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10.8: Advanced topics, Summary and key points, Further Reading, Bibliography - Biology

10.8: Advanced topics, Summary and key points, Further Reading, Bibliography - Biology



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There still remain a host of other problems that need to be solved by studying RNA structure. This section will profile some of them.

Other problems

Observe some of the problems depicted graphically below:

Relevance

There are plenty of RNAs inside the cell aside from mRNAs, tRNAs and rRNAs. The question is what is the relevance of all this non-coding RNA? Some believe it is noise resulted through experiment, some think its just biological noise that doesn't have a meaning in the living organism. On the other hand some believe junk RNA might actually have an important role as signals inside the cell and all of it is actually functional, the truth probably lies somewhere in between.

Current research

There are conserved regions in the genome that do not code any proteins, and now Stefans et al. are looking into them to see if they have structures that are stable enough to form functional RNAs. It turns out that around 6% of these regions have hallmarks of good RNA structure, which is still 30000 structural elements. The group has annotated some of these elements, but there is still a long way to go. a lot of miRNA, snowRNAs have been found and of course lots of false positives. But there exciting results coming up in this topic! so the final note is, it’s a very good area to work in!

Summary and key points

1. The functional spectrum of RNAs is practically unlimited

(a) RNAs similar to contemporary Ribozymes and Riboswitches might have existed in an RNA world. Some of them still exist as living fossils in current cells.

(b) Evolutionarily younger RNAs including miRNAs and many long ncRNAs form a non-protein based regulatory layer.

  1. RNA structure is critical for their function and can be predicted computationally

    (a) Nussinov/Zuker: Minimum Free Energy structure (b) McCaskill: Partition function and pair probabilities

    (c) CYK/Inside-Outside: probabilistic solution to the problem using SCFGs

  2. Phylogenetic information can improve structure prediction
  3. Computational biology of RNAs is an active eld of research with many hard algorithmic problems still open

10.10 Further reading

• Overview
– Washietl S, Will S. et al. Computational analysis of noncoding RNAs. Wiley Interdiscip Rev RNA. 2012, 10.1002/wrna.1134
• RNA function: review papers by John Mattick

• Single sequence RNA folding

– Nussinov R, Jacobson AB, Fast algorithm for predicting the secondary structure of single-stranded RNA.Proc Natl Acad Sci U S A. 1980 Nov; 77:(11)6309-13

– Zuker M, Stiegler P Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan; 9:(1)133-48

– McCaskill JS The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers. 1990; 29:(6-7)1105-19

– Dowell RD, Eddy SR, Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics. 2004 Jun; 5:71

– Do CB, Woods DA, Batzoglou S, CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics. 2006 Jul; 22:(14)e90-8

• Consensus RNA folding

– Hofacker IL, Fekete M, Stadler PF, Secondary structure prediction for aligned RNA sequences. J Mol Biol. 2002 Jun; 319:(5)1059-66

– Knudsen B, Hein J, RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. 1999 Jun; 15:(6)446-54

• RNA gene finding

– Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D Identication and classication of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006 Apr; 2:(4)e33

– Washietl S, Hofacker IL, Stadler PF, Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A. 2005 Feb; 102:(7)2454-9

Bibliography

  1. [1] R Durbin. Biological Sequence Analysis.
  2. [2] W. Gilbert. ”origin of life: The rna world”. Nature., 319(6055):618, 1986.
  3. [3] Rachel Sealfon, 2012. Extra information taken from Recitation 5 slides.
  4. [4] Z. Wang, M. Gestein, and M. Snyder. Rna-seq: a revolutionary tool for transcriptomics. Nat Rev Genet., 10(1):57–63, 2009.
  5. [5] Stefan Washietl, 2012. All pictures/formulas courtesy of Stefan’s slides.
  6. [6] R. Weaver. Molecular Biology. 3rd edition.

Summary

Summary is indispensable in preparing for and writing an argumentative essay. When you summarize a text (or describe visual material), you distill the ideas of another source for use in your own essay. Summarizing primary sources allows you to keep track of your observations. It helps make your analysis of these sources convincing, because it is based on careful observation of fact rather than on hazy or inaccurate recollection. Summarizing critical sources is particularly useful during the research and note-taking stages of writing. It gives you a record of what you've read and helps you distinguish your ideas from those of your sources.

Summaries you write to prepare for an essay will generally be longer and more detailed than those you include in the essay itself. (Only when you've established your thesis will you know the elements most important to retain.) It is crucial to remember, though, that the purpose of an analytical essay is only partly to demonstrate that you know and can summarize the work of others. The greater task is to showcase your ideas, your analysis of the source material. Thus all forms of summary (there are several) should be tools in your essay rather than its entirety.

True Summary

True summary always concisely recaps the main point and key supporting points of an analytical source, the overall arc and most important turns of a narrative, or the main subject and key features of a visual source. True summary neither quotes nor judges the source, concentrating instead on giving a fair picture of it. True summary may also outline past work done in a field it sums up the history of that work as a narrative. Consider including true summary—often just a few sentences, rarely more than a paragraph—in your essay when you introduce a new source. That way, you inform your readers of an author's argument before you analyze it.

Immediately after his introduction to an essay on Whittaker Chambers, a key player in the start of the Cold War, Bradley Nash included four sentences summarizing the foreword to his main source, Chambers's autobiography. Nash characterizes the genre and tone of the foreword in the first two sentences before swiftly describing, in the next two, the movement of its ideas:

The foreword to Chambers's autobiography is written in the form of "A Letter to My Children." In this introduction, Chambers establishes the spiritual tone that dominates the body of his book. He initially characterizes the Cold War in a more or less standard fashion, invoking the language of politics and describing the conflict as one between "Communism and Freedom." But as the foreword progresses, Chambers introduces a religious element that serves to cast the struggle between communism and capitalism as a kind of holy war.

Every essay also requires snippets of true summary along the way to "orient" readers—to introduce them to characters or critics they haven't yet met, to remind them of items they need to recall to understand your point. (The underlined phrase in the paragraph introducing Nash's summary is an example of orienting information.) True summary is also necessary to establish a context for your claims, the frame of reference you create in your introduction. An essay examining the "usable past" created by the Vietnam Veterans Memorial, for example, might begin by briefly summarizing the history of the idea of a usable past, or by summarizing the view of a leading theorist on the topic.

Interpretive Summary

Sometimes your essays will call for interpretive summary—summary or description that simultaneously informs your reader of the content of your source and makes a point about it. Interpretive summary differs from true summary by putting a "spin" on the materials, giving the reader hints about your assessment of the source. It is thus best suited to descriptions of primary sources that you plan to analyze. (If you put an interpretive spin on a critical source when you initially address it, you risk distorting it in the eyes of your reader: a form of academic dishonesty.)

The interpretive summary below comes from an essay examining a Civil War photograph in light of Lincoln's Gettysburg Address. The essayist, Dara Horn, knew she needed to describe the photo but that simply "walking through" its details would bewilder and bore her readers. So she revealed the point of her description in a pair of topic sentences (solid underline), summarized the details of the photo (double underline), and gave the description some interpretive "spin" (throughout).

As skeptical moderns, we often have trouble accepting drawings or paintings as historical records, but we tend to believe in photographs the way that we believe in mirrors we simply accept them as the truth. Alexander Gardner's photograph Trossel's House, Battle-Field of Gettysburg, July, 1863 might therefore be viewed as evidence rather than commentary. Unlike some of Gardner's other "sketches," this picture includes no perfectly positioned rifles, no artistically angled river, no well-posed men in uniform—indeed, no people at all. The photograph's composition could barely be more prosaic the horizon slashes the picture in half, and the subject, a white colonial-style house, sits smack in the center. Yet this straightforward, almost innocent perspective sets the viewer up for the photograph's stealthy horror. At first glance, the photograph appears to be a portrait of a house, perhaps even a poor portrait of a house in a Òsketch bookÓ of war, one might flip right by it to the gory pictures before and after. But the terror in this photograph lies in its delayed shock, the gut-wrenching surprise when the light on the house leads the eye to the light on the fence and the viewer notices that the backyard fence is broken, and then thatthe backyard is a mess, littered with—what are those?—horses, dead horses, twelve dead horses. What must have happened to topple twelve nine-hundred-pound horses, and where are the people who rode them? Crushed underneath? The viewer doesn't know, because Gardner's picture doesn't tell us. All we see is a house, a broken fence, twelve dead horses, and an empty sky.

Some Cautions

Remember that an essay that argues (rather than simply describes) uses summary only sparingly, to remind readers periodically of crucial points. Summary should always help build your argument. When teachers write "too much summary—more analysis needed" in the margin, generally they mean that the essay reports what you've studied rather than argues something about it. Two linked problems give rise to this situation. The first is a thesis that isn't really a thesis but rather a statement of something obvious about your subject—a description. (The obvious cannot be argued.) A statement of the obvious tends to force further description, which leads to the second problem, a structure that either follows the chronology of the source text from beginning to end or simply lists examples from the source. Neither approach builds an argument.

Copyright 2000, Elizabeth Abrams, for the Writing Center at Harvard University


INTRODUCTION

According to the National Assessment of Education Progress, the science proficiency of high school seniors dropped from 21% in 1996 to 18% in 2000 and remained at 18% in 2005 (Grigg et al., 2006). As a result, the public's science literacy is remarkably low. Only one in five Americans comprehends or appreciates the value or process of scientific inquiry (National Science Board [NSB], 2000). To combat this, the NSB on Communicating Science and Technology to the Public has underscored the need to communicate the fascination, joy, and utility of science (NSB, 2000). Traditional textbooks do not always make this possible, especially if students are already uncomfortable with the material. According to the NSB's Science and Engineering Indicators for 2004, textbooks now contain more content that is presented with less coherence (NSB, 2004). In this paper, we report data that suggest comic book stories can play a significant role in conveying content in a coherent manner and, in the process, improve the attitudes that non–science majors have toward biology.

The potential value of comics in education and student literacy is not a new concept. Educators have been using comics in the classroom for over 60 years. Instructors who incorporate comics into their curricula suggest that comics generate increased individual student interest (Sones, 1944) and, according to at least one teacher, make “learning too easy” (Hutchinson, 1949). Comics have been used to motivate children to read (Haugaard, 1973), train students in the language arts (Williams, 1995), teach collegiate physics (Kakalios, 2002), outline business ethics (Gerde and Foster, 2008), and explain the maintenance of military equipment (Eisner, 1944). Comics are also being used in medical education and patient care (Green and Myers, 2010). The Maryland State Department of Education (MSDE) even started the Maryland Comic Book Initiative in which it piloted the use of comics such as Jim Ottaviani's Dignifying Science (biographical comic stories about women scientists) in middle school classrooms (MSDE, 2004 Ottaviani, 2009).

Few science educators could dispute the explanatory power of images and figures in traditional textbooks. The complex interplay of words and images in comics has the potential to go beyond the traditional textbook by weaving text and images into a story that can help generate coherence and context for the information. A pedagogical tool that engages students, motivates them to read, helps them remember content, and makes the whole process fun would be quite useful in the science curriculum. It is not surprising then that comics have found their way into some science classrooms. The literature concerning science education and science comics has recently been reviewed by Tatalovic (2009), and although there have been a number of articles published that suggest comics can be used in the classroom to motivate students, these arguments usually rely on anecdotal evidence for support and do not assess what role, if any, comics play in student success.

In this paper, we report the results from a comparative study to assess the pedagogical effectiveness of a comic book textbook called Optical Allusions. We focus on the role comics might play in engaging non–science majors. Relative to science majors, nonmajors are less motivated and interested in science and spend less time studying it (Knight and Smith, 2010). We hypothesized that using a comic book story to deliver scientific information would provide imagery and context that would enhance student learning and attitudes about biology.


Key Points: Advanced Mathematics Revision Guide

Covering the content units is fundamental to students achieving good marks in Grade 12 Mathematics assessments and end-of-the-year examinations. Here are three pointers about the use of the mathematics study guide for grade 12. The topics are from the Advanced Mathematics Upper Secondary School Syllabus (Grades 11 and 12).

Advanced Mathematics topics form the basis of classroom teachings and assessments. It is important for students to use the topics as guides when revising for major mathematics examinations.

The new and experienced Advanced Mathematics teachers at Grade 11 and 12 levels should (and must) cover the topics in-depth and at greater length. Where there are GAPS in learning, students can use their initiatives to learn. Therefore, this guide will help students to identify topics of interests and revise accordingly.


Reviews

"Giddens′s book is composed with verve and panache, yet it is extraordinarily learned and reliable. It really is fun to read . We need to applaud Giddens for a superb text as well as his singular contribution to the standing of sociology today."

Frank Webster, Times Higher Education Supplement

"There s no one on the planet with such a refined grasp of the practical and political significance of sociology as Anthony Giddens. This new edition of his best–selling textbook is his best yet."

Anthony Elliott, Flinders University Australia

"With this new edition of Sociology, Anthony Giddens has done the seemingly impossible. He has lifted the best introductory text in sociology in the world to yet a further level of excellence. It is a great achievement."

Ulrich Beck, London School of Economics

"I have a high opinion of Giddens s book, which I consider to be a comprehensive and lucid introduction to the major topics, debates and theoretical perspectives in sociology. It combines a detailed overview of the contemporary sociological landscape with sensitivity to the enduring debt that the discipline owes to earlier theorists."

Mike Hawkins, Kingston University

"This new edition is fresh, engaging and topical. One particular feature is worth a mention: a striking introduction that catches the reader s attention right at the start is very effective educationally. I remain a fan of such pedagogical devices. The point is made economically and strikingly at the very beginning and is then carried through the chapter. Some of the chapters do this in an exemplary fashion."

Nick Abercrombie, University of Lancaster

"The main reason for recommending Giddens s text over many of its competitors lies in the way that the book handles the various sociological specialisms. Although structured through specialist fields such as crime and deviance, families, gender and sexuality and so on, Giddens never loses sight of the general sociological perspective amid the welter of detailed and specialized knowledge. This introductory textbook stands out as a welcome antidote to the impression of fragmentation and diversity of the discipline which students often come away with from textbooks. Giddens still succeeds in demonstrating the continuing intellectual excitement of the sociological enterprise to all new students. For me, this is the foremost consideration when choosing a core introductory textbook and Giddens s Sociology is peerless in this regard."

Phil Sutton, The Robert Gordon University

"The chapter [ Theoretical Thinking in Sociology ] is clearly written with a strong thread running throughout. Students will like the way in which it brings together many diverse social theories highlighting some of their main similarities and differences in a single chapter. This chapter was towards the end of the book in the fourth edition moving it nearer to the front of the book in this new edition is an excellent idea and will give students an insight into the theoretical interpretations used by sociologists as they look at the issues discussed in the remaining chapters."

Steve Williams, University of Glamorgan


❓ Summary Making FAQs

To create an original summary, follow these tips:

  • Read the article several times to have a clear idea of its content
  • Inspect the introduction, find the thesis statement and rephrase it
  • Write down the article’s key points and phrases so as not to forget them
  • Compose your summary without peeking at the source text, relying only on your notes
  • Cite all the sources used

Alternatively, you can use our online tool, which creates summaries of source texts automatically.

To shorten a paragraph, cut the unnecessary or redundant information. Your paragraph should contain only one idea, outlined in an introductory sentence. Make sure to elaborate on it in 2 to 3 sentences, cutting out phrases or ideas t that deviate from the core subject.

Then, eliminate words that don’t add any value to the text, stating the obvious or excessive information. Get rid of unnecessary determiners and modifiers and cut repetitive phrases or words.

To create a summary, you need to divide the research paper into key sections and elaborate on each one. You then compose a brief overview of everything that’s crucial in the document.

In your summary, include the following parts:

  • An introduction, in which you engage the reader in your study
  • An explanation of the hypothesis, or purpose of your research
  • Description of the methods used
  • A review of the results that ties directly to the hypothesis
  • A conclusion in which you outline your interpretation of the results and plans for future study

Yes, of course! There are plenty of summary makers available in the App Store or Google Play. Furthermore, you can find some great summarizing tools online that don’t require payment or registration. Or use our automatic summary generator above to get an original summary of your text.

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