issue-3-july-september-1993/agrobacterium-a-natural-genetic-engineer-of-plants/</link>
		
		<dc:creator><![CDATA[Louima Cunningham]]></dc:creator>
		<pubDate>Thu, 01 Jul 1993 00:00:00 +0000</pubDate>
				<category><![CDATA[Issue 3 (July - September 1993)]]></category>
		<category><![CDATA[agro]]></category>
		<category><![CDATA[bacteria]]></category>
		<category><![CDATA[bacterium]]></category>
		<category><![CDATA[breeding]]></category>
		<category><![CDATA[cell]]></category>
		<category><![CDATA[cells]]></category>
		<category><![CDATA[crop]]></category>
		<category><![CDATA[disease]]></category>
		<category><![CDATA[dna]]></category>
		<category><![CDATA[engineered]]></category>
		<category><![CDATA[gene]]></category>
		<category><![CDATA[genes]]></category>
		<category><![CDATA[genetic]]></category>
		<category><![CDATA[genetically]]></category>
		<category><![CDATA[inserted]]></category>
		<category><![CDATA[plant]]></category>
		<category><![CDATA[plants]]></category>
		<category><![CDATA[resistance]]></category>
		<category><![CDATA[Science]]></category>
		<category><![CDATA[traits]]></category>
		<category><![CDATA[transfer]]></category>
		<guid isPermaLink="false">http://107.21.79.195/all-issues/1993/issue-3-july-september-1993/agrobacterium-a-natural-genetic-engineer-of-plants/</guid>

					<description><![CDATA[Plants are the key to life on earth. They are, directly or indirectly, the primary source of energy for all terrestrial animals; for instance plants supply directly 90% of calorific intake, and 80% of the protein intake of man. Breeding of crop plants has been carried out by man for thousands of years. It is, [&#8230;]]]></description>
										<content:encoded><![CDATA[<p>Plants are the key to life on earth. They are, directly or indirectly, the primary source of energy for all terrestrial animals; for instance plants supply directly 90% of calorific intake, and 80% of the protein intake of man. Breeding of crop plants has been carried out by man for thousands of years. It is, however, only over the last 50 years, as a result of highly sophisticated breeding processes, combined with improved agricultural methods and modern technology, that this has brought about a dramatic increase in yield and quality of crops. Generally, though, these improved crop plants are often susceptible to many diseases caused by fungi, insects, bacteria, nematodes and viruses. The tendency for crop plants to be threatened by many diseases and pests compared to wild plant species is due mostly to the breeding programmes, whereby selection for characteristics such as yield take priority over those for disease and pest resistance. For many years this has been overcome by the use of pesticides, but there is now increasing concern about the environmental safety of these chemicals, which can persist in the food chain and may be toxic to plants and animals. Given that pesticides have been largely successful only in the control of fungi and insects, and offer little protection against viruses, viroids and bacteria, it is now more urgent than ever to find alternative methods of protecting crop plants from disease.</p>
<p>Plant breeding has several other serious limitations for use as a tool to increase disease resistance. There are only a limited number of plant species which are able to cross-fertilize, thus restricting the transfer of potentially useful traits. Moreover, having found useful traits, it is impossible to prevent the co-transfer of undesirable ones, which can take many years to breed out again by back-crossing.</p>
<p>How can genetic engineering be of use in the quest for new answers to the problems of providing plants with the ability to resist disease? The aim of crop plant genetic engineering is to insert a gene (or genes) which improve an existing plant variety whilst retaining the desirable genetic make up of the original plant.</p>
<p>The main tool at the disposal of the scientist is the use of nature’s own genetic engineer, Agro-bacterium tumefaciens. The manipulation of this bacterium’s natural functions has allowed the biologist to transfer many foreign genes into plants. The bacterium is soil-borne and infects plants at the crown, usually through a wound site, causing cancerous growths of proliferating plant cells known as crown gall tumors. This disease in itself is ergonomically important and effects most dicotyledonous plants causing millions of dollars’ worth of damage to plants. In the 1940s, from experimental observations, it was concluded that a factor is transmitted from the invading bacteria to the host plant cell. Further studies demonstrated that the disease is actually the direct result of the transfer of a particular DNA fragment (genes) from the bacterium to the plant cell. In addition to its chromosomal DNA, Agro-bacterium contains a much smaller circular DNA molecule called a Ti (tumor-inducing) plasmodia, of which a small piece, called the T-DNA (Transferred-DNA), is the factor transferred into plant cells (see Figure 1). The T-DNA becomes stably integrated into the plant’s chromosomes, from where it is able to perturb the natural functions of the plant. The T-DNA encodes genes, which, when expressed, bring about the production of new enzymes that are able to alter the hormone balance within the infected cell. This brings about de-differentiation and cell division, leading to proliferation of cells and the formation of tumors. This appears to be of little benefit to the bacterium. However, other genes are also present in the T-DNA which, when expressed, are able to synthesize novel compounds from naturally occurring plant precursors. These novel compounds cannot be metabolized by the plant but are a good source of nutrients for the bacterium.</p>
<p>Mutation analysis of the T-DNA revealed two regions, the left and right borders, which were essential for integration into the chromosome. It was also found that any piece of DNA inserted between these borders was stably inserted into the host chromosome on transformation. Deletion of the genes for tumor formation (Disarmed Ti-Plasmid) were found to have no effect on the transfer efficiency from bacterium to plants. Availability of disarmed Ti-plasmids, tissue culture methods for the regeneration of whole fertile plants from single cells, and marker genes (such as antibiotic resistance) for the selection of transformed cells, have allowed for the production of a whole new range of plants containing foreign genes. Several genes responsible for pathogen and herbicide resistance proteins have been isolated from the bacteria and viruses. These genes have then been inserted into the T-DNA region of Agro-bacterium and introduced into plants, giving rise to insect, virus or herbicide resistant plants.</p>
<p>By using Agro-bacterium as a plant genetic engineer, many crop plants such as the tomato, potato and cucumber have now been engineered for virus resistance. Field tests showed that these genetically modified plants appeared to be highly resistant to viral infections. Similarly genetically-engineered cotton plants have proved to be resistant to insect attack and many herbicides (weed killers).</p>
<p>Another powerful new genetic engineering technique is ‘antigens’ technology, whereby specific gene transcripts are prevented from being translated into proteins. By using antigens technology, it has been possible to produce genetically engineered tomato plants that have a much increased shelf-life. Although many aspects of gene transfer from Agro-bacterium to plants are not fully understood, the use of Agro-bacterium for gene transfer will continue to increase; and it is likely that genetically engineered crops carrying traits for resistance to herbicides, insects and viral diseases will soon reach the market-place.</p>
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