View source for Genomic Essay Sungbin Lim

<p>[[Sungbin Lim]]</p>

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<p><strong>How genomic prove evolution?</strong></p>

<p>20131501 Sungbin Lim</p>

<p>1. Introduction</p>

<p>There are a lot of way to answer the question &lsquo;Why?&rsquo;. Evolution theory is important because it provide unique way to answer the question &lsquo;Why?&rsquo; in biology.</p>

<p>Question &lsquo;Why?&rsquo; require reason. This reason can be historical one, or mechanical one, or so on. For example, If I buy some hamburger from Burger King, you can ask to me &lsquo;Why do you get burger?&rsquo;. I can answer in several way.</p>

<p>1) Because I give money to Burger King.</p>

<p>2) Because I was hungry.</p>

<p>3) Because worker of Burger King gave it to me.</p>

<p>All of these answer can be rational but we can choose better answer to choose by knowing contest of question. If you was curious about capitalism and that&rsquo;s the contest, answer 1 will be proper one.</p>

<p>At this view, most of biology give answer to &lsquo;Why?&rsquo; in Mechanical process. For example, if we question &lsquo;Why human have two sex?&rsquo;. Then answer will be it&rsquo;s because division of XX chromosome and XY chromosome, and following difference of hormone and so on. This answer is still valuable but not enough. Someone could say &lsquo;Yes, I know the mechanical process but why not 3 sex or 5 sex? If se have more chromosome combination isn&rsquo;t it able to make more sex?&rsquo;. This question require in different context then mechanical process. It require the reason of existence and the reason of history.</p>

<p>Before evolution theory came, people explained by existence of god. But not now. Existence of evolution theory give it. This is why evolution theory is important. It give us new context of question and answers which was not scientifically held.</p>

<p>As it is science, Evolution theory need to be scientifically proved. There are a lot of refutation and support and debates. As tool of scientific discovery is getting improved, Evolution theory get more supported.</p>

<p>In past days, people tried to prove evolution in several ways. But as I will explain, there were still remained question unsolved. After time goes, Recent technologies and knowledge give new way of proving. And one of new ways was using genomic.</p>

<p>Genomic give us new context of answers and it widen the explanation of evolution theory. Following reports shows how genomic support evolutionary theory as method of discovery.</p>

<p>Plus, genomic in prokaryote will be focused. It&rsquo;s because in prokaryote genomic not only add explanation, but it also give totally new logic to analysis prokaryote evolution. Genomic improved evolution theory more greater in prokaryote than eukaryote.</p>

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<p>2. Traditional method of discovering evolution</p>

<p>2. 1. Methods and Logic</p>

<p>Idea of Evolution was suggested from Darwin, 1859 through &lsquo;The origin of species&rsquo;. Yet there were Wallace cooperated, Darwin is kind of Symbol and usually mentioned and it is useful to simplify to focus on Darwin.</p>

<p>Darwin suggested some important concepts. One is the concept of evolution, which argue that all of species have common ancestors and they are divided in past. The other is the detailed process of evolution, natural selection.</p>

<p>After Darwin, there are some concepts combined with genetics and evolution. Mendelian genetics, and concept of mutation add more detail on evolution.</p>

<p>Mendelian genetic give new big concept of evolution that there will be some way to prove evolution in genetical way. Mendelian genetic argue that there are genes which delivered from parent to offspring. And this gene is revealed by phenotype. Watching phenotypic change, we can guess individual&rsquo;s gene.</p>

<p>Evolution occurs through generation. Mendelian genetic suggest genetical relationship between generation. Thus, Evolution get potential to be analyzed by genetical view.</p>

<p>2. 2. Limitation, Criticism</p>

<p>There were big limitation before genomic to explain evolution. All evolutionary idea started with phenotype. Especially the only phenotype what people can easily observe. Thus, although we can make a hypothesis that sudden phenotype is came from common ancestor, it had to be remained in hypothesis. Because, to prove certain phenotype is came from common ancestor, it is crucial to explain it through genetical history.</p>

<p>But it cannot be actually work because there were no techniques to analyze certain species or phenotype in gene level.</p>

<p>There are criticism that evolution theory is hypothesis. Because although it gives reliable story but there are no significant evidence. Significant evidence contains logical processes. Logical process that supposing variation and reveal relationship clearly between them. In this case, genetical change through generation need to be suggested because genetical change is variation between parent and descendant. This change always follow in part of evolution. Thus, to identify evolutional event, it is necessary to explain it through genetical analysis and make scenario using gene. Without gene, explanation will lose their power of persuasion because they don&rsquo;t use valuable variation that always give unique explanation on each events.</p>

