Statistical Biology Lab Report. UTSC Journal of Plant Biology

BIO A01 2018- Fall; 1(1): 1-6

Insert Principal Author’s Name/Student Number

Paper title (The title should be specific and concise-Do not use “Formal Lab Report” in the title. All words except the first word should be in lower case-except for proper nouns.)[endnoteRef:1] [1: Template modified from the following resources: “Manuscript Template,” Science Publishing Group, The Open Access Publisher 2012 URL http://www.sciencepublishinggroup.com/journal/guideforauthors.aspx?journalid=173; Guidelines for Writing Scientific Papers, Honors Organismal Biology Laboratory (no date), URL http://www.bms.bc.ca/resources/library/pdf/GuidelinesScientificPapers.pdf; Guidelines for Writing a Scientific Paper, Maloy 2001, URL http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/scientific-writing.pdf; and Writing a Scientific Research Paper, Massachusetts Institute of Technology 2000. URL http://umech.mit.edu/freeman/6.021J/2000/writing.pdf. ]

Author’s Name (Principal Author), 1, Author’s Name (Bench-mate 1), 1 Authors Name (Bench-mate 2), 1 Author’s Name (Bench-mate 3), 1 Author’s Name (Bench-mate 4), 1 Author’s Name1 (Bench-mate 5) 1 – If you do not know your bench-mates names, please write your name + 4 other BIOA01 students in PRAXX

1Dept. of Biological Sciences, University of Toronto Scarborough, Toronto, Canada

UTSC BIOA01 Lab PRAXX, BENCHX:

PRAXX TA:

Abstract: An abstract is a one-paragraph summary of your report. It should begin with a few introductory remarks that introduce the significance of the study. It should include (in this order) the background of the study (1-3 sentences), mentioning of the study system/species/object (1 sentence), the question investigated (1 sentence), the general methods used (1 sentence), the principle results (1 sentence) and the conclusions (1 sentence). The reader should be able to determine the major points of your report without having to read further. The language should be concise and no citations should be included in the abstract. The abstract is located at the beginning of your report, however it is usually written once you have finished writing your paper.

Keywords: Include at least 3 keywords or phrases (specific to your paper), which must be separated by commas to differentiate them.

Introduction [Page limit-1 page]

This template is set up to provide you with an example of the format expected for your Formal Lab Report (FLR). The template provides you with the specifications needed for preparing your FLR. You can save this file as a separate document and type your report directly into the template. You can then submit your edited version of this file to Quercus. Please note that Quercus will only accept Word (.docx or .doc) files or PDF (.pdf) files.

The introduction provides a context for the research. This section should include the following: 1) Description of the current state of knowledge or understanding at the beginning of your investigation (i.e., background information synthesized from the existing literature – think about what information readers would need to know to be able to understand your lab report); 2) Background information about study species used; 3) The purpose of the experiment and/or the question being asked; 4) Hypothesis/hypotheses written as statements. Null hypotheses may be included here; 5) Brief description of the approach being used to test your hypothesis/hypotheses statement; 6) Predictions written as explanatory statements (“If…then”) that focus only on experimental treatment groups (not controls) and are backed up with relevant references.

It is imperative that you include properly formatted in-text citations to support all non-original ideas within your introduction. Failure to include in-text citations will result in a grade penalty and could possibly lead to an academic offence.

Materials and Methods [Page limit – 1/2 page- 1 page]

The purpose of this section is to describe the experimental procedures, including any controls. This section should be written in the past tense (and first-person if applicable); the remainder of the paper should be written in the present tense. The description should be complete enough to allow someone to repeat your work. The Methods section should describe the chronological process that you used to complete the research, how all of the data was collected, and a short description of the statistical analyses you completed. It should be written in complete sentences, not bulleted lists. Do not include lab coat, gloves, or safety goggles in your materials description-the use of personal safety equipment is assumed.

Be certain to include any software used to produce graphs and analyze data (e.g., Excel, GraphPad). Also, be certain to include an in-text citation of the lab manual in this section (and a corresponding complete reference in your reference section) but summarize the methods in your own words.

