Category Archives: Education

Writing the Materials and Methods Sections

This is part of a tutorial series I’m writing for my students on scientific manuscript preparation. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

This section should include information on every experimental procedure used in the work. You don’t have to include experimental details of everything that was in your lab notebook or all of the optimization work you did for the project. Yeah, readers don’t care about the two-years’ worth of failed protein purification methods in your notebook. You will only include the short paragraph of what did finally work. Refer to your figures. Whatever experiments yielded data that is ultimately found in your figures should have details in your Materials and Methods section. If certain reagents were critical to completion of the experiments, then include your sources for them (commercial or donations from other labs). The Materials and Methods section is written in the past tense without the use of personal pronouns. It may seem awkward to get into this point of view, but there is an omniscient perspective from which your methods can be written. I’m not sure where this convention originated, but remove yourself from the experiment and it seems more legitimate.

Subdivide this section into useful parts. This kind of organization also helps the reader pinpoint details for replication or evaluation of experiments. Often readers will be looking at your work to perform similar experiments or repeat your work.

It’s not exactly a protocol, but it should be complete. You don’t have to tell your readers every step of a protocol, but it should be complete enough for someone else with comparable training to replicate. The literature varies widely in the usefulness and clarity of methods descriptions. For more complex procedures, authors are often contacted directly for lab protocols or additional information not included in the materials and methods section. As methods have become more complex, fewer details are included. This is especially true of molecular biology work. Typically primer sequences are given and specific vectors are mentioned, but it can be especially irksome to figure out others’ cloning construction strategies. Usually, though, this information can be obtained directly from the authors. In general, I would err on the side of completeness (vs. concise) because this makes it easier for your experimental strategies to be evaluated and replicated. This strategy can run afoul of the journal’s character limits, but in this age of online publication, supplemental information is allowed. You can write a ‘Supplemental Methods’ section which will be available online only and can be as long as you’d like.

Referencing previous literature is a convenient way of being concise. It is acceptable to say something like, “This experiment was performed as in Reference (1).” However, if you go this route, make sure that the reference you are citing in this case does have the necessary information on experimental details. The scientific literature is infamous for pulling this trick only to reference yet another paper that says “This experiment was performed as in Reference (2).” You may have to follow this rabbit hole back a couple of decades before you find any real useful information on performing the experiment. (This is a personal pet peeve of mine that just makes me feel stabby when I encounter this nonsense.) So save your readers some trouble and either include the necessary info or cite a direct source. For many labs, there are standard references and descriptions for routinely used methods that appear in almost all of the manuscripts. It’s fine to revert back to previously published articles to see how things were worded and what references were cited, but it’s always a good idea to verify these references yourself. Otherwise, a mis-referenced citation will be propagated many times over. (This is also a good practice for any citation anywhere in a manuscript- to make sure the reference is really saying what you think it does.)

Offer your pro-tips for methods-writing in the comments section below.

Johnna

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Citations and Reference Formatting in Manuscripts

This is the next post in a series of tutorials I’m writing for my students related to scientific manuscripts. This series is compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

For every statement of fact in your introduction, results or conclusions sections or for every method, it is important to cite the appropriate reference, which provides the basis for this fact or method resource. Thus, references are given throughout the manuscript to direct the reader to previous literature to independently verify the facts or otherwise track down more information. Providing references for information in a scientific manuscript is somewhat different than providing references in a research paper for the humanities. While there may be some similarities with MLA style, there are specific requirements for scientific manuscripts that are determined by the choice of journal for submission.

Acceptable references are books and other peer-reviewed articles. You’re not allowed to get facts from random sites on the internet and other unreliable sources. Scientific literature is vetted by a peer-review process, in which other scientists evaluate the merit of submitted work. While it’s not perfect, this arduous process of evaluation and revision is science’s way of validating reports of experimental work. It means you can trust the information within peer-reviewed journal articles more than you can the random blog post or Wikipedia entry.

Specific formatting for references can be found in the instructions for authors. Some journals prefer using numbers in parentheses, some use superscripts, and some use an (author, year) formatting within the text of the manuscript. Reference lists are likewise variable according to journal- numbered lists, alphabetical lists, include titles, no titles, full journal names, abbreviated journal names etc. etc. In any case, the format will include enough basic information for a reader to look up the exact reference and check your facts. You have to follow the exact style for the journal of choice or the editor in charge of looking over new manuscript submissions will notice and kick your manuscript back to you- not reviewed, not accepted, not any further beyond your lab notebook than your computer files.

Citation management software should be your new best friend. Chances are the previous written assignments you’ve had haven’t required dozens of citations backing up various facts in your manuscript. You also probably worked on all of your previous manuscripts from start to finish in the order in which they will appear. As stated in my previous tutorial, you generally work on the sections of your scientific manuscript in a very different order than the one in which it will be finally assembled. Not to mention that working with multiple authors means merging sections from different writers and major rearrangements of written work. All of these complications mean that it is futile to try to manually keep track of all of the references that go along with these edits.This is a waste of your time and will lead to errors. Use citation management software. Citation management software like EndNote allows you to search for literature, manage all relevant information for a citation and integrate it into your handy text editing software (MS Word) in a way that lets you point-and-click which references to incorporate. This software will re-order citations in the reference list as sections are rearranged. The citation management software also already knows the exact details of each journal’s citation style. Simply select the appropriate journal option in the citation management software and EndNote will keep track of journal abbreviations, what should be italicized, what things are separated by commas and where periods should go. And if you decide to switch the journal for submission, all you have to do is click a different button and at least the reference section is done. Using citation management software ensures that no random numbers in parentheses are forgotten in the middle of your text.

Here’s a brief tutorial for using EndNote.

The EndNote software allows you to create a library of citations that can be used in your writing projects. There are two general strategies for EndNote library usage. (1) A single EndNote library containing every citation you will ever use. (2) Multiple EndNote libraries with one for each writing project. Each has its own merits and drawbacks. I know people that use both successfully, so if you feel strongly one way or the other, go with the one that seems most intuitive to you.

Citations can be added to your EndNote reference library by using the on-line search function. The most useful searches for scientific manuscripts are the PubMed (NLM) and Web of Science (ISI) searches. If you enter an author, publication year, journal name and some relevant keyword, EndNote should easily identify the necessary reference, which can then be saved in your library. It should be noted that I find this search feature useful for finding specific references (like those you’ve already read and know you want to use) rather than a general search to keep up with the literature (then again, I’m a type 2 EndNote user).

Reference entries can be added manually to an EndNote library also. If the paper is ancient or otherwise impossible to find with the search tools, you can manually type in all of the fields.

Duplicate entries within a library can be identified and eliminated. This should be done or it can cause problems when trying to use these entries while writing in MS Word.

The EndNote program also integrates itself as an add-on feature in MS Word. Once installed, it will have its own tab in the top toolbar. While working on a manuscript in MS Word, open the EndNote program and the appropriate library. From the EndNote tab in MS Word, all you have to do is click the ‘Insert Citation’ button to select the appropriate reference from the library. Note, the reference must be a part of the library at this point (already captured from an on-line search) because you can’t do an on-line search via EndNote from MS Word. Once selected, a reference placeholder will appear in the text (whether (#) or (author, date)) and a reference list will be started at the end of the text portion of your MS Word file. All of the details are determined by the designated style, given in terms of the journal title, which can also be changed from a drop-down style menu in the EndNote tab in MS Word.

Finer points of citation formatting with EndNote…

You can make some changes to the style if it’s not exactly correct based on the most up to date info on the journal’s website.

If you are citing multiple references at the end of a particular sentence, you can reorder them according to the stipulations of the journal style (usually in chronological order, oldest to most recent).

An EndNote library can be exported from an MS Word file. So, if you get a written portion from another author, you can recreate their EndNote library of citations even if they didn’t send you their library file.

A note on plagiarism: Don’t do it. Just because you are citing a reference in order to substantiate a statement in your manuscript doesn’t mean that you can copy their exact words. Use your own words and incorporate their work as it relates to yours. Don’t sweat whether minor wording changes are enough. Since you are building on these previous facts, the context will be different than the original paper, but there’s no excuse for copying things word for word. Sure, there are limited numbers of ways of saying any given truth clearly and concisely, but you can find a way of stating a necessary fact in your own words. Plus, you should really understand the previous literature well enough to restate necessary information in the context of your research manuscript without stealing someone else’s words.

Share your reference, citation and EndNote pro-tips in the comments section below.

Johnna

Clear and Concise: General Suggestions for Manuscript Preparation

Today’s post is the first tutorial on some general good practices of scientific writing and manuscript preparation. Many of the suggestions are based on common errors I’ve seen so far in very rough drafts from my students. If you have other suggestions, please offer them in the comments section. This is part of a series of posts compiled on the page A Beginner’s Guide to Writing Scientific Manuscripts.

Congratulations, you have some research to report to the rest of the world. No one knows it better than you, and it’s your job to educate the rest of us. The whole point is to clearly convey what you did, what it means and why it’s important.

It may seem overwhelming where to begin, but the specifics of sections and formatting have largely been decided for you depending on the journal you have chosen* for your manuscript submission. Each scientific journal provides detailed ‘instructions to authors’ on their websites. It includes everything you need to know about putting your manuscript document(s) together- section headings, font and size, citation formatting and figure guidelines. Some even provide a useful template document for MS Word. It is imperative that you follow these guidelines explicitly (yes, all of them. yes, exactly) or your research manuscript will be bounced back to you by the editor without review until you make it conform to their requirements. If you have any questions about how your document should look, download an article from that journal and/or have a look at an available pre-publication accepted manuscript version; each readily available at the website for that journal.

Outside of the requirements of the journal, it’s up to your good practice and judgment to put together a written document that clearly conveys your research. There are typically character or page limitations so it is important to be concise. State your thoughts in the most direct and clear way. This style may not win you a Pulitzer prize, but your audience is reading for information content, not necessarily pleasure. Verbose descriptions or filler sentences that don’t really say much can be a frustrating waste of time for the reader.  At the other end of the spectrum, it shouldn’t be so terse as to be incomprehensible due to missing information or no connection with anything of greater significance. (It should be noted that your manuscript’s first readers will be an editor and reviewers that will decide whether your research ever sees the light of day beyond your lab notebook and documents on your computer. So, yeah, at the very least- it shouldn’t be difficult or frustrating to read.)

Another good piece of general advice is ‘be consistent.’ Consistency- in terms of abbreviation usage and nomenclature in the text and presentation in the figures. If you refer to an organism one way in one paragraph, it should be same in subsequent paragraphs, unless you are talking about a different organism. While synonyms can be useful to break up the monotony, for important things like technique names and critical variables, refer to them in the exact same way or the reader may think you’re talking about something else. It is also useful to consistently order/label samples in your figures. If untreated sample is a solid black line and treated sample is a dashed line in Panel A, then don’t switch them for Panel B. This consistency should propagate across figures as well. If wild type is to the left of the mutant in images or lanes on a gel for a figure, then don’t switch the orientation in subsequent figures.

Abbreviations- you should use them. For any uncommon and long gene/protein names or techniques names, use an abbreviation. Write out the full-length version of the name or technique at its first usage and follow it by the abbreviation in parentheses. Then, just use that abbreviation in the rest of the manuscript. The general rule is, if you’ll need to use cumbersome wording 3 times or more, use an abbreviation. There are a number of very commonly used abbreviations within a scientific field that are widely understood and do not need definitions (ex: DNA, RNA, ATP etc) and these are generally listed somewhere on the website for each journal. Manuscripts also have an abbreviations section somewhere at the very beginning or end where all abbreviations are defined in one place. If the reader missed the definition in the text, they can refer to the abbreviations section. Abbreviations should be used consistently and exactly as defined. (Ex: Photosystem II = PS II; not sometimes PSII or PsII etc).

Specific usage and nomenclature- organisms, genes, proteins. This nomenclature often gets mixed in biochemistry literature. The full proper names of any organisms should be given the first time they are mentioned with the genus name capitalized and italicized and the species name lowercase and italicized. (Ex: Drosophila melanogaster, Zea mays, Arabidopsis thaliana) Then, if you plan on referring to this organism other places throughout the manuscript, designate the shortened version in parentheses after the first usage. (Ex: …. Drosophila melanogaster (subsequently Drosophila)….) Just make sure you use exactly that shortened designation consistently throughout the rest of the manuscript because any deviation from that usage will make the reader wonder if you are referring to another species. The specific shortened designations can vary widely, some people just stick with Genus others G. species and for some reason some organisms are so commonly known by their genus name that it has become acceptable to write Genus (nonitalicized) like Arabidopsis. There are strict conventions for the proper designations of gene or protein names/abbreviations. In a more genetics/cell biology manuscript, the rules are stricter**, but in more biochemically-focus papers, we’re not such sticklers. That being said, again, consistency is key and it should be clear whether you are talking about a protein or a gene. Typically genes are italicized (Ex: adh, Adh, ADH) and proteins are nonitalicized and at least the first letter is capitalized (Ex: Adh, ADH).

Scientific writing is generally written in third person format without any personal pronouns. It may take some getting used to this style, but eventually you will find ways of writing methods and results without any mention of yourself. (Ex: The colonies were screened using PCR. vs. We isolated DNA and did PCR.) Also, the Methods and Results are typically written in past tense because you are reporting observations that were made before you started writing the manuscript. The Introduction and Conclusion sections can be a mix of both, but be careful how you marry tenses. If you are writing a statement that is a known fact in the field or some conclusion you are now making from your data, write about these things as if they were always true and in the present tense. (Ex: ADH requires an NAD cofactor for activity.) However, if your wording choice mentions them as a previous finding, the past tense may also be appropriate. (Ex: Cheng and co-authors (#) showed that pyrazole was a competitive inhibitor of ADH.) Sometimes the use of personal pronouns is used in the conclusion section as a way of really owning a claim, but these instances are generally few and far between (Ex: From blah, blah, blah results, we conclude the following model…).

Repetition is necessary. It may seem like you are repeating yourself in various places throughout the manuscript. While absolute monotony is discouraged, repeating key assumptions, rationales or findings in the abstract, introduction, results and conclusions is useful for guiding the reader through your work. Remember, no one else knows the topic as well as you. So, someone reading your work for the first time may not make the necessary connections from rationale to conclusion, especially if those things are only mentioned once and separated by very many sections and experiments. You have to help the reader along or they will get frustrated or start coming to their own alternative conclusions. If this happens during the review process, it means more work for you- re-writing and usually additional experimentation. If it happens after publication, readers will still have doubts about your work.

In this course, you are given small tasks throughout the semester to guide you to the ultimate finished product. Generally, here is the order in which researchers typically work on sections of a manuscript (Note: this is completely different from the order in which they are presented in manuscript form to be submitted to a journal!).

  1. Figures, Tables and Legends: All of that data from your notebooks need to come together in some fashion to tell a story to support your new conclusions. The order of the figures in your manuscript will probably NOT be the order in which you actually did them. Data in figures are used to make the frame for the way you will present your work. I hope your notebook is complete enough to provide the necessary details to render the data into figures. Do you remember what sample was in lane three on that gel you ran 6 months ago? Probably not; hope you wrote it down or you will have to repeat it. If you do have to repeat it, I hope the samples for that gel are in appropriately labeled tubes in a box in the freezer. The figure legends should clearly state what the reader is looking at. Sometimes key details of the method are mentioned when appropriate for evaluating the data. Do not write any lengthy analysis of the results. At this point the researchers that will be authors on the paper will agree upon overall conclusions based on the data and how they will presented in the manuscript.
  2. Title and Author List: The figures should give you an idea of the story you need to tell, so come up with a descriptive, but concise title that captures all of it. Considering the data to be used, the analysis of the results and the writing to be done, authors and their relative ranks in the list according to contribution should be decided.
  3. Materials and Methods: It’s a good section to start with and transition yourself from experimental mode to writing mode. Since you’ve already decided on the figures you need to tell your research story, simply write about the methods you used to generate those figures. Scientific literature varies widely on the useful content within this section. While this section is not a complete protocol, it should give enough highlights of the techniques (and details critical for your experiments) for someone of reasonable ability to repeat your work.
  4. Results: Now that you are in writing-mode, explain all of your results, referring to the data in figures and tables as necessary. This section can be divided into relevant subsections to group findings as they support the various conclusions of your work. It is important to briefly state the purpose for each experiment and the experimental results. Very briefly, conclusions may be mentioned, especially as they lead into later experiments. If this is a pure results section, you won’t want to expound at length on the conclusions or models drawn from your data, but you should say briefly what they mean so it’s not a frustrating cliffhanger for the reader until the next section. Some journals have combined results/conclusions sections and, in that case, it is appropriate to discuss the meanings of your results.
  5. Conclusions: After you have written up all of your results with supporting data in your figures and tables, use this section to talk about what it all means. You may have briefly mentioned the significance of your findings in the results, but here is a chance to put it all together again. This will be the last thing you leave your readers with, so make sure your conclusions are clear and supported by your data. If multiple conclusions are possible, then you’ll have to split the difference and give a little bit of space to each possibility that your experiments haven’t differentiated. Now is the time to relate your conclusions to other published work (which you will cite), supporting or possibly contradictory, as well as offer a possible future direction or application of the research. If you are specifically working on additional experiments along this vein, then it is OK to mention this here or just speak more generally about what your conclusions mean for your field. Research will always keep moving forward; there will always be more experiments to be done, but at some point, you need to stop and write it up. It’s up to you to define the scope of your work. Reviewers may suggest other reasonable experiments, but you can often successfully argue against them if they are beyond the scope you have defined.
  6. Introduction: The background information on your research topic should be sufficient enough for a reasonable person to understand the scope and significance, but not an overly exhaustive review. In theory, it can be written in parallel with your Results and Conclusions sections. It should be complementary to your Results and Conclusions. While it should start with the bigger picture of a research area and its significance, it should ultimately hone in on the problem addressed specifically by your experiments. Usually, the end of the Introduction has a small paragraph describing the current work with respect to techniques and purpose, but not completely giving away the final conclusions. The Introduction and Conclusions sections may need to be edited for content simultaneously so they can most appropriately complement each other.
  7. References: Should be included throughout the writing process- Methods, Results, Conclusions and Introduction. They should include enough information for a read to find the citation and relate it to the claim you have supported in your writing.
  8. Abstract: Take the most important points of the entire work and fit them neatly into a single paragraph of 250 words or less. Your audience should be able to read the abstract and know the gist of what you’re interested in, what you did and the conclusions you made.

Johnna

*Deciding on a journal for submission is a tutorial topic unto itself. I’m avoiding this discussion at this point, since I’ve made the arbitrary decision for my students to prepare according to the Journal of Biological Chemistry.

**If anyone wants to list these rules in the comments section, please do. Gene names are generally italicized, but capitalization/lowercase varies in usage between prokaryotic and eukaryotic systems. As a biochemist, I try to focus on the protein so as not to have to worry about italicization at all.

Suggestions for Science Writing

In the biochemistry lab course I’m teaching, I’m trying to incorporate more scientific communication skills. The basic structure of this lab involves cloning a gene for recombinant protein expression, purifying the protein using affinity chromatography and analyzing the hell out of its kinetics with different substrates and inhibitors. This overall context gives the students insights into the larger scope of a research project instead of discrete, unconnected experiments for each class. It’s challenging enough to make sure the students understand the theory behind all of the techniques and learn some good lab practices along the way. This semester I’m including an extra challenge in terms of scientific writing. Their results will not be confined to their lab notebooks, but will be turned into a manuscript in the style of the Journal of Biological Chemistry.

As part of their lab notebook grade, the students must answer questions related to the experiment of the day. Many of these have been designed to get them to work on their manuscript in a piecemeal fashion throughout the semester (i.e. make this figure, write these methods, etc), so they get feedback from the TAs and myself on all sections before they are assembled into the final manuscript format. It may sound quite organized on paper, but I’ve definitely underestimated the amount of guidance novice authors need to produce quality work. So, I’m trying to come up with a better way of teaching all the things that I’ve learned informally about manuscript-writing over the last decade. I’ll be posting my various tutorials on this blog as a way to further crowdsource useful pro-tips and topics I may not have thought to address. I know many people may have strong opinions on this, so feel free to comment or offer other useful links in the comments section.

Here are the topics/posts/tutorials I’ve got in mind so far…

General Science Writing and Manuscript Preparation

Literature Searching and Reading

Citations and Reference Management

Figures and Figure Legends

Writing Materials and Methods

Writing the Results Section

Writing the Conclusions/Discussion Section

Writing the Introduction

Writing the Abstract

Peer Review and Revisions

My students are mostly seniors on the verge of graduating and moving on to medical and graduate schools or other employment in a health/science field. While they may not all go on to regularly prepare scientific manuscripts, at least they will have a greater appreciation of what it takes. As an exercise, they will get some experience with the process, but I’m not following all of the real life rules. If I did, then the first of my groups to submit would get an A, maybe the second group would get a C and the rest would just fail. And those graded groups would only earn their A or C after an exhausting revision process. For those students choosing to pursue a research career, they’ll learn those harder lessons eventually. As an educational bonus, I’m hoping that working on a manuscript from the side of an author will also allow them to be critical consumers of scientific literature. We should all expect high quality communication of research.

Johnna

References and Links:

https://ugr.ue.ucsc.edu/sites/default/files/jyi_guide_to_scientific_writing.pdf

http://www.studentgroups.ucla.edu/usj/The%20Ins%20and%20Outs%20of%20Scientific%20Manuscript.pdf

http://www.aaeditor.org/StepByStepGuide.pdf

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3626472/pdf/blt-11-217.pdf

The Instructor Chronicles: Semester 1, Part 2

We last left Superhero PhD and her troop of Superhero TAs in a morass of educational glitches

The semester had not gotten off to a smooth start. Surely this trend would change, but there was no data indicating otherwise. Then, there was a glimmer of hope. The powers that be in the department had pity on our hero’s plight and found a way to pay for a new ice machine in her teaching lab. Without hesitation, she calls the refrigeration company and orders a replacement. It is installed as the molecular biology segment of the semester is ending. Now that the traditional biochemistry experiments are set to begin, the students can be properly trained to be Fast. And. Cold. “Now, if only the hefty charge on the university-issued procurement card will clear without holding me personally liable,” thinks Superhero PhD.*

It was a great victory, but not a sign that the fortune was changing for our heroes. Meanwhile, back at the lair, a problem was waiting in Superhero PhD’s mailbox. Superhero PhD rarely checks her mailbox as it is never filled with anything of great importance, only local store ads and unwanted credit card offers. This week an official envelope is there summoning Superhero PhD to jury duty the week of midterms and that changing of the guard from Superhero TAs #1 and #2 to Superhero TAs #3 and #4. “Noooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo!” she yells shaking her fist at the sky frightening Junior PhD. Canis familiaris even howls along with her gut-wrenching cry. She composes herself as she remembers, “It’s a government agency. There’s always fine print. A way out.” She is in luck. She is within 24 hours of the deadline to fax over a postponement request to the clerk. She quickly pens the numerous specific reasons why the 19th Judicial District would have to wait until the semester break to conscript Superhero PhD into service. She calls a few hours after it has been faxed away. Success! The Clerk of Court has heard Superhero PhD’s pleas and had mercy. Her service is postponed until the semester break.

Superhero TA #4 was diligently preparing the experiments he would lead for the first time this semester, and something was terribly wrong. The first enzyme inhibition lab exercise is not matching the data in the TA Manual. There’s no inhibition. Superhero PhD invokes her first rule of biochemical troubleshooting, “Make everything fresh and repeat.” Superhero TA #4 also follows this rule with no success, and it is time to invoke the next rule, “Order new reagents, make everything fresh and repeat.” “It’s still not working.” reports Superhero TA #4. “Now it’s time to put out the ‘PhD Signal’.” Superhero PhD states. E-mails are sent to Retired Instructor and Recently-Graduated-Former-Superhero-TA detailing the problem and our futile attempts at troubleshooting. What critical step was being overlooked? Was this merely another revolt of the Teaching Lab to its new master? Over the next week, everyone tried their hand at the troublesome inhibition with no luck. A remarkably detailed e-mail outlining the experiment’s execution from Recently-Graduated-Former-Superhero-TA arrived in Superhero PhD’s inbox, but it did not illuminate any significant differences in our attempts. Late one afternoon, Superhero PhD enters the Teaching Lab only to find Retired Instructor herself performing the vexing inhibition assays. Alas, she is also unsuccessful. Inhibition could not be observed by anyone, with any reagents, nor any enzyme, nay even preparations previously showing inhibition. It is a defeat, but the lab must go on.

After midterms, the students realize that they should come to see Superhero PhD in her office. There she answers the lingering questions they had but did not ask during class. She illustrates biochemical concepts on the newly-hung white board. She calculates ways for them to improve their letter grades with the remaining graded activities. They seem to be calmed. Yet, Superhero PhD soon learns that the vast majority of students are poor project managers, relying on short bursts of intense cramming rather than steady attention to the course and its assignments. Much of their misery is of their own making. Superhero PhD also occasionally sends out e-mails with important information. It is clear that some of the students do not read them; they are unprepared for scheduling changes, oblivious to related content for exams and unaware of upcoming important dates. Superhero PhD is beginning to think that Moodle mail uses some unfortunate translation tool after she hits the ‘send’ button that rewords her carefully crafted e-mails into “Blah, blah, blah, important date, blah, blah, blah, exam info…” but she has no time to take this up with IT services.

On report due dates, Superhero PhD sighs, “Less than an hour before the listed deadline and still half of the students have yet to click the submit button, and five submitted in the last five minutes.” She muses this is not so different from real science and grant deadlines. A briefly evil thoughts cross her mind as to how to change the course to better prepare her students for a career in professional science. Of the reports submitted 10% would be sent back with no grade at all because of formatting issues, 80% would be reviewed favorably but still not receive a passing grade because of the few available to go around, and the final 10% would be both favorably graded and receive A’s. In the lab, exercises would be graded as follows: the first group to finish collecting data for the day and write it up in their notebook would receive an A (the equivalent of publishing findings first in a decent journal), second place would receive a C (because good 2nd place research could probably be dumped into some lower tier journal) and everyone else will fail. Of course, some of the later finishing groups could decide to hold onto their work, opting to file for a patent thereby subverting the advancement of the work of the 1st and 2nd place finishing groups in the future. These patent-holders would then get a guaranteed A for the course. Then Superhero PhD remembers, it’s only an undergraduate course, “They can figure out how science really works after they graduate.” Plus, this alternative system would surely negatively affect instructor evaluations at the end of the semester.