<p>Also studying relationship between species using phenotypic observation is a problem. Because phenotypic observation can be subjective. Someone may say existence of wing is more important than existence of bone. Then bird will be more highly related with insect rather than human. There are no significant evidence that bone is more important criteria than wing. It is trap when we use phenotypic analysis.</p>

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<p>3. Genomic method of discovering evolution</p>

<p>To use genomic as successful tool to prove evolution, there should be some criteria.</p>

<p>First, genomic analysis should reveal core concept of evolution. Though new discovery can change original theory, it should be finally strengthen core idea of evolution. Unless if new discovery that refuse core idea of theory, then new kind of debate will occur and break original theory. Yet genomic discover the facts by supporting evolution.</p>

<p>Second, genomic have to make view of evolution broader. Genomic will provide genetical view of evolution. Thus genomic will be useful to develop evolution.</p>

<p>&nbsp; Genomic is powerful tool for evolution theory because it gives genetical relationship between species, population, and individuals. Before genomic, evolution theory explained relationship of species through phenotypic observation. As it mentioned before, phenotypic observation has typical limitation and genomic breakthrough this limitation.</p>

<p>3. 1. Methods and Logic</p>

<p>Genomic in evolution theory basically work by understanding relationship of species genetically. Which we call, Comparative genomics. Comparative genomic is focusing on common and different feature of genome between species. To be simplified, if two genome is similar than another third genome, we conclude that former two genome is more closely related than another genome. In evolutionary explanation, two genome have common ancestor after branching out from common ancestor of all of them.</p>

<p>Also, if we sequence further species, we can find some highly conservative region, and also highly diverse region. Through highly conserved region, we can find which function is common feature for certain species and their relatives.</p>

<p>There are lot of method and projects. Sequencing alignment, ENCODE project, BLAST and so on. There could be more details provided. But as this report is purposed to give general concept, the detail will be skipped.</p>

<p>3. 2. Contribution of Prokaryotic evolution</p>

<p>Evolutionary study was mainly focused on eukaryotes. Especially human. Because phenotypic analysis is easy to processed what we can directly see. Beside, it is totally difficult to identify phenotype of prokaryote. Thus, evolution of prokaryote was less studied. But after genomic, study of evolution of prokaryote was highly developed. Because the feature reveal identical in level of gene whether it is prokaryote or not. Which means, if we use genomic, we can analyze detail as much as eukaryotes.</p>

<p>As it mentioned on 3.1, Scientist find powerful tool to search relationship between prokaryote species. It&rsquo;s 16S rRNA. 16S rRNA have highly conserved region and also have highly diversed region. More important, it exist universal at prokaryote. Furthermore, it is abundant. Thus, scientist can now make taxonomy of prokaryote using 16s rRNA.</p>

<p>Discover existence and method to use 16s rRNA is totally started with genomics. Scientist applied genomic analysis method to prokaryote and find those tools.</p>

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<p>4. Further subject of evolutionary genomic</p>

<p>Still there are a lot of potential to study evolutionary theory using genomic. What I am most curious about is revealing history of species using genomic. There are recent movement to study anthropology by mitochondria genome, sex chromosomes. I think this kind of concept have great potential. If this kind of study accumulate data, we can know that what region of certain genome means. The meaning that where did gene originated, and the functions, uniqueness, and so on. Thus, in the end, we can use individual genome as history book.</p>

<p>Another point is to understand dynamic of gene in prokaryote. Prokaryote often transform their genome such as horizontal gene transfer. So in view of genome, it is far unstable than eukaryote genome. It gave genomic big trouble to analyze prokaryote genome. Because there are too many variation and variety change of genome. I think understanding genetic variation of prokaryote and analyzing will be hard task for genomic. But this task can be overcome by understanding physiological principle of genomic dynamic in prokaryote.</p>

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<p>5. Acknowledgement</p>

<p>Genomic is improved as days go by. Some information on report can be a story of past or some estimation may be already studied. There are limitation by gathering information of genomics.</p>

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<p>6. References.</p>

<p>M.LEST <em>Introduction to GENOMICS Second edition</em>. Oxford.</p>

<p><a href="https://en.wikipedia.org/wiki/Comparative_genomics">https://en.wikipedia.org/wiki/Comparative_genomics</a></p>

<p><a href="https://en.wikipedia.org/wiki/History_of_evolutionary_thought#1859 1930s:_Darwin_and_his_legacy">https://en.wikipedia.org/wiki/History_of_evolutionary_thought#1859 1930s:_Darwin_and_his_legacy</a></p>

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