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10.6: Conclusion and Resources - Biology

10.6: Conclusion and Resources - Biology


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10.6: Conclusion and Resources

Introduction

Less than two years ago, the author published an online bioinformatics curriculum in this journal and made the claim (with some important caveats) that a sufficient number and variety of free video courses had made their way to the web that it was possible to obtain a reasonably comprehensive bioinformatics education on one's laptop [1]. In that compilation of courseware, only a few entries originated from the then-nascent Coursera platform (https://www.coursera.org), and none came from its academic competitor edX (https://www.edx.org). In the intervening time, these platforms and several others have fairly exploded with new content, such that on the order of a thousand courses are now available online from over a hundred academic institutions. That fact alone justifies an update to the curriculum and a reassessment of the viability of online education in this field.

To begin with the latter, it should first be acknowledged that MOOCs are controversial in many regards. This article will not attempt to review or comment on the generic issues beyond making a few general observations in the Conclusion below. It is the opinion of the author that MOOCs are indeed a valuable resource even if they are not a magic bullet. The general limitations as regards bioinformatics were discussed in the previous article [1] and in a companion piece giving practical advice to online learners [2] and need not be recapitulated here. Certainly the sizeable increases in content that have occurred in the interim have improved the prospects, yet they have also raised the bar, and it is now clearer than ever where the gaps and shortcomings are in the available curriculum. Specific instances will be commented upon in the appropriate contexts below. One general observation is that the MOOC universe provides good coverage at the introductory level and plenty of specialized “elective” courses, but comprehensive intermediate and advanced courses are thin on the ground in some areas, including biology. For example, as of this writing there are no MOOCs dedicated to the subject of structural biology, which is surprising given the importance of visualization in the field and the availability of excellent online resources. Nevertheless, the sizeable expansion of courses available, particularly in allied fields such as neurosciences and evolutionary biology, has been deemed sufficient to widen the scope of this edition to encompass the more expansive term “computational biology” as opposed to “bioinformatics” (for those who consider the distinction important).

MOOCs continue to generate large enrollments, at least initially, and these numbers together with anecdotal evidence from course discussion forums indicate active interest in online education among a certain population. This evidently extends to the readership of PLOS Computational Biology, judging from article-level metrics for the original curriculum [1], which has now attracted over 60,000 views and as of a year after its appearance was the 12th most viewed article in the history of the journal (per data available from http://www.ploscompbiol.org/static/almInfo).

Those same metrics reveal high levels of interest in skills improvement and career advice, a conclusion that is based upon the popularity of the “Ten Simple Rules” series, which accounts for six of the ten most viewed articles. The topics of these six include giving talks [3], making posters [4], getting published [5], obtaining grants [6], selecting postdoctoral positions [7], and choosing between career paths in academia and industry [8] (the final article also having been written by this author). To better accommodate these interests, the current edition of the curriculum has been extended in two ways. First, articles have been included (at the end of the catalog) that specifically address nonscientific skills likely to be useful in career development. Second, the commentaries on individual courses now include not only evaluations of their content but also career advice and other personal comments tied to that subject and based on the experiences of the author, both in the classroom (real and virtual) and over the course of a varied career in bioinformatics. These features are described in more detail below.


Introduction

Writing and reading papers are key skills for scientists. Indeed, success at publishing is used to evaluate scientists [1] and can help predict their future success [2]. In the production and consumption of papers, multiple parties are involved, each having their own motivations and priorities. The editors want to make sure that the paper is significant, and the reviewers want to determine whether the conclusions are justified by the results. The reader wants to quickly understand the conceptual conclusions of the paper before deciding whether to dig into the details, and the writer wants to convey the important contributions to the broadest audience possible while convincing the specialist that the findings are credible. You can facilitate all of these goals by structuring the paper well at multiple scales—spanning the sentence, paragraph, section, and document.

Clear communication is also crucial for the broader scientific enterprise because “concept transfer” is a rate-limiting step in scientific cross-pollination. This is particularly true in the biological sciences and other fields that comprise a vast web of highly interconnected sub-disciplines. As scientists become increasingly specialized, it becomes more important (and difficult) to strengthen the conceptual links. Communication across disciplinary boundaries can only work when manuscripts are readable, credible, and memorable.

The claim that gives significance to your work has to be supported by data and by a logic that gives it credibility. Without carefully planning the paper’s logic, writers will often be missing data or missing logical steps on the way to the conclusion. While these lapses are beyond our scope, your scientific logic must be crystal clear to powerfully make your claim.