Results [Page limit – 1 ½ – 2 pages (written ½-1 page, figure ½ page, table ½ page)]

The results section describes the results of, but DOES NOT interpret, your experiment. You should present your table and figure in this section. The ‘Results’ section should always begin with text and not your table and figure. You should describe your findings to the reader – you should refer the reader to your table and figure in your results description (e.g., see Table 1 or Figure 1). By referring to your table and figure appropriately, you can concisely present your results in several paragraphs. If you do not refer to the appropriate figure or table in your results section, you will be penalized.

For the purpose of this report, your table and figure should be embedded within your results section. Be certain that there is not a page break in the middle of your table or figure and do not wrap text around the outside of the table and figure. (Note that some journals require that the tables and figures be included following the reference section.) The table caption should appear above the table, whereas the figure caption should appear below the figure. Insert your table and figure after they are cited in the text.

Be sure to record all your class data on the Table 3.2 in your lab manual. You will need these data to do the statistical analysis to produce the Table and Figure for your ‘Results’ section of your Formal Lab Report. See tips for the Table caption below.

Table 1: Your caption should be above your table and include details of what is included in your table. The information in your caption/table should be complete enough and presented in a way that the reader can easily understand the information presented without referring to the text of your report.

INSERT TABLE HERE – Your Statistical Worksheets should not be used for your Table in your Formal Lab Report. You must select information from your Worksheets to make a Table for your FLR. Your Table should include the following columns for each t-test comparison. You will be comparing each of the four treatment groups (light intensity in lumens) with the negative control (dark), as well as the positive control (outside light). Thus, you will have 8 comparisons.

Your Table should include the following columns for each t-test comparison:

a. n

b. critical t- value

c. calculated t-value

d. df

e. actual p-value (p > 0.05 or p < 0.05 or p = 0.05)

f. conclusion (did you reject or fail to reject the null hypothesis?)

INSERT FIGURE HERE – Prepare a bar graph with standard deviation error bars using the total oxygen produced (ml) for your complete data set (posted on Quercus for your lab practical). This means that the columns will be an average of all 8 values for each control and each experimental treatment group. You will have a total of 6 bars in your bar graph. Treatments should be shown as categories on the x- axis, mean total oxygen produced (ml) should be on the y- axis. The controls and the 4 treatments should be discernable by clear labels on the x-axis.

Note: If treatments cannot be discerned from your figure, you will be penalized.

Figure 1: Your caption should be below your figure and include details of what is depicted in your graph. The information in your caption/graph should be complete enough and presented in a way that the reader can easily understand the information presented without referring to the text of your report.

Discussion [Page limit – 1 – 1 ½ pages]

The discussion section is where you report on the interpretation and conclusion of your results. This is your opportunity to demonstrate your ability to analyze, evaluate, interpret and reason effectively. The discussion should relate your findings to your original question, hypothesis (or hypotheses if you had more than one), and predictions, which means that you evaluate your results in terms of your original question/hypothesis/predictions and point out the biological relevance of your findings. Avoid redundancy between the sections, especially the ‘Results’ and ‘Discussion’, of the lab report.

In addition, you should generalize the importance of your findings, discuss ambiguous data, and relate your results to other published studies (i.e., results published in primary scientific literature). Is your work in agreement or in contrast with previously published work? You should also discuss any sources of experimental error or limitations. You should end your discussion by summarizing the main points that you want the reader to remember; you should provide closure for the report and by extension, the reader. You should also recommend specific areas of further research based on your results and the findings of other published studies.

It is imperative that you include properly formatted in-text citations to support all non-original ideas within your discussion. Failure to include in-text citations will result in a major grade penalty.

Acknowledgements [Page limit – 1 paragraph, optional]

The acknowledgements section is where you can choose to acknowledge people who contributed to your work in some way but do not fit the criteria to be included as authors. This is also where you would include information about funding sources.

References [Page limit – 1/2 – 1 page]

You must include at least three primary scientific literature sources (which you are responsible for finding) as well as the BIOA01 lab manual in the proper format (Name-Year System, CSE Style- see Section C of the FLR Information page). Further resources can be included in addition to the three required primary sources. This style combines in-text parenthetical citations with a reference list at the end of your report (Walker and Rapley 2009). The references should be organized in alphabetical order by the primary author’s surname (last name) – DO NOT alphabetize the names within each citation. Be consistent when writing journal titles – write all journal titles out in full (e.g., European Food Research and Technology) or all abbreviated (e.g., Eur Food Res Technol).

Tip: Complete the online Library Research module and associated quiz to help you find relevant primary resources.

See examples below and more by using library resource document included with other FLR files on Quercus. Remember to remove subheadings when preparing your reference list. Reference list should be a single alphabetized list.

Scholarly Journal Article (primary source)

Ma Q, Scanlan C, Bell R, Brennan R. 2013. The dynamics of potassium uptake and use, leaf gas exchange and root growth throughout plant phenological development and its effects on see yield in wheat (Triticum aestivum) on a low-K sandy soil. Plant Soil 373:373-384.

Scholarly Journal Article (primary source found on the internet)

Mattupalli C, Genger RK, Charkowski AO. 2013. Evaluating incidence of Helminthosporium solani and Colletotrichum coccodes on asymptomatic organic potatoes and screening potato lines for resistance to silver scurf. Am J Potato Res [Internet]. [Cited 20 June 2013.] Available from http://link.springer.com/content/pdf/10.1007%2Fs12230-013-9314-3.pdf

Scholarly Journal Article (review, not a primary source)

Miao Y, Stewart BA, Zhang F. 2011. Long-term experiments for sustainable nutrient management in China. A review. Agronomy for Sustainable Development 31:397-414.

Chapter in Book (not a primary source)

Denison RF. 2012. Selfish genes, sophisticated plants, and haphazard ecosystems. In Darwinian Agriculture: How Understanding Evolution can Improve Agriculture. Princeton (NJ): Princeton University Press. Pages 76-94.

Chapter in Book Series (not a primary source)

Fageria NK, Moreira A. 2011. The role of mineral nutrition on root growth of crop plants. Advances in Agronomy (Book series) 110:251-331.

Internet Resource (secondary or tertiary source)

Williamson RC. 2004. Deciduous tree galls [Internet]. Madison (WI): University of Wisconsin-Madison; [cited 2013 Sep 12]. Available from http://labs.russell.wisc.edu/pddc/files/Fact_Sheets/FC_PDF/Deciduous_Tree_Galls.pdf

Statistical Biology Lab Report

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Kukai’s TenKukai’s Ten Mindsets (Japanese Buddhist Philosophy)Mindsets (Japanese Buddhist Philosophy). Kukai’s background and summary of Shingon Buddhism

In the Japanese philosophy and humanitarian history, there has been a series of religious people who have taken part in sharing and teaching about different humanitarian ideas and theories. One of these individuals was the Buddhist tantric monk Kukai. Kukai was born in 774 in a sea-village known as the Gbu-ga-ura a village that is not far from the Tadotsu, in Sanuki. The boy Kukai was born into a family called Saiki and his father, was Yoshimichi who was a nobleman from the ancient emperor descendent. The birth of Kukai is said to be miraculous in nature. The reason is because before conception; his mother saw a vision in her dream of a saintly monk coming to her house and monk using supernatural powers made Kukai’s mom pregnant. Again, when the boy Kukai was born, his hands were held together as if he was in prayers (Casal, Ugo Alfonso, 1959). Kukai was baptized to a name Henshg King which means “worldwide shining diamond.” Locally, during his growing up, he was also given a nickname that people used to call him “TotGmono” which means “out treasure.”

Kukai started his mission when he was young, and he could he have visions like being seated on eight-petalled lotus flower having a dialogue with the Buddha. Kukai joined the University when he was twelve years in preparations for his career in Confucianism. However, being unsatisfied with the career, Kukai privately studied Taoism because it was the job that he felt was in alignment with his reasoning. In great curiosity to learn the truth, Kukai left his city at a tender age and became a member of the Buddhist temple as an acolyte. His great passion in Buddhism made him to mode clay images of Buddha. With the images, he established a shrine from where he could do his Adoration to Buddha. This great step of faith in Buddha subjected Kukai to trials of the devil as he was continually tried. However, it is believed that Buddha protected him from the trials and tribulations and he was granted special power to overcome spiritual battles. His great commitment and adoration led to his ordination as a Buddhism priest by priest Gonso of Iwabuchidera (Casal, Ugo Alfonso, 1959).

As a priest, Kukai worked together with Ambassador Fujiwara, and together they traveled to different countries like China between the years 778-818. Upon his return to Japan, Kukai founded an independent Buddhist institution by the name Heian Buddhism which focused on teaching about the truth. In his works at the Heian Buddhism ministry, Kukai engaged in a lot of teachings which among them was the understanding of human mind where he came up with ten different mindsets development  and the different personal characteristics and behaviors associated with the different mindsets. According to Kukai’s teachings through his school of thought, the ten different mindset stages that individuals go through before they can achieve full consciousness of issues as they are naturally.

The philosophy claimed that more one moves to another step the more developed one’s brains get, and the more real the world becomes (Casal, Ugo Alfonso, 1959). Notably, each stage has its specific characteristics and behaviors that a person tends to show. Kukai’s state of mind teachings came to be taught and known a big number of people, and they are instructions that are known to have realized massive respect and value from the Japanese people. However, opposition towards Kukai’s view of mindset was highly present from some Ryuichi who was a Buddhist revisionist. Nevertheless, Kukai’s teachings came to be recognized as the Japanese Buddhist philosophy.

Apart from the teachings, priest Kukai did a lot of Buddhism services to people like communicating with different gods like the god of rain, soil, the sun, and harvest among many other gods and goddesses. Kukai constantly did a lot of supernatural powers that made the people believe in his powers and consider him a saint. The reason is that it was hard in Buddhism to communicate and have a response from the gods without being a saint. Also, for people to believe in his exorcism Buddhism, he also had to write a lot of literature and philosophies. However, this essay shall focus on Kukai’s ten mindsets successfully articulate the state of mind achieved through his school of thought.

Kukai’s ten mindsets

According to Dalisay, (2014); Priest Kukai who was born like a saint established ten different mindsets. The various mindset stages have a lot to do with humanity and a person’s state of mind. Each mindset has its specific characteristics and behaviors that a person shows when he/she belongs to that particular mindset category. Progressing to different mindset stages comes along with different features and behaviors. The following table shows all the different mindsets and their respective characteristics and behaviors.

Stage 1: unstable, goatish mind

According to Kukai, the unstable, goatish mind is the first step of mindset and according to Kukai is the toughest step in the entire development process. The reason is that it is the stage that presents individuals with the crudest and bleak visions of life. This is in regards to personal paths to follow and the starting point. Moreover, it is the stage when a person is presented the most challenging and complicated life visions that determine who a person is. Nevertheless, it is the mindset step that has a profound honesty starting point (Dalisay, 2014). The reason is that, despite a person feeling that he/she is sophisticated; the first level of mind is always familiar and strangely real. The danger about this stage is that instincts normally drive a person. So if the instincts are misleading, it is likely for one to have an entirely wrong mindset. The reason is that, in this step, people tend to act like sheep, and hence they tend to show ignorance and stupidity.

Stage 2: foolish abstinent mind

According to Kukai, a foolish abstinent mind is the second stage of mind development. In this stage, self-awareness hastens, and it is at this stage that a person realizes that there is more to life than just following the fickleness on the untrained and ordinary mind. Kukai also stated that it is at this stage that a person starts refraining from over-indulgence as well as harmful actions hence making a person start turning away from the first level of mind and instead starts seeking for something more meaningful in life (Casal, Ugo Alfonso, 1959). This stage was also named as gudo jisai-shin, and a person starts to restrain oneself from self-instincts. The reason is that the stage of mind development makes one realise the different foolish things that one was engaging in and the desire to stop them is triggered.

Stage 3: Childlike fearless mind

This is a stage of mind development a person seeks to believe in an eternally unchanging god or salvation doctrine. During this third stage of mind development, Kukai stated that a person in this state is normally wearied with human suffering and it is for this reason that the person starts to seek the peace of dwelling in heaven with the only thing being salvation (Casal, Ugo Alfonso, 1959). It is this mind that first awakens the need for religion because one in this mindset development stage makes a person to feel like a child and hence increased need to seek comfort for the mother’s embrace. Unfortunately, a person in this stage fails to realize that the mother too is subject to death, old age, and sickness and hence the only option is to believe in a forever spiritual doctrine or unchanging god. The need is even more desperate when the mind is at this stage, and one performs the four mental concentrations together with the six practices (Matsuda, 2003). The reason is that these practices increases the disliking of the world below and instead increases the need to love and gain more knowledge about heaven (Taoism and Hinduism).

According to Kukai, in this third stage of mind development, a person starts to have amazing spiritual visions. However, these visions are only practicable in another world and not the present world that the individual is in. However; a person’s vision of what can be achieved expands to infinite even though the confidence involved makes it possible for the vision to happen in life or fail to occur in this life.

Stage 4: Mind of selfless aggregates

According to Kukai’s philosophy, the fourth stage of mindset development makes one see oneself as impermanent, but the person still thinks that the five aggregates have a real existence. These five aggregates include; perception, mental activity, consciousness, form, and will. The realization of the five aggregates, a person’s mind can think more clearly and realize the notion of a permanent ego is in the real sense unreal. The realization further makes a person see the need and benefits of the eightfold anticipation as well as the six supernatural powers (Dalisay, 2014). This means that the development of the brain makes the mind to recognize the existence of components and denies a permanent ego any form of recognition. According to Kukai, a person meets Buddhadharma for the first time in the fourth stage of mindset. It is the stage that people tend to practice all the core principles and values taught by Shakamuni. More so, the system of practice is normally characterized by the three mysteries which are; Samadhi, sila, and prajana. This stage is also the personal obstacle overcoming stage and awakens a person’s abilities to handle challenges (Matsuda, 2003).

Stage 5: Mind free of karmic seeds

The fifth stage of mind development makes a person destroy all the arrogance and ignorance which are said to have been planted by the bad karma. Just like in the fourth stage of brain development, in this stage also the brain lacks any form of compassion towards other beings (Casal, Ugo Alfonso, 1959). This means that in as much a lot of arrogance is uprooted; other mental weaknesses develop hence hindering total effectiveness on how the brain works.

Stage 6: Compassionate Mahayana mind

According to Kukai in his Japanese Buddhist Philosophy, the compassionate Mahayana mind is the level of mind where the mind becomes compassionate about all living things in the world. The mind becomes conscious of all things despite the realization that all objects are void and hence the mind tends to see all objects as real (Dalisay, 2014). Kukai stated in his philosophy that in the entire brain development process, this is the first time that great compassion takes place and one takes the action of granting aid to other people who might be in need of any help.

Stage 7: Mind awake to the unborn

According to Kukai, when the mind gets into this level of development, it is the time that an individual gets into an actual realization about the void nature of both the mind and objects. In this stage, Kukai elaborates that with the unborn, he means the false predictions that are made clear by the absolute emptiness that one feels in mind and objects (Matsuda, 2003). It is the stage of mind awakening to face the truth, and the mind in this stage becomes unproduced. More so, it is the stage that the mind comes to the realization that no dramas exist beyond the mind.

Stage 8: The mind single way

According to the philosophy, the eight step of mind development leads to a single way of thinking. Kukai defined mind single was as the way to the truth. The reason is because he believed that the brain can only perceive issues from one single way for the truth to be determined. According to Kukai, this level of mind development can understand and acknowledge that the world of delusion and enlightenment is the world of mind and matter, an all possible world, and all thoughts are contained in one individual mind (Casal, Ugo Alfonso, 1959). In this stage of mind development, the mind can come together and put more efforts and concentration on the true issues and minimizes the void felt in the seventh stage of mind development. The reason is that according to Kukai, the brain can consolidate and narrow down the wide perception to a narrow perception hence making things to have meaning and purpose,

Stage 9: Mind of ultimate no-self nature

According to Kukai’s Japanese philosophy, the mind in the ninth stage of development has gone through different stages, and the mind can push through all things around it. Nevertheless, the brain is still limited by its duality, and this is something that further hinders the brain from functioning or perceiving issues from a perfect point of view (Dalisay, 2014). The reason is that when the mindset is limited to duality, it means that the mind is being affected by two different issues hence compromising the way of perceiving problems.

Stage 10: secret sublime mind

This is the last stage of mindset, and in this stage, the mind has already gone through all the process, and the stage brings the brain to a breakthrough. The reason is that the mind has been able to follow illusions, comes to realize and overcome them among many other challenges. It is for this reason that Kukai stated that this stage of mind development is marked with a breakthrough of the duality and finally the mind can realize the true nature (Matsuda, 2003). With the duality challenge overcome, the much searched for truth is eventually realized, and the mind can settle after obtaining the truth.

Treatise on the Ten Stages of the Development of Mind

Just like everything else in the world that develops, the mind also has different stages of development. It is by going through all the stages of development that the mind is grown fully and can distinguish between good and bad or something acceptable and things that are not acceptable (Dalisay, 2014). When one is young, the mind is not fully developed, and it means that as one grows up, the mind continues to grow as well as go through the different stages. First, when the mind is young, there is a lot of confusion and the confusion is the one making one to feel the void or the emptiness. The reason is that one from the onset normally has a purpose and before the purpose is obtained it is hard for one to get the real world. Thus, one ends up going through different stages and satisfaction is realized when the brain becomes fully developed. The reason is that this is the time that from one’s thinking; things in life starts making sense and more clear. It is also the time one is sure of the feelings and it like the reality dawns hence making one have a better sense of direction and purpose.

This difference in characteristics and behaviors that come with each stage of mind development according to Kukai is the reason that makes people who belong to different mind development stages to behave differently from each other. The latter is in the sense that the actions that one engages in according to how the brain is receiving and interpreting information are different from the actions that another person who belongs to another brain development level would show (Casal, Ugo Alfonso, 1959). For example, a person whose mind is in the first stage of development would innocently act on instincts. On the other hand, a person who has already passed the first stage of brain development and now is in the third stage of mind development would not act by instincts but would apply morals and ethics earned in stage two and also act in a manner that will please the heavens. The reason is that this stage makes a person to seek salvation as the best way out.

Social cycles

From the different stages of mind development and the different actions associated with the stages, the social cycles are created. The people from the same level of mind development tends to behave in the same manner and share similar characteristics something that makes them belong to the same social cycle (Matsuda, 2003). The more reason is that they are likely to get along easily because of the similarities in behavior and characteristics as compared to dealing with an individual with an entirely different way of perceiving issues and behaving. However, the different social groups are important because when they come together, they form the society. This means that according to Kukai, the community is made of people from different levels of brain development and social cycles (Casal, Ugo Alfonso, 1959). In as much, each human being that makes up a social cycle or society has his/her characteristics, so it is the same case with the society. In most cases, the members of the community come together and form different laws and traditions that help the people despite from the fact they belong to different mind levels; they can interact and live together in harmony. In the world today, there are high-minded societies which have already gone through the maturing process like the European Union, and the low-minded societies that are still in the development process yet to mature like the warring nations.

The warring nations and countries practicing discrimination and other malpractices are classified as low-minded societies because they have not reached the maturity stage where all malpractices would lose meaning (Matsuda, 2003). This means that these societies have not been able to break through the limitedness of duality, and hence they continue being held back. After the breakthrough, the society is also able to perceive issues from a positive point of view, and the malpractices become irrelevant hence making the members of the society even without being commanded to act responsible and argue from an ethic, moral, and religious point of view.  The latter is in the sense that going through the development process helps the society to continue learning new things hence changing perception and way of thinking.

Work cited

https://logisticsofbelonging.com/2016/12/20/kukais-writing-praxis/

Casal, Ugo Alfonso. “The Saintly Kôbô Daishi in Popular Lore (AD 774-835).” Folklore Studies (1959): 95-144; https://web.archive.org/web/20070927213255/http://www.nanzan-u.ac.jp/SHUBUNKEN/publications/afs/pdf/a117.pdf

Dalisay Jr, Juan. “Understanding Humanity: An Analysis of Human Minds and Societal Patterns.” (2014); http://gurukul.edu/wp-content/uploads/2014/05/Understanding-Humanity-Jan-20141.pdf

Matsuda, William J. The founder reinterpreted: Kukai and Vraisemblant narrative. Diss. The University of Hawaii at Manoa, 2003; https://scholarspace.manoa.hawaii.edu/bitstream/10125/7110/2/uhm_ma_3075_r.pdf

Kukai’s TenKukai’s Ten Mindsets (Japanese Buddhist Philosophy)Mindsets (Japanese Buddhist Philosophy)

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