Troubles continue to plague the experiments entrusted to Superhero TAs #3 and #4. At the conclusion of the protein purification exercises, the students subject their purified enzyme to dialysis so that it will be in the most appropriate buffer for the subsequent enzymatic activity assays. This experiment takes a significant amount of time, so care must be taken to be cold. Unfortunately, the deli-cooler cold box in the lab used for this purpose died the day before Superhero PhD assumer her new role as Instructor because of course it did. Other departmental cold rooms were available, but these were less conveniently located and the buffer contained a foul-smelling reagent that would preferably be contained in a smaller space. Superhero TA #4 offers the cold box in his lab. Unbeknownst to him, the required stir plate had recently started malfunctioning such that when the necessary stirring function was initiated, so was the heating element. By the time the Superhero TAs retrieved the students’ precious enzyme samples, the solution was boiling. The first rule of biochemistry had been violated in horrific fashion. Superhero PhD and the Superhero TAs could only stare in shock at the dialysis bags containing the students’ boiled protein, looking like scrambled eggs and utterly ruined for future activity experiments. Superhero TA #3 offers, “There’s still a ton of enzyme from our previous preps and the other half of their precipitated sample for a different experiment. We could just divide that up among the groups for them to have.” “Let’s do it. They’ll never know and we won’t speak of this again,” says Superhero PhD. The lab goes on with the students none the wiser that an equipment glitch had ruined weeks-worth of their efforts. Superhero PhD also muses that this could be another opportunity for re-structuring the teaching lab to be more like real life science. When the experiment fails, go back to the beginning and repeat all of your work.

In a separate exercise, the students use a mutant enzyme to compare to the wild-type version they have meticulously purified and analyzed. This enzyme is prepared by the Superhero TAs and generally lasts for a few years before activity drops below a useful value. When Superhero TA #4 checks the activity of the purified mutant enzyme available in the freezer, it is insufficient because of course it is and by now this semester is just snake bit. Superhero PhD locates what should be the corresponding mutant DNA, but it is not useable. Attempts to locate other freezer stocks of the critical bacterial strain fail. Once again, Superhero PhD calls upon Retired Instructor, who has superior abilities at deciphering the glyphs on tubes in the bowels of the -80 freezer. A tube is found and Superhero PhD quickly determines it will express the necessary mutant protein. Superhero TA #4 isolates the enzyme and verifies that it behaves as expected. As Superhero PhD receives this news, the Hallelujah Chorus rings in the background and a bright light appears ahead- it is the light at the end of the semester. Everyone just might survive and manage to learn some biochemistry along the way.

Meanwhile in the laboratory, the students have finally entered the home stretch of their experiments- the doldrums of enzyme kinetics. It’s a greater than two week stint of exercises in which their hands must perform the same tedious assays with various reagents to understand the details of how their enzyme works. Even with the help of numerous others, Superhero TA #4 is unable to troubleshoot the problematic inhibition experiment. Superhero PhD decides to cut that experiment short and rely on data found within the Holy TA Manual for the students to analyze. It is within this series of experiments many students are reconsidering their choice of major.

The repetitious lull of kinetics assays on the spectrophotometer dulls their senses. They are less vigilant about manually recording their data in their notebooks. Inevitably, the unthinkable happens. After more than two hours of data collection, one group asks to be checked out to leave. “Do you have your data for the day? Make sure everyone in your group gets a copy of the Excel file you were working on.” says Superhero PhD. “Yes Ma’am.” they reply, but as they try to add the attachment, the file is nowhere to be found and the spectrophotometer files are woefully incomplete. They begin to panic, but Superhero PhD says, “That sucks if the computer ate your file, but you can re-enter your data from your notebook.” She is met with only blank stares and a rising sense of panic. “You did record all of your data by hand in the notebook you are keeping for the course? At least one of you did, right?” she asks. More uncomfortable silence. “Not one of the three of you wrote down any numbers today?” she asks rhetorically. “I will see if IT Services can possibly recover your file, but it appears that it has been improperly saved and no longer exists. Fortunately for you, this is the inhibition experiment for which we will be providing you with data, so you can use that. You’ve just wasted two hours of your life. If you continue to pursue a career is science, I doubt it will be your last. This is an important lesson in data management that you have learned in class instead of real life.” As it turns out, IT Services could not recover their data. There may be computer forensic scientists at the FBI that may have been able to recover the students’ file, but these methods are not routinely available to public universities. This instance has forced Dr. PhD to append the Rules of Biochemistry to include #6: Thou shalt manually record thy data. Always.

As the semester winds down, Superhero PhD can begin to think about the next semester. Some experiments will be adjusted. Also, Superhero TA #3 will transition full time into Dr. Postdoc, and at least on new TA, preferably with powers of chromatographic separation will be needed. Tenured PI’s Graduate Student is willing to take on the role, but Tenured PI is not in agreement with this decision. Graduate Student’s research is at a critical point and she won a student award that will allow her to give up her double life as a TA. Fortunately, Superhero TA #2 is able to recruit another graduate student from his lab to join the team. Superhero TA #1 will also be available for one more semester. It looks as if the team will be ready for the next semester. That is, of course, if Superhero TA #2’s visa renewal goes smoothly between semesters and he is able to travel back to the university as intended the day before classes start. “Only if my luck changes significantly,” thinks Superhero PhD. She does not underestimate the bureaucracy involved in coordinating paperwork between two sovereign nations over the holiday season. So, she writes a polite but persuasive letter addressed to the Visa Officer requesting expeditious resolution of this matter.

The battle of Semester 1 is over. All students, Superhero TAs and Superhero PhD have survived… barely. “Take that Chaos and Ignorance,” muses Superhero PhD as she indulges in the fine chocolate cookies stashed in her office.** More biochemistry majors have been indoctrinated in the practice of good laboratory techniques. The mysteries of the pKa, molecular biology and Michaelis-Menten enzyme kinetics have been unraveled for a new generation. Off they will go to Medical School, Graduate School and The Job Market empowered with this new biochemical knowledge. Superhero PhD has taught them the most important thing about biochemical research,

“It is tedious and awful both at the bench and digging through primary literature, but if you’re paying attention and you persevere, you can synthesize prior knowledge and new results into a better future.”

Stay tuned next time for new and exciting adventures in the Instructor Chronicles: A New Hope Springs. Will the new Superhero TA exhibit chromatographic supremacy? Will they ever get that one inhibition experiment to work again? Will they find a replacement for that debacle of a gel filtration lab? Will Superhero TA #1 get his visa renewal in time to return for the Spring semester? What new obstacles await our team? But before any of these questions can be answered, stay tuned for Superhero PhD: Call of Civic Duty as she serves her mandatory jury duty.

Johnna

*It did.

**A 2nd place prize for her ugly Christmas sweater-wear at the Departmental Holiday Party.

The Instructor Chronicles: Semester 1, Part 1

We last left Superhero PhD leaving the funeral of her research career for a new adventure in biochemistry laboratory instruction…

The course she was entrusted with has a really great structure- starting from cloning a gene to expressing a protein to enzymology and protein crystallization. There was just precious little time between Superhero PhD’s start date and the first day of class. She just really needed an electronic version of the manual to get it churned out for the students or instead of alcohol dehydrogenase, biochemistry majors would be working on Photosystem II* (Dr. PhD’s forte). Fortunately, Retired Instructor was willing to be incredibly helpful, she had just been out of town visiting grandchildren. There was no time for significant edits, but it was much better than the other nightmarish scenarios that flashed through Superhero PhD’s brain.

With the lab manual in hand, Superhero PhD felt confident in her prospects for successfully completing the semester’s lab exercises. There was only one thing standing in her way, the thing that stands in the way on anyone that’s ever walked into a new lab- finding out where the hell everything is. The room was lined with benches containing identical equipment, tons of cabinets filled with God knows what, and freezers and refrigerators possessing an uncalled-for amount of previous years’ samples.** If only X-ray vision were one of Superhero PhD’s superpowers! Alas, she had to rely on the lesser power she did possess- painstakingly opening each cabinet and drawer, taking an inventory and labeling the contents on lab tape.

Of course, Superhero PhD was not alone in this new quest. The class came with 4 Superhero TAs with tons of experience running the lab exercises. Thankfully, they knew the location of everything Superhero PhD couldn’t find. However, there was one major concern held among all the TAs. The great secret to their power resided in a trilogy of binders they reverently called the ‘TA Manuals.’*** These holy books were nowhere to be found since the teaching lab had been vacated by Retired Instructor. “By the power invested in me by the search committee, I swear I shall deliver these holy texts to you by the start of class.” promised Superhero PhD. So she embarked on a crusade to acquire the TA manuals. It turned out that another e-mail to Retired Instructor specifically requesting them and coordinating delivery of the precious relics between Retired Instructor’s visits to her grandchildren was all that was required. With that, the Superhero TAs set about prepping for the semester’s labs.

The first day of class started with a strange omen. As Superhero PhD was driving on campus to her usual parking spot, she nearly hit two cyclists that thought it was appropriate to blow through a 4 way stop as if they were not vehicles. It was a sign of other obstacles to come. All seemed to be well with the TAs until Dr. PhD’s second day on the job when Superhero TA #3 mentioned he was trying to graduate and had, in fact, found a local postdoc job starting immediately. Superhero PhD isn’t one to begrudge anyone with a PhD finding gainful employment, but on the inside she felt like this. On the outside, her panic was probably only a brief eye-twitch. The next day, while she was still thinking of the lies she would have to tell to recruit another TA on such short notice, a miracle of miracles happened. Since Superhero TA #3 had not yet defended, he still qualified to be a TA and his new employer was willing to accommodate his schedule such that he could be both a Superhero TA and a Dr. Postdoc simultaneously. At this news, Superhero PhD smiled and began breathing again. “Now, we are really ready for the semester,” she thought naively.

As part of her new role in the Department, Dr. PhD actually got her own office. The space was glorious by postdoc standards- 4 walls, a small window with a view of the stadium, and a door. Even when she first laid eyes on it, filled as it was with file cabinets that seemed to be holding up the walls, flood damage along the exterior wall, and ductwork to who knows where in the corner. Her eyes welled up with tears and not solely due to the decades’ worth of dust that had accumulated. Nothing comes without a price of some kind and this room came with a whole other to-do list to manage: painting, sheet-rocking, cleaning, a computer, a printer, a phone, a phone number, a key, transferring all those file cabinets to surplus property. Each job meant a separate person handling it.

The office was not move-in ready on the first day of class, but it didn’t take too long before 90% of things were in place. Surplus furniture was moved into the hallway. A better desk chair was inherited from the Departmental Office. The whiteboard was not re-hung, but Superhero PhD owns a drill and a Home Depot card, so no big deal. Someone else a Facility Services even fixed the interior side of the door knob (Superhero PhD had some concerns that she would accidentally become trapped inside when it fell off). Surely at any moment, her new students would come pouring in for office hours seeking biochemical laboratory guidance. Alas, the only person to visit her office in the first month was Tenured PI.

As the semester began, chaos ensued. Superhero PhD received a minor in Chaos Management at the Evening Academy of My Family Circus, so most of the instances about to be described in no way affected the learning environment for the students, but nevertheless took years off of Superhero PhD’s life.

Critical reagents needed to be ordered for the lab, reagents with a hefty price tag for special expedited handling. In one case, the shipping company failed to deliver the package on time and in another, the reagent was backordered indefinitely. Superhero PhD managed to get a refund of the shipping charges for the late package and Superhero TA #3 suggested doing away with the backordered reagent entirely for the other experiment.

The teaching lab uses an ancient glass still to produce the dH2O necessary for experiments. It is a finicky contraption whose secrets were relayed to Superhero PhD by Retired Instructor. The plumbing connections are not to be trusted. Sure enough, the first day Superhero PhD started it running, the tubing for the cooling water jacket source blew off as she dropped off her laptop in her office. It was a mess, but luckily no damage was done to any equipment or labs on lower floors. Dr. PhD did not even enlist the help of janitorial staff.

On the first lab exercise doing molecular biology work, Superhero TA #1 opened the ice machine to find it empty. This ice machine that had worked perfectly for all prep work until then was now broken. Again, if only Superhero PhD had more traditional superpowers like Elsa’s freezing powers she and Superhero TA #1 and #2 would not have had to cart ice from the common equipment room for every class thereafter. Perhaps it was just a maintenance error light. Superhero PhD’s power of randomly pressing buttons failed to resurrect the ice machine. The refrigeration serviceman was contracted to revive the ice machine. It was not in need of routine maintenance. It needed a completely new motor and a new unit was the most cost effective way of doing that.

Another experiment was giving us more trouble than it should have. The second transformation by electroporation to generate the expression cell line was not working. After re-making reagents and new competent cells, it turned out to be the electroporator. Luckily again, the lab had another fully functional back-up instrument.

Now that Superhero PhD’s schedule was more inflexible due to class schedules, all manner of personal emergencies seemed to occur. In her spare time, Dr. PhD’s life involves a lot of child-, pet-, and elder-care. And honestly, for someone who’s not-that-kind-of-doctor, she still ends up dealing with more bodily fluids than one can imagine. Nevertheless, quick texting allowed her to communicate with other caregivers and coordinate emergency room situations from the classroom. If only the superpower of being in two places at once was something Superhero PhD possessed, she’d have tenure a Nobel Prize by now. Since she does not possess this power, she is just ecstatic to have made it through so far without having to pay per minute overage charges for Junior PhD’s after care.

At some point Superhero PhD decided that her office was in fact stable enough without half a dozen file cabinets crammed in it. There was no way she wanted another piece of furniture in it and it was time to rid the hallway of the extras. The proper forms had to be filled out detailing the property inventory numbers for each. One perk of Superhero PhD’s new position is a handful of undergraduate minions to help with support tasks. With the forms filled out and sent away to the appropriate university office, the months-long wait for retrieval began. Upon inspection of the copies of the forms, Superhero PhD notices that her undergraduate minion was a little overzealous in listing items- not all of the furniture in the hallway was her surplus. Neighboring lab had a nice lunch table and other cabinet in the hallway for their convenience. Superhero PhD was their neighbor for less than a month and she’s already giving away their property. “I’ll just have to be on the lookout for Facility Services again.” she thinks. The next day there is a crash outside her office, the sound of metal being unceremoniously moved about. “They’re here already?!?” she thinks. She walks into the hallway to explain the mistake on the paperwork. Speaking quickly to the man in the hallway, he appears to listen briefly before signing that he is deaf. Finally, a situation appears for which Superhero PhD can summon one of her lesser-used powers- a basic understanding and use of ASL. She manages to point to the paper and the misidentified furniture and sign, “Wrong. Must Stay. Thank You.” It worked! “Now that the hallway is clear, my students will surely come to my office hours,” she thinks to herself.

Just when Superhero PhD thinks all office-related work has been completed, other workmen from Facility Services show up to replace a 6 ft stretch of plastic baseboard along the back wall where sheet rock had been replaced. Every little bit helps. While they are there, they notice that no one has re-hung Superhero PhD’s white board. They just so happen to have the appropriate clips and bolts in the truck and hang it up for her. “This will really come in handy when I have to explain biochemistry to my students during office hours,” thinks Superhero PhD.

In some ways, research labs can be like the Mafia- they never really let you leave The Family. Superhero PhD still attends the lab meetings of Tenured PI to keep tabs on the research projects she left behind, offer insightful experimental suggestions and tell others in the lab where to find things. One week both Tenured PI and Lab Manager will be absent and Superhero PhD is called upon to preside over lab meeting. Experiments are reported without much incident. Superhero PhD and the Research Team retire back to the lab. Just as she is leaving, Superhero PhD hears the one sound that strikes fear into every researcher- the piercing cry of the high temperature alarm of the -80 F freezer. Graduate Student says, “By the way, this alarm was going off before lab meeting, but it doesn’t seem to be getting better after being shut for another hour.” Superhero PhD can sense the precious biochemical samples thawing and decades of freezer stocks becoming perilously warm. There’s no way Tenured PI or Lab Manager will be around to handle this. Superhero PhD and the Research Team**** spring into action securing additional freezer space in other departmental labs’ freezers. All samples are safely stored in time. Scientific crisis averted.

Stay tuned for the next installment of Superhero PhD’s inaugural semester in the Instructor Chronicles. How can she be Fast. And. Cold. without a functional ice machine? What will become of Tenured PI’s freezer? Will students ever come to her office hours? Is anybody really learning anything about biochemistry? What new slings and arrows of outrageous fortune await Superhero PhD and her TAs for the remainder of the semester? All of these questions will be answered in the next episode of the Instructor Chronicles.

Johnna

*Working with a large membrane protein complex whose substrates are water and light definitely qualifies as the deep end of the biochemistry techniques pool, so it’s probably not the best place to start.

**They took Rule #2 to the extreme, even for molecular biology samples and cultures that could never hope to be resurrected.

***The TAs were awesome apart from the TA Manual, but it contains all manner of useful information for managing the course that makes their lives a lot easier.

****Collectively, the new name for the group is the Chlorophyll-a Team. Homage to @AmeliaRWright who came up with that gem for #ScienceAMovieTitle. When I have spare time, I’ll write a spin-off with this title.