Here we present ten simple rules for structuring papers. The first four rules are principles that apply to all the parts of a paper and further to other forms of communication such as grants and posters. The next four rules deal with the primary goals of each of the main parts of papers. The final two rules deliver guidance on the process—heuristics for efficiently constructing manuscripts.


Teaching an Online Introductory Biology Lab Using Cellular and Molecular Biology Resources

This playlist can be used in an online, undergraduate (majors-level) introductory biology lab to incorporate core topics in cellular and molecular biology. Using case studies, multimedia, and interactive resources, it engages students in data analysis and critical thinking. The topics covered include the process of science, cellular energetics/photosynthesis, metabolism, meiosis and patterns of inheritance, and biotechnology.

This playlist can be used to teach five 3-hour (180-minute) labs in a lab course for a total of 900 minutes of instruction over a semester.

Lab 1: Process of Science

By completing the resources in this lab (resources 1–3 in this playlist), students will be able to:

  • Compare and contrast questions that can be analyzed using the methods of science and those that are outside the scope of science.
  • Develop testable scientific questions.
  • Use data to propose hypotheses, make predictions, and justify claims with evidence.
  • Identify, evaluate, and predict the scientific questions that drove research, based on data or figures from the scientific literature.

Lab 2: Cellular Metabolism and Photosynthesis

By completing the resources in this lab (resources 4–6 in this playlist), students will be able to:

  • Summarize the overall purpose of photosynthesis, including the inputs and outputs of matter at various steps in the process.
  • Identify the structures that perform photosynthesis in plants.
  • Summarize the main components of the light reactions and Calvin cycle, and how they contribute to photosynthesis.
  • Analyze and interpret data from a scientific figure.
  • Explain and contrast the impact of environmental factors on the function of the electron transport chain.
  • Design a research protocol using the basic principles of experimental design.

Lab 3: Macromolecules and the Digestion of Carbohydrates

By completing the resources in this lab (resources 7–8 in this playlist), students will be able to:

  • Analyze and interpret data from a scientific figure.
  • Graph data and appropriately label all graph components, including title, axes, units, and legends.
  • Make claims based on scientific evidence and support those claims using scientific reasoning.
  • Discuss the role of enzymes in metabolism.

Lab 4: Mendelian Patterns of Inheritance and Understanding Sex and Gender

By completing the resources in this lab (resources 9–10 in this playlist), students will be able to:

  • Study a pedigree to make an evidence-based claim about the mode of inheritance of a trait.
  • Determine the most likely inheritance pattern of a trait tracked in a pedigree and the genotypes of individuals included in the pedigree.
  • Analyze variations in DNA to make claims about which variants are associated with specific traits.
  • Explain how biological sex and gender differ.
  • Summarize how mutations in a variety of genes can affect the development of internal and external sex characteristics.
  • Explain how characteristics associated with biological sex may affect athletic performance.

Lab 5: Biotechnology

By completing the resources in this lab (resources 11–14 in this playlist), students will be able to:


10.6: Conclusion and Resources - Biology

Many students just beginning their science education may be unfamiliar with the concept of an abstract in a lab report it is often not required in introductory science courses because of its level of difficulty. As one takes higher level classes the teacher will specify if he or she wants an abstract to be included in the written reports. If it is required, it is the first part of your report, directly following the title page and proceeding the introduction.

The abstract, although it comes first logistically, always should be written last. It needs to be written last because it is the essence of your report, drawing information from all of the other sections of the report. It explains why the experiment was performed and what conclusions were drawn from the results obtained. A general guideline for an abstract has five sections or areas of focus: why the experiment was conducted the problem being addressed what methods were used to solve the problem the major results obtained and the overall conclusions from the experiment as a whole. Do not be misled, however, from this list into thinking that the abstract is a long section. In fact, it should be significantly shorter than all of the others. All of this information should be summarized in a clear but succinct manner if the abstract is going to be successful. An estimated average length for all of this information is only a single paragraph. Although this may seem as though it is a short length to contain all of the required information, it is necessary because it forces you to be accurate and yet compact, two essential qualities.

The best way to attempt to go about writing an abstract is to divide it into the sections mentioned above. The first two sections are very similar and can be grouped together, but do not have to be. If you decide to address them separately, make sure that you do not repeat anything. Often a section can be mentioned in only one sentence. Remember, brevity is the key to a successful abstract. Each section is addressed below to help clarify what needs to be included and what can be omitted.

The most important thing to remember when writing the abstract is to be brief and state only what is pertinent. No extraneous information should be included. A successful abstract is compact, accurate and self-contained. It also must be clear enough so someone who is unfamiliar with your experiment could understand why you did what you did, and what the experiment indicated in the end. An additional note is that abstracts typically are written in the passive voice, but it is acceptable to use personal pronouns such as I or we.

General questions to be addressed in the abstract section

1. Why it was done and what is the problem being addressed?
These two sections can be grouped together into one brief statement summarizing why the experiment was performed in the first place? What was the question trying to be answered? Science is an exploration for truth. It is all about curiosity and answering questions to find out why and how things work. The scientific method is a clear example of this first state a problem or question and then try to determine the answer. This section is the statement of the original problem. It is the reason behind why an experiment is being done. This should not include many details, rather it should be a simple statement. It can even be stated in one or two sentences at the most.

2. What did you do?
This part of the abstract states what was done to try to answer the question proposed. It should in no way be very detailed. It contains a brief outline of what was done, highlighting only crucial steps. It is the materials and methods section of your abstract, but it is only one or two sentences in length. It is a description of how you decided to approach the problem.

3. What did you find out?
In other words, what did all of your hard work and preparation tell you about the question you set out to answer. This contains only the crucial results obtained. The crucial results are those that are necessary to answer your original question posed. Without these results, the experiment would have been useless. The results should be stated briefly and should not be explained they should only be mentioned. It is very similar to the results section of your paper, but it highlights only pertinent results used to draw conclusions. An average length for this section is two or three sentences at the most. This number can vary however, depending on the complexity of the experiment, and so these length guides are just that, guides, not rules.

4. Conclusions?
This is the end of your abstract, directly hinging on the results obtained. This is the "so what" part of your experiment. "So what" refers to what the results mean in the long run. You need not include how you drew your conclusions, only the final conclusion. This should directly follow the results so the reader knows what results led to what conclusions. This is the equivalent to the discussion part of the paper, but again, like the rest of the abstract, it needs to be stated briefly and succinctly. You do not need to explain how you deduced the conclusion from the results obtained, only the end conclusions. After you have stated this, the abstract is complete.

Here are two examples of the same abstract, sample one is an example of a badly written abstract, while sample two is an example of a well-written abstract. Italicized words are links to explanations describing why the sentences are a good or bad example of an abstract.

Sample 1 : This experiment will determine what will make enzymes effective and what will make them ineffective. We tested different samples of enzymes in a spectrophotometer and recorded their absorption rates. Six samples were placed in the spectrophotometer but two contained no enzyme these acted as blanks for the other samples. The four remaining samples contained Catecholase ranging from 0.5 ml to 1.75 m. The second half of the experiment contained four test tubes with a constant amount of Catecholase, but the pH levels ranged from four to eight. It was found that if the enzyme was present in large amounts, then the absorption rate was high, and if the pH level ranged from 6 to eight then the absorption rate was high. Therefore it can be said that enzymes work well in neutral pH levels and in large amounts.

Sample 2 : This experiment was performed to determine the factors that positively influence enzyme reaction rates in cellular activities since some enzymes seem to be more effective than others. Catecholase enzyme activity was measured through its absorption rate in a spectrophotometer, using light with a wavelength of 540 nm. We compared the absorbance rates in samples with varying enzyme concentrations and a constant pH of 7, and with samples with constant enzyme concentration and varying pH levels. The samples with the highest enzyme concentration had the greatest absorption rate of 95 percent compared to the sample with the lowest concentration and an absorption rate of 24 percent. This suggests that a higher concentration of enzymes leads to a greater product production rate. The samples with a pH between six and eight had the greatest absorption rate of 70 percent compared to an absorption rate of 15 percent with a pH of 4 this suggests that Catecholase is most effective in a neutral pH ranging from six to eight.

Explanations of the Example Links

Ineffective : This sentence is in the present tense and needs to be switched to the past tense. In addition to tense problems, the sentence does not tell the reader much about what is meant by the term effective. What exactly is an effective enzyme? The author needs to be specific and try to avoid generic terms such as effective. Also, the author never states why the experiment is being conducted. Why is enzyme effectiveness so important? What makes it important enough to be studied? (return to Sample 1)

Rates : This sentence is addressing what was done, yet it barely conveys any information. The author states that different samples of enzymes were tested, but mentions nothing about the contents of the samples. Was the same enzyme used in every sample? What was in each sample, and what varied in each sample? Also, what does absorption have to do with enzyme activity? This correlation needs to be explained to the reader. One last detail that should be included is the wavelength of light that was used in the spectrophotometer. Did it remain constant or was it a variable as well? (return to Sample 1)

Eight : This is too long and detailed to be in an abstract it sounds as though it was pulled from the methods and materials section of the paper. The amounts of enzyme do not need to be stated, nor do the pH levels. The number of samples tested do not need to be included either it is just extraneous information that is not crucial to understanding the experiment as a whole. The information contained in this sentence can be pulled out and rearranged to say that some samples had a constant pH and varying enzyme concentrations and other samples had constant enzyme concentrations and varying pH levels. With the controls and the variables stated you can move on to your results. (return to Sample 1)

High : This is just too general, although it conveys the right information. When stating results it is okay to use actual numbers. Instead of saying that the absorption rate was high, specify how high in comparison to samples with low absorption rates. (return to Sample 1)

Amounts : An experiment is never final, nor is it ever positive. Always avoid saying that the results you obtained are correct or definite. Instead just say that the data supported or did not support your hypothesis. (return to Sample 1)

Others : This sentence is clear and concise, telling the reader why the experiment was carried out. It postulates the question of why some enzymes are more effective than others and it explains that the experiment was set up to determine what causes these differences. (return to Sample 2)

540 nm : This sentence introduces the specific enzyme being studied and how it was studied. The light wavelength used in the spectrophotometer was also specified telling the reader that wavelength was not one of the variables manipulated in the experiment. (return to Sample 2)

Levels : It is okay to use personal pronouns in the abstract and this sentence uses "we" effectively. It also defines what was done without going into great detail. The controls and the variables are stated clearly and succinctly so the reader knows what factors are being tested to determine enzyme productivity. (return to Sample 2)

Clear summary : These two sentences combine the results with the conclusion. This helps to make the conclusions drawn from the results very clear to the reader. The author also stated concrete numbers in the results so the reader is aware of just how much the absorption rates changed in each sample. (return to Sample 2)

All citations from Pechenik, Jan A. A short guide to writing about Biology. pp. 54-102, Tufts University: Harper Collins College Publishers . 1993.


The Lab

For the lab book, I recommend using a bound notebook instead of of loose paper or a word processor. We use composition books that can be found in most stores that sell school supplies. If you prefer loose paper, then below are some lab sheet forms.

2010 Exploring Creation with Biology Lab Forms

Each file has two pages as shown in the images. Mix and match the pages to suit the lab.

First Page Ruled, Second with Grid

First Page Grid, Second Page Ruled

Table of Contents Form the the Lab Book
Experiments are listed- Based on Edition 2. The optional experiments are included in the list.

I recommend using the DOC file and reformatting the list in such a way that when the page numbers are added by the student, there is more height for the number.

Notes: May 2002

We are almost finished with our biology book. I can see that the schedule could use changes. One change is that it takes only one day to complete a dissection instead of the several that I allowed in the schedule. Each dissection takes more time than the previous one. We thought the fish was the most difficult because the dissection tools were inadequate for some of the cutting required. The fish scales slowed the cutting a great deal. We had to use sharp household scissors for some of the cutting. It took us around 2 hours to complete the fish dissection because of the cutting difficulties. An optional bonus of the fish dissection is the fish eyes. My son dissected the eyes and found the lenses, which he found very interesting.

The frog was the best dissection because we used the specimen with latex injected organs which made them easy to identify. Cutting the frog was not difficult except for the neck and shoulders of the frog. These areas were more difficult due to the bones present in that area.

Random Comments

Comment regarding specimens: I purchased our dissection specimens at the beginning of our school year. The dissections did not begin until months later. The worm was dry and dusty and a poor specimen. It is possible that it was bad in the first place or that we bought it too soon - I can't say which. I wonder if a freshly killed worm would make a good specimen if it is big enough?

The Drawing Assignments: My son found the labeled drawings that I required of him tedious but his grades improved by doing them.

Somewhere midway in the book I began to write the schedule of the module on the back of the vocabulary bookmark.

We started our leaf collection early so we could collect the spring leaves as well as the fully-grown leaves. Observing the trees when they 'wake up' in the spring helps me to identify them easier because there is more to go by such as their blooms and spring leaf color as well as emerging pests that live on the trees.

See also from Apologia's Knowledge Base this article: Two Example Biology Lab Reports


Watch the video: Activity. Light Reflection and Refraction. Class 10 Science. CBSE BSEH NCERT STATE BOARD (May 2022).


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