For anyone who has hesitated to teach evolution, closes down at the idea of drift, or uses the term "% homology," Jim Smith and I wrote this review to help clear up common confusions and make evo life a bit easier.
The Perspective, published this month in ASM's education journal, discusses why evolution is so critical -- but still underused and misunderstood -- in the biomolecular sciences. We share our vision for how to teach and think evolutionarily, and we review a slew of published studies and resources for doing so.
I'm pretty excited about this "Side Project" especially Table 1, which I see as a handy guide to speaking the Language of Evolution, equally useful for research as for teaching.
We hear more about antimicrobial resistant infections every year. Where are these pathogens coming from? In a new article published in Evolution, Medicine, and Public Health, I explain the role of horizontal gene transfer in the evolution of antibiotic resistance. Check it out it at: Burmeister, A. 2015 Horizontal Gene Transfer. EMPH doi: 10.1093/emph/eov018.
I just came from a productive and fun lab meeting that involved everything from celebrating a labmate's research highlight, learning about python config files, talking about parallel evolution, eating pita chips, and hearing a fascinating story about how metapopulation sequencing was used to solve the 2001 anthrax mystery.
But aside from the pita chips, lab meetings vary from week to week and lab to lab. I have a small sample size, -- and this Ph.D. Comic is part of that sample -- so I made a poll (choose up to 3):
My objective for this post is to address the presenter's block voice that cries out "Nothing to present!" and seems to happen to many grad students in the week leading up to lab meetings and other informal presentations. (At MSU, these include BEACON, MMG's GSW, and the "Bad Bug Club.") I hope these ideas will encourage optimism and confidence, which make us better scientists and help us feel better as people.
I like Dynamic Ecology’s list of lab meeting ideas, especially popcorn meetings, ethics, elevator pitches, non-academic careers, the publishing process, and classic papers. I also like round tables and in-depth research discussions. For cultivating lab culture -- no, not E. coli -- during lab meetings, this short guide from Lena Ting has useful tips.
Here are topics that I think work well when one person is in charge of presenting or leading a discussion:
New literature: Presenting a paper is a great way to get some presentation practice, try out assertion-evidence slide design, and/or to begin thinking about a new research area. I’ve seen this method used in at least one journal club, a lab group I’ve been part of, and two of my ecology courses.
Paper/proposal drafts: I like the idea of sharing progress on written work, but I don't think that group reading sessions are the most efficient way to communicate. Instead, I suggest turning a written proposal into an oral presentation, using figures of previously published work, diagrams of experiments, hypothetical results, etc. For manuscripts, consider making a conceptual diagram or graphical abstract that summarizes your findings.
Everyday results: These include what’s working and what isn’t working. They include protocol development, preliminary results, surprising observations, and many other things. Even if I haven’t stepped in lab yet, I may have new insights from a BLAST search or genome alignment. Some of my projects have started with simple observations, like some phage genotypes decaying faster than others during stock storage. I may or may not have an interpretation for these types of observations yet, nor a clear idea of how they might turn into an avenue of research, but I can usually come up with a couple of concrete ideas to start a discussion. Also, scientists (your labmates) like weird results and puzzles.
Experimental design: There are times I wish I had sat down for 30 minutes to plan out my approach for lab work or computing and then run my plan by my lab group. Best-case scenario: the plan is sound and the lab agrees. Another great scenario: There are ways the plan could be better, and the lab catches them before I waste a lot of time.
Practice talks: My first practice talk was to be my first committee meeting presentation. The practice round didn’t go well, mostly because I didn’t realize that the presentation should be a well-organized narrative, not just bits and pieces of data and ideas. But, I took the feedback from my lab and flipped the presentation, resulting in a happy committee and my P.I. noting that I did a great job during the quick revision process.
Practice (parts of) talks: I also think it’s great to begin practicing parts of talks – for example, by preparing two or three intro slides for whatever bits of research-in-progress data you might have.
Side projects and course projects: Research is research, whether it's a main dish, side, or snack. My program has several courses that involve independent research projects. In one, I reanalyzed data from a previous publication from the lab. In another, I made an analytical model of host-parasite interactions. When I'm unsure whether or how these types of projects could be further developed and published, I consider them good candidate topics for lab meeting.
Computation demo: Labmates have shared demos of useful tools, including Github and software developed internally. I think this works well for tools in development, as it's an easy way to get feedback on features, priorities, tips on how to code something, and volunteers to help review. That lab meeting I mentioned at the top of this post was one of these.
Research results: If the above practices work and we do ours, eventually we end up with results. These likely include the final outcome of a well-developed protocol with a well-planned experiment. Even at this point, there’s work to do. Maybe the results could be represented in different graphical form, interpreted in another way, or put in the context of the literature -- that’s where your labmates are again useful.
Overall, I think it’s probably pretty rare when we have absolutely nothing to present, or that we have nothing interesting we could come up with to turn into an informal oral presentation. I suggest envisioning what you see as a successful lab meeting, trying not to worry about whether X, Y, and Z are enough or whether you'll be able to fill 90 minutes (or whatever amount of time your meetings usually run). In my experience, less can be more, except in the case of pita chips.
While preparing for my department's Hsiung-Kimball award seminar, I learned a lot about the award’s two namesake scientists. Inspired by their stories, I share them here.
Dr. Gueh-Djen (Edith) Hsiung (1918-2006) and Dr. Margaret Everett Kimball (1924-2011) attended Michigan State University together in the late 1940s. The Hsiung-Kimball award was endowed by Hsiung, who named the it for Kimball and her family. The two women were friends and roommates during their time at State, ~1947-1951, and their careers highlight biology’s 20th century triumph over infectious disease.
I found Dr. Hsiung's obituary from Yale, where she spent most of her career on the faculty as a virologist and professor of laboratory medicine. As far as obituaries go, it’s the most lively and inspiring one I’ve read. Here's an excerpt with one of my favorite stories about Dr. Hsiung, a vaccine, and a goat:
“Gueh-Djen (Edith) Hsiung, an internationally recognized virologist and professor emeritus of laboratory medicine, died of cancer on Aug. 20 at Connecticut Hospice in Branford. She was 87.
I had only 10 minutes for my awards seminar, but I took a minute to share the great goat story and highlight Dr. Hsiung's career. After all, she graduated with Ph.D. in microbiology, from MSU (the degree I'm seeking) in 1951, which was the year Ester Lederberg discovered virus phage Lambda (my Ph.D. study organism) at the University of Wisconsin-Madison (where I earned my undergrad degree), making the award especially meaningful to me. And, the audience loved the goat.
The other half of the award’s namesake is Dr. Kimball, who graduated from MSU in 1949 with a Doctorate of Veterinary Medicine. She went on to test cattle for tuberculosis across the state of Michigan, practice veterinary medicine, and work as a meat processing plant inspector. She also made it to all 50 states! The MMG website says that “Dr. Kimball's family hosted Dr. Hsiung during her graduate career, and the two became close friends,” and Dr. Kimball’s obituary specifically mentions a trip to China with Dr. Hsiung, so it seems the friendship was a long and meaningful one.
I’d love more details about Hsiung and Kimball’s friendship, perhaps because as I’m mid-grad school myself and have a hunch that grad school friendships are much the same now as they were 70 years ago. I would guess that then, as now, the academic environment forges lifelong friendships. Did these women talk about their research and emerging diseases over drinks? Did they review one another’s manuscripts? Did they go on autumn walks through the Baker woodlot? Did they celebrate with dinners out when they had a success?
Maybe friends or family of Dr. Hsiung and Dr. Kimball will have stories or pictures to share. As I write my thank-you letter simply to “whom it may concern,” I would guess that some of those people include Dr. Hsiung’s nieces and nephews and their children, as well as Dr. Kimball’s children and their children. To all of you: your aunt and mother were two cool women I look up to and gain inspiration of as I walk across Michigan State’s campus today. Thank you for the award named in their honor!
Arrowsmith: The Classic Microbiologist Hero
Arrowsmith (Sinclair Lewis, 1925) tells the story of an academic microbiologist and his research in early 20th-century middle America. The tale contains one of my favorite passages of academic fiction, encompassing math, imposter syndrome, late nights, and friendship all against a backdrop of phage research. I thought of this passage often as I relearned calculus in graduate school, coded differential equations into Mathematica, and read phage modeling papers. In the story (excerpt abridged below), Max Gottlieb is the senior scientist (think PI), Martin Arrowsmith is the new scientist (think grad student/postdoc/associate professor), and Terry Wickett is the guy working down the hall.
I share these quotes here for educational use, mostly to encourage those of us going through similar challenges. Behold the new scientist grappling with math and imposter syndrome while trying to invent phage therapy and making a friend along the way...
Gottlieb observed, “Martin, I haf taken the privilege of talking you over with Terry, and we concluded that you haf done well enough now so it is time you stop puttering and go to work.”
How The U.S. Naturalization Test Fails Itself: A Perspective From An Education Assessment point of View
Arizona just became the first state to adopt the U.S. Naturalization Civics test for high school completion, and other states are quickly following. Here's why the test fails.
Before deciding my opinion (as a U.S. citizen and Michigan resident) whether this test should be required here, I assessed the test itself. The test has two major flaws: 1) The test has confusing instructions with often arbitrary answers; 2) the test is subjective, leaving test-takers vulnerable to discrimination.
Instructions for the test are confusing and result in arbitrarily incorrect answers. The test prompts: “As you study for the test, make sure that you know the most current answers to these questions. Answer these questions with the name of the official who is serving at the time of your eligibility interview with USCIS.” For example, an acceptable answer to “What is the name of the Vice President of the United States now?” (Q.29) includes Joe Biden, the current Vice President. But other questions do not follow the format. “If the President can no longer serve, who becomes President?” (Q.30) Here, the correct answer listed is NOT “the name of the official who is serving at the time,” but instead lists the more general form “the Vice President.” Another example with the current Vice President question (Q.29) is that “Joe Biden” and ”Joseph R. Biden, Jr.” are acceptable answers, but “Joe R. Biden” