Using The Scientific Literature PDF

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Lab Homework for Introduction to Biology. Covers a variety of different topics. ...

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Fynn Jacobsen September 29, 2017 Biology 171 Lab Yosuke Kawai

Using the Scientific Literature 1. A browser is a piece of software that allows individuals to “browse” and view the internet. Good examples of browsers that we use on a daily basis are Internet Explorer, Google Chrome, Safari, and Firefox. The role of a search engine is to allow one to search and find information on the internet. A search engine is more specific as it guides you to websites that include or cover the items that you typed in to the search bar. A good example of search engines that we use on a daily basis are Yahoo, Bing, and Google. A database usually incorporates information from pieces of writing such as newspapers, journals, books, and magazines. A database is considered a more reliable source of information than a browser and search engine because all material has undergone the editorial process. Library databases, such as those of UH Manoa, are a great tool for students to use for a wide array of subject topics.

2. Yahoo, Bing, and Google are among the top search engines used by individuals around the world. Though these search engines were created by different developers, they are all very similar as to how they look on screen and the results they discover. It seems that search engines such as Yahoo and Bing have really used Google’s model and have designed their programs to look and run like their competitor’s. They do this because Google is the most widely used search engine and people are most comfortable with it. If one was to conduct a search on all of these search engines, not much would vary between within the results on

screen. The websites that are displayed in the results are almost always identical other than a link for a video or a definition that is out of place on the screen. When one searches something in a search engine, the search engine has to work to decide what website will most likely contain the information you are looking for. It then has to rank this website, along thousands of others, and decide what pops up at the top of the screen. The way in which Yahoo, Bing and Google rank the websites differ greatly from time to time.

3. A periodical is piece of writing that comes out in regular issues. Magazines and newspapers are great examples of periodicals. They are often scholarly journals which can display and discuss a set of findings or data. Examples in the Hamilton Library include “Hawaii Ocean Time Series Data Report” (call # GC781.h388), “Journal of Medicinal and Aromatic Plant Sciences” (call # GK99.A1C87), and “American Family Physician” (call # R11.A44). Popular periodicals include magazines such as Vogue, and National Geographic, thought the Hamilton Library at UH Manoa does not keep periodicals like these.

4. A library database is a body of information from a wide variety of edited, published, and credible pieces of writing. Like any database, it usually incorporates information from newspapers, journals, books, and magazines. Library databases are very user friendly and allow one to fine tune their search. By entering keywords, or selecting the subject topic or author, a student can find unbelievable amounts of information on their topic within seconds. One is sure to discover a new source that they did not know about prior to using the library database.

A good database to use when attempting to locate articles on biomedical topics is the “U.S. National Library of Medicine Database”. This database allows for access to thousands of edited and peer reviewed biomedical journals. The “American Psychological Association Databases” are a great place to find articles on social issues. The articles in this database analyze social issues, how they come to be, and what psychological factors drive them. When trying to find information on plant physiology, the UH Manoa Voyager Database is great resource. It may not be as big as some of the other databases, but it has many articles full of information on this topic.

5. A piece of writing is considered primary literature when the information provided is original and comes directly from the primary source. A piece of primary literature is usually the first official show of various types of results for experiments, surveys, etc. A lab report is a good example of an appropriate use of primary literature. Secondary literature is the evaluation of primary sources. Authors in secondary literature take someone else’s results and re-convey key aspects of that primary literature piece in a different environment. It would be most appropriate to use secondary literature when writing things such as newspaper and magazine articles. Tertiary literature collects and analyzes information that has come from both primary and secondary sources. It allows for a wide overview on information that has come to be accepted by the general public. It is most appropriate to use tertiary literature when writing pieces such as textbooks or guides.

6. When attempting to determine if a source is appropriate for your research, you want to consider the type of source, its contents and structure, the author, and where the author got his/her information. Trying to find appropriate sources can be tricky but narrowing down sources by their types can really help. When trying to find information for your experiment, it helps to look for lab reports from individuals who may have already completed that experiment or one that is similar. Magazine or journal articles which analyze other individual’s results, are also a good place to look for information for your experiment. To make sure that your source is appropriate, you need to make sure that the source actually contains what you are looking for and that the contents and structure make the information you are looking for easy to comprehend. The author of the source should be knowledgeable on the topic of discussion and be accredited to a recognizable degree. You want to make sure that your information if not coming from a random user on some public blog. Where the author got his/her information or results is extremely important as it is able to tell someone if the source is credible or not. If all the information comes from very public websites with little credibility then it is best to re-consider that source.

7. According to the criteria listed in the previous question, one can tell that the website, “http:/www.lifeextension.com/ClinicalResearch/Clinicaltrials” is a good source for information. The main purpose of this website is to advertise clinical trials and sell health products to consumers however, a large array of credible information can be found behind this distraction. In the portions of this website listed as “Health” and “Magazine”, many articles are posted about current trending medical information or new exciting health studies. The purpose of these parts of the website are to make readers aware of current health

phenomena and analyze the issues. The reliability of the information stated in these articles is very high as the authors always include a large list of credible sources that relate to the topic. Articles within this website are great when researching for a paper because they are structured with images and graphs to make information easier to understand.

8. After analyzation, one can see that Miguel Madariaga’s journal article, “Ebola Virus Disease: A perspective for the United States”, is very different to Times Magazine’s, “Ebola in the United States: What You Need to Know”. Though both pieces of writing cover the same general topic, they serve very different purposes for the reader. Miguel Madariaga’s, “Ebola Virus Disease: A perspective for the United States”, is a journal posted on the American Journal of Medicine which dives deep in to the Ebola virus, how it works, and what can be done to diagnose and treat the disease. The author has done extensive background research on the topic, has included solid data and graphs, and fully analyzes all components of the disease. Time Magazine’s, “Ebola in the United States: What You Need to Know”, is very different as it does not analyze what Ebola is or how it works. This magazine article focuses on the transmission of the Ebola virus and making the public aware of the dangers of this disease. There is no complex information or mention of any types of studies or results in this magazine article.

9. In the life sciences section of UH Manoa’s Voyager database, there an electronic journal called, “Isotopes for Medicine and the Life Sciences”. Its call number is RC78.7.R4 I76 1995.

10.“Pattern and Process in Land Mollusk Diversity” (call # fQL430.4. P2872005), is a scientific journal from the Western Australian Museum that is only available in paper format in the Hamilton Library. The abstract of the second article in the journal reads, “Land snails constitute a significant and characteristic element of the world’s terrestrial fauna, and may be the most diverse group after arthropods and nematodes. They feature rather seldom, however, in general accounts of biodiversity and its causes, despite the fact that they appear to be amongst the most vulnerable to human-induced extinction (Groombridge, 1992). Amongst other reasons, this results from our very incomplete, and often confused, knowledge of patterns of distribution and diversity found between regions, and amongst different groups of snails.” The reference citation is, Cameron RAD, Nekola JC, Pokryszko BM, Fells FE. Pattern and process in land mollusk diversity. West Austr Mus. 2005 Oct, V.68

11. The journal, “The Adaptive Accuracy of Flowers: Measured and Micro Evolutionary Patterns”, written by W. Scott Armbruster, speaks about Darwin’s theories explains deviations of optima through flower pollination. This journal article is available both in hardcopy at the Hamilton library (call # QK656.E512009), and in electronic form on the library database. When comparing the two types of copies of the article, the main thing one will realize is how reading comprehension increases when a hard copy paper format is used.

Since both the types of copies are the same article, all the contents will remain the same. Page size and where figures lie on the pages are slightly different between the two copies. When one choses to read from a source that is in paper format, the connection of feeling and writing on paper creates markers in the human brain which result in better reading comprehension. Students who read information from hard copy textbooks are also found to score higher than students who read the same information through an electronic source. The source citation for paper version of “The Adaptive Accuracy of Flowers: Measured and Micro Evolutionary Patterns” is, W. Scott Armbruster. “The Adaptive Accuracy of Flowers: Measured and Micro Evolutionary Patterns.” Stylidium Annals of Botany, Vol. 103, no. 9, 2009, pp.1529-1545. The Source citation for the electronic version of “The Adaptive Accuracy of Flowers: Measured and Micro Evolutionary Patterns” is, Armbruster, W. Scott. “The Adaptive Accuracy of Flowers: Measured and Micro Evolutionary Patterns.” Stylidium Annals of Botany, Vol. 103, no. 9, 2009, pp.15291545, https://academic-oup-com.eres.library.manoa.hawaii.edu/aob/articlelookup/doi/10.1093/aob/mcp095.`

12.

“The Rhythms of Life” written by Edward S. Ayensu and Philip Witfield . Call number fQH527.A93

“Progress in Photosynthesis” written by Günther O, Schenck. Call number fQH515I571972a

“Electric Field Phenomena in Biological Systems” written by the Static Electrification `Group of the Institute of Physics. Call number - fQH509E4341989

“The Chemical Basis of Life – An Introduction to Molecular and Cell Biology” written by Scientific American, Philip C. Hanawalt, and Robert H Haynes. Call number fQH501H35

“Introduction to Genetics” written by D.G. Mackean. Call number – fQH530M25 13.

A style guide is there to provide the writer with rules to follow for a specific topic. The goal is to provide and make the information given recognizable to those who are also studying that topic. The MLA style of citation is mainly used within subjects of humanities and liberal arts. MLA style provides rules for written pieces such as the page layout and format, how sources must be cited, and what writing styles are to be used when. The fundamental work cited format for a book includes the last name of the author, the first name of the author, the title of the book, the publisher, and publication date. The Chicago Manual of style is most commonly used in the humanities and places rules on grammar, page layout, publication, and citation. The general format for a works cited list in Chicago Manual style includes both a footnote or endnote and a bibliographical listing. The foot/end note for a citation in CMS format includes the first and last name of the author, the title of the book, the place it was published, the publisher name, year of publication, and page number. The bibliographical listing includes all of these aspects except for the page number. The American Psychological Association style guide (APA) provides rules for creating written works in the subject fields of nursing, social sciences, and business. To follow strict APA guidelines, one’s piece of writing must have 4 parts; a

title page, abstract, main body, and references. Writing should be double spaced, within one inch margins, and include a page header on the top of each page. The Council of Science Editors Manual for Authors, Editors and Publishers style format (CSE), is most commonly used in the natural and physical sciences, and mathematics. It places rules on the reference list and how in-text citations are to be cited. To cite a reference in-text in CSE format, you must place a number next to it. On the reference sheet at the end, you must have the list of references in the same order as they were added to the text. The author, title, place of publication, name of publisher, and date all need to be included in a general citation for a book. CSE writing style is very similar to that of Chicago Manual of Style. Source Used - “Research and Citation.” The Purdue OWL: Research and Citation, Purdue Online Writing Lab, owl.english.purdue.edu/owl/section/2/.

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When searching both the words, “osmosis” and “membranes” on Bing and Google Scholar, you get very different sets of search results. A Bing search, much like a Google search, is very broad and is often not very specific to the topic of discussion. When these two words were entered in the Bing search engine, a wide array of information is displayed. This includes definitions, websites with articles about those topics, video explanations, and even many advertisements which include those key words. When these two words were entered in the Google Scholar search engine, thousands of pieces of writing appear that often relate better to your topic than those of the Bing search. The Google Scholar search is much more direct as it immediately immerses you in a pool of accredited pieces of work. Google Scholar works by finding credible sources and

matching the key terms in your search to the articles in the search engine. It would be most useful to use Bing when trying to understand the general concept of a topic. If one needs to become more immersed in the topic to write an essay or such, then completing a Google Scholar search is most useful.

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The advantage of being logged in to your UH account when you are on Google Scholar is that you are able to fine tune your display results. By entering information in your scholar profile, you are able to state what topics interest you the most and what types of information that you need. By being logged in to your UH account on Google Scholar, you are able to compile articles and save them in a folder to read later.

16.

A works cited page works by listing the sources that have been directly referenced within a piece of writing. A bibliography differs from a work cited page because it must list all the sources that have been used for gathering information and ideas on the topic of discussion, and not only those that have been directly mentioned in the writing.

17.

After having read lab 7, “The Effect of Light Color on Photosynthesis” and chapter 10 of “Campbell Biology 11/e”, I was able to come up with five subject terms that relate to the key concepts described. These subject terms are absorption, photosynthesis, wavelengths, light reactions, and photons.

Using the same guidelines that were used in the first part of this question, I have developed a list of 20 key words that might be used to find information on the material listed in both pieces of writing. These key words are; pigments, photosynthetic membranes, light energy, incident light, transmitted light, chloroplasts, chlorophyll, ATP,

NADPH, synthesis, glucose, Calvin cycle, stroma, thylakoids, light reaction, cellular respiration, carotenoid, photosystem, linear electron flow, and action spectrum.

Absorption, light reaction, carotenoid, cellular respiration, and pigment are the subject terms or key words that I believe will give me the best search results when trying to find information on the material listed in the two pieces of writing.

“Seasonal patterns of reflectance indices, carotenoid pigments and photosynthesis of evergreen chaparral species” and “Understanding photosynthesis, pigment and growth-responses induced by UV-B and UV-A irradiances”, are the two articles I have located that I believe will be beneficial for reference in lab 7.

“Seasonal patterns of reflectance indices, carotenoid pigments and photosynthesis of evergreen chaparral species”

Abstract

This study examined the ability of the Photochemical Reflectance Index (PRI) to track seasonal variations in carotenoid pigments and photosynthetic activity of mature evergreen chaparral shrubs. Our results confirm that PRI scales with photosystem two (PSII) photochemical efficiency across species and seasons, as demonstrated by PRI's strong correlation with de-

epoxidized (photo protective) xanthophyll cycle pigment levels (normalized to chlorophyll) and with the chlorophyll fluorescence index. DeltaF/Fm'. PRI and carotenoid pigment levels (deepoxidized xanthophyll cycle pigments normalized to chlorophyll or total carotenoid pigments normalized to chlorophyll) were correlated with seasonal fluctuations in midday net CO2 uptake of top-canopy leaves. By contrast, chlorophyll levels (as measured by the Chlorophyll Index) were not as strongly linked to photosynthetic activity, particularly when all species were considered together. Likewise, the Normalized Difference Vegetation Index (NDVI, an index of canopy greenness) did not correlate with net CO2 uptake. Canopy NDVI also did not correlate with canopy PRI, demonstrating that these indices were largely independent over the temporal and spatial scales of this study. Together. these patterns provide evidence for coordinated regulation of carotenoid pigments, PSII electron transport, and carboxylation across seasons and indicate that physiological adjustments are more important than structural ones in modifying CO2-fixation capacity during periods of photosynthetic down-regulation for these evergreen species.

“Understanding photosynthesis, pigment and growth-responses induced by UV-B and UV-A irradiances”

Abstract

Plant response to UV-B (0.290-0.320 mu m) irradiation in controlled environments has been difficult to assess, possibly because plants also respond to UV-A (0.320-0.400 mu m) and visible radiation. Photosynthetic dysfunction is often reported, but effects on photosynthetic pigments have been equivocal. Because UV-A/blue radiation is involved in pigment synthesis, the experimental UV-A irradiation was controlled and this study was conducted under high ambient photosynthetic photon flux (mid-day PPF greater than or equal to 1400 mu mol m(-2)...