BISC 219/F10: Assignment Series2 Classical Genetics Paper: Difference between revisions
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1) '''Remember your audience for this paper is not your lab instructor or a classmate who knows all about these experiments;''' rather, the audience is a group of scientifically literate strangers who don’t necessarily know anything about your project and its goals or about genetic tools, laws, or worms. The introduction is the place to spell out your experimental goal: structural characterization of a functionally significant mutation in ''C. elegans'' through finding the location of the gene responsible for the dumpy phenotype. | 1) '''Remember your audience for this paper is not your lab instructor or a classmate who knows all about these experiments;''' rather, the audience is a group of scientifically literate strangers who don’t necessarily know anything about your project and its goals or about genetic tools, laws, or worms. The introduction is the place to spell out your experimental goal: structural characterization of a functionally significant mutation in ''C. elegans'' through finding the location of the gene responsible for the dumpy phenotype. | ||
2) Your introduction, also, must attempt to develop the audience’s interest in the topic by explaining to prospective readers (who aren’t students in this course) why they should care about your project’s goal. | 2) '''Your introduction, also, must attempt to develop the audience’s interest in the topic by explaining to prospective readers (who aren’t students in this course) why they should care about your project’s goal.''' This is not so easy; since, if we’re honest, your readers are pretty sure they can live quite full and productive lives without knowing anything about dumpy worms--- unless you convince them otherwise. So why do geneticists spend so much time hunting for functionally significant (those that cause a phenotype change) mutations and then sleuthing out the location of the genetic change that cause them? It is crucial to keep in mind that the big picture here is not to learn about the mutation in a lowly soil worm, but rather, to learn as much as we can about the normal gene, particularly if that gene and its function are relevant to other eukaryotes. We do that by purposely causing a gene to be altered or broken a little bit (mutagenesis) and then hunting for a change associated with an interesting phenotype change. If we mutate a gene and see what its encoded protein or regulatory product is now now unable to do, does differently, or does better, then we have learned a lot about the role of the normal gene. It's particularly important to find out where that gene is located relative to other genes because genes exchange bits most readily in nature with other genes in close proximity and alter their function too. The goal and the significance of your forward genetics project is to map or locate and characterize a phenotypically significant gene mutation using classical and modern genetic tools such as linkage analysis, mapping from reference markers, complementation analysis, and DNA sequencing. Once you know the location and the gene change, you can do research on public databases to find out if this gene and mutation you studied is new or previously characterized. You are will end by doing some preliminary investigation to see what is known about similar genes and mutations in other species. Because the ''C. elegans'' homology with humans (and with most other eukaryotic organisms) is astonishingly high, genetic researchers, like you, can apply quite often aspects of worm genes structure and function to other organisms, including ''Homo sapiens''. | ||
3) '''Do not assume that your reader understands what you did and why you did it.''' Remember that it is not intuitive to those who didn’t hear Prof. Koniger's lectures on laws of inheritance that certain ratios of progeny from certain crosses means that genes are linked or that assortment is independent. In your Results section, you will have to BRIEFLY explain your crosses and your experimental design to understand how the resulting progeny allowed you to figure out the main conclusion: where your particular dumpy mutation is located in the ''C. elegans'' genome, exactly what the gene and protein change is, if it is a new or a previously charaterized dumpy mutation. Your discussion will revolve around some conjectures about this mutation's function significance in the worm and in other eukaryotes. Concise "explaining" in a logical and progressive sequence is the most difficult and important part of a scientific research report . Just because you are allowed to omit the Materials and Methods section of this paper, that does not mean that your reader does not need to know what you did to be able to make conclusions from experimental evidence. The Results section should begin with a general synopsis of your experiments (but not in anywhere near the level of detail that you would write about what you did in M&M). You need not be specific in the Results narrative about media recipes, incubation times, etc. However, future investigators, who are also working in this field, need for you to be specific about strain names and crosses. You must use established nomenclature and you must make sure that any acronyms (dpy for dumpy, for example) are clearly defined at first use and wherever ambiguous. '''Avoid non-specific words like “plates” when you describe your experiment.''' Plates are just pieces of plastic. It is the culture conditions (medium, worm strain, bacterial food) on the plates that need to be named because that's what's important. | 3) '''Do not assume that your reader understands what you did and why you did it.''' Remember that it is not intuitive to those who didn’t hear Prof. Koniger's lectures on laws of inheritance that certain ratios of progeny from certain crosses means that genes are linked or that assortment is independent. In your Results section, you will have to BRIEFLY explain your crosses and your experimental design to understand how the resulting progeny allowed you to figure out the main conclusion: where your particular dumpy mutation is located in the ''C. elegans'' genome, exactly what the gene and protein change is, if it is a new or a previously charaterized dumpy mutation. Your discussion will revolve around some conjectures about this mutation's function significance in the worm and in other eukaryotes. Concise "explaining" in a logical and progressive sequence is the most difficult and important part of a scientific research report . Just because you are allowed to omit the Materials and Methods section of this paper, that does not mean that your reader does not need to know what you did to be able to make conclusions from experimental evidence. The Results section should begin with a general synopsis of your experiments (but not in anywhere near the level of detail that you would write about what you did in M&M). You need not be specific in the Results narrative about media recipes, incubation times, etc. However, future investigators, who are also working in this field, need for you to be specific about strain names and crosses. You must use established nomenclature and you must make sure that any acronyms (dpy for dumpy, for example) are clearly defined at first use and wherever ambiguous. '''Avoid non-specific words like “plates” when you describe your experiment.''' Plates are just pieces of plastic. It is the culture conditions (medium, worm strain, bacterial food) on the plates that need to be named because that's what's important. | ||
4) Students are often confused about what goes into results and what should be saved for discussion. In the results section, you should make and include conclusions if your data allow them. If you can answer the main question or any part of it from your experimental data, do so! You should be able to use the data to conclude the location of your unique dumpy mutation in the ''C. elegans'' genome, to explain exactly what the gene and protein change is from wild type. Deciding if it is a new mutation or a previously characterized one is also something you can conclude from your mapping work and WormBase, so make those conclusions as part of the process of explaining your results. Don’t just describe your data in Results and leave your reader scratching her head, thinking, “ok, but what does that data mean”? | 4) Students are often confused about what goes into results and what should be saved for discussion. '''In the results section, you should make and include conclusions if your data allow them.''' If you can answer the main question or any part of it from your experimental data, do so! You should be able to use the data to conclude the location of your unique dumpy mutation in the ''C. elegans'' genome, to explain exactly what the gene and protein change is from wild type. Deciding if it is a new mutation or a previously characterized one is also something you can conclude from your mapping work and WormBase, so make those conclusions as part of the process of explaining your results. Don’t just describe your data in Results and leave your reader scratching her head, thinking, “ok, but what does that data mean”? | ||
5) Your discussion should briefly reiterate your main findings and then propose potential relevance, significance, or broader application of your findings. You should use other researchers work (citing those sources correctly!) to strength or weaken your arguement, however, the discussion is centered on YOUR thoughts about your findings in relation to others or as it paves new ground. Previous research by others is integral to the discussion, but NOT it's focus. | 5) '''Your discussion should briefly reiterate your main findings and then propose potential relevance, significance, or broader application of your findings.''' You should use other researchers work (citing those sources correctly!) to strength or weaken your arguement, however, the discussion is centered on YOUR thoughts about your findings in relation to others or as it paves new ground. Previous research by others is integral to the discussion, but NOT it's focus. | ||
6) Your references should be formatted according to the journal "Genetics". The Wellesley College Library allows electronic access to this journal; therefore, you should download a few recent articles in pdf format and use them as models for how to structure your references. Attention to detail is expected and required so make note of exactly where commas and periods are located | 6) '''Your references should be formatted according to the journal "Genetics".''' The Wellesley College Library allows electronic access to this journal; therefore, you should download a few recent articles in pdf format and use them as models for how to structure your references, both in-text and in the reference page. Attention to detail is expected and required, so please make note of exactly where commas and periods are located. Note that ''Genetics'' uses hanging formatting in its Literature Cited page. (In this journal, the references section is called Literature Cited rather than References.) This structure is far from universal so you must pay attention to getting it right ---or use a reference manger system like ''EndNOTe'' that automatically formats everything correctly when you tell it which journal to mimic. | ||
'''More Resources for Writing Help:'''<br> | '''More Resources for Writing Help:'''<br> | ||
Revision as of 08:29, 15 August 2010
Grading Rubric & Information for Scientifi Paper on Classical (Forward) Genetics Project – 50 points
Title, Abstract, Introduction, Results, Discussion, References – due week of 10/29 at the beginning of lab
Please refer to the general Guidelines for Scientific Writing, found in the Resources section, for tips on how to write each required section (Title, Abstract, Introduction, Results, Discussion, References). You may omit the Materials and Methods section.
Note that there are links in the Resources section of this Wiki to a page of instructions for finding sources using the Wellesley College library e-databases and another link to a page from the Wellesley library web site with instructions for using EndNote™ reference manager software for citing those sources correctly. In this paper, you will use the reference format of the journal Genetics. The best way to learn to format your reference citations in this style is to find recent articles in Genetics to use as models; or, (even easier) instruct EndNote™ to format them for this journal.
The Guidelines for Scientific Writing section on the Resources page of the Wiki goes into exhaustive detail about the general requirements and expectation for each section of your paper. You should spend significant time digesting all of that information and putting it to use in the drafts of your paper. Included below is additional advice (dos and don’ts) for writing this paper on your classical (forward) project.
1) Remember your audience for this paper is not your lab instructor or a classmate who knows all about these experiments; rather, the audience is a group of scientifically literate strangers who don’t necessarily know anything about your project and its goals or about genetic tools, laws, or worms. The introduction is the place to spell out your experimental goal: structural characterization of a functionally significant mutation in C. elegans through finding the location of the gene responsible for the dumpy phenotype.
2) Your introduction, also, must attempt to develop the audience’s interest in the topic by explaining to prospective readers (who aren’t students in this course) why they should care about your project’s goal. This is not so easy; since, if we’re honest, your readers are pretty sure they can live quite full and productive lives without knowing anything about dumpy worms--- unless you convince them otherwise. So why do geneticists spend so much time hunting for functionally significant (those that cause a phenotype change) mutations and then sleuthing out the location of the genetic change that cause them? It is crucial to keep in mind that the big picture here is not to learn about the mutation in a lowly soil worm, but rather, to learn as much as we can about the normal gene, particularly if that gene and its function are relevant to other eukaryotes. We do that by purposely causing a gene to be altered or broken a little bit (mutagenesis) and then hunting for a change associated with an interesting phenotype change. If we mutate a gene and see what its encoded protein or regulatory product is now now unable to do, does differently, or does better, then we have learned a lot about the role of the normal gene. It's particularly important to find out where that gene is located relative to other genes because genes exchange bits most readily in nature with other genes in close proximity and alter their function too. The goal and the significance of your forward genetics project is to map or locate and characterize a phenotypically significant gene mutation using classical and modern genetic tools such as linkage analysis, mapping from reference markers, complementation analysis, and DNA sequencing. Once you know the location and the gene change, you can do research on public databases to find out if this gene and mutation you studied is new or previously characterized. You are will end by doing some preliminary investigation to see what is known about similar genes and mutations in other species. Because the C. elegans homology with humans (and with most other eukaryotic organisms) is astonishingly high, genetic researchers, like you, can apply quite often aspects of worm genes structure and function to other organisms, including Homo sapiens.
3) Do not assume that your reader understands what you did and why you did it. Remember that it is not intuitive to those who didn’t hear Prof. Koniger's lectures on laws of inheritance that certain ratios of progeny from certain crosses means that genes are linked or that assortment is independent. In your Results section, you will have to BRIEFLY explain your crosses and your experimental design to understand how the resulting progeny allowed you to figure out the main conclusion: where your particular dumpy mutation is located in the C. elegans genome, exactly what the gene and protein change is, if it is a new or a previously charaterized dumpy mutation. Your discussion will revolve around some conjectures about this mutation's function significance in the worm and in other eukaryotes. Concise "explaining" in a logical and progressive sequence is the most difficult and important part of a scientific research report . Just because you are allowed to omit the Materials and Methods section of this paper, that does not mean that your reader does not need to know what you did to be able to make conclusions from experimental evidence. The Results section should begin with a general synopsis of your experiments (but not in anywhere near the level of detail that you would write about what you did in M&M). You need not be specific in the Results narrative about media recipes, incubation times, etc. However, future investigators, who are also working in this field, need for you to be specific about strain names and crosses. You must use established nomenclature and you must make sure that any acronyms (dpy for dumpy, for example) are clearly defined at first use and wherever ambiguous. Avoid non-specific words like “plates” when you describe your experiment. Plates are just pieces of plastic. It is the culture conditions (medium, worm strain, bacterial food) on the plates that need to be named because that's what's important.
4) Students are often confused about what goes into results and what should be saved for discussion. In the results section, you should make and include conclusions if your data allow them. If you can answer the main question or any part of it from your experimental data, do so! You should be able to use the data to conclude the location of your unique dumpy mutation in the C. elegans genome, to explain exactly what the gene and protein change is from wild type. Deciding if it is a new mutation or a previously characterized one is also something you can conclude from your mapping work and WormBase, so make those conclusions as part of the process of explaining your results. Don’t just describe your data in Results and leave your reader scratching her head, thinking, “ok, but what does that data mean”?
5) Your discussion should briefly reiterate your main findings and then propose potential relevance, significance, or broader application of your findings. You should use other researchers work (citing those sources correctly!) to strength or weaken your arguement, however, the discussion is centered on YOUR thoughts about your findings in relation to others or as it paves new ground. Previous research by others is integral to the discussion, but NOT it's focus.
6) Your references should be formatted according to the journal "Genetics". The Wellesley College Library allows electronic access to this journal; therefore, you should download a few recent articles in pdf format and use them as models for how to structure your references, both in-text and in the reference page. Attention to detail is expected and required, so please make note of exactly where commas and periods are located. Note that Genetics uses hanging formatting in its Literature Cited page. (In this journal, the references section is called Literature Cited rather than References.) This structure is far from universal so you must pay attention to getting it right ---or use a reference manger system like EndNOTe that automatically formats everything correctly when you tell it which journal to mimic.
More Resources for Writing Help:
Resources section of the WIKI
Your lab instructor!
Science Writing Peer-Mentors- The Writing Program provides free help from Writing mentors. The student writing advisers have scheduled hours in Sage Lounge and elsewhere on campus. Appointments can be made through an on-line appointment scheduler at: www.rich65.com/wellesley
Grading Rubric for Partial Paper-Gene Mapping – 50 points
| At or Above Standard | Below Standard | Points
Earned | |
|---|---|---|---|
| Title/ Abstract |
5.5-7.5 pts. Title reflects paper’s conclusions. Concisely summarizes in appropriate format: topic, experimental questions, general outline of methods, major findings (specific!), conclusions & implications of the findings in relation to what is known or expected. Information is brief but intelligible to novice reader. | 0-5 pts. Title stresses techniques or general goals rather than conclusions. Abstract omits topic, experimental goals, or a concise description of the experimental design with key results. Does not include conclusions or significance of those conclusions. Information unintelligible to novice reader. Includes tangential information or too much detail; misinterprets information and/or implications. | __/7.5 |
| Introduction | 8.5-10 pts. Identifies central topic, includes appropriate background information from primary sources, & a synopsis of the experimental design. Writing style uses correct vocabulary, grammar, spelling, punctuation, and is clear and concise. Reference citations in proper format (Cell style) in the body of the paper for all information not common knowledge. | 0-8 pts. Does not correctly identify central topic; does not include appropriate background information, or a synopsis of the experimental design; does not explain relevance of the experiments; does not use primary sources or give properly formatted reference citations for information not common knowledge. Includes background info. unrelated to topic; related background info is in too much detail or too general. Writing style is not clear or concise and/or uses incorrect vocabulary, grammar, spelling, or punctuation. | __/10 |
| Results/ Conclusions |
17.5-20 pts. Includes sufficient appropriate figures and tables designed for maximum clarity and ease of interpretation. All figures & tables are numbered & have correctly formatted legends; all data is labeled & includes correct units or appropriate info. on statistical tools used. The narrative describes accurately, clearly, and succinctly the rearch goals and an adequate description of the experimental methods before describing the major findings with specific references to figures/tables.
All major findings are evaluated appropriately for meaning and importance in answering experimental questions and explained for a reader who does know the topic or research methods well. Appropriate conclusions are drawn. |
0-17 pts. Key figures and/or tables omitted. Unprocessed data included. Figures &/or tables difficult to read or to interpret due to missing information and/or poor design. The narrative omits research goals, experimental design synopsis, key findings, describes the data inaccurately or unclearly, includes irrelevant information, or is repetitive. Data analysis does not include an adequate explanation of the concepts behind the experimental design or those required for the data interpretation. Not all major findings are evaluated for meaning & importance, or are incorrectly interpreted. Conclusion omitted, or, if present, conclusions are incorrectly drawn, unexplained and/or not related to experimental data. Future research directions or possible significance omitted. Writing style is not clear or concise and/or uses incorrect grammar, spelling, punctuation & vocabulary. |
__/20 |
| Discussion | __/10 | ||
| References | 2-2.5 pts. Includes complete, properly formatted citation for each work cited in body of report modeled after style of journal Cell. Includes an appropriately formatted Reference page at end of paper in Cell style. Includes all material that is not commons knowledge. Uses an adequate number of reliable, appropriate sources. | 0-2 pts. Does not include complete, properly formatted citations for all references in Cell style in body of paper and/or in References page at end of paper; lists works in Reference page not cited in body of paper, or fails to give reference citation for information not common knowledge. Does not use reliable or appropriate sources. | __/2.5 |
| Total | __/40 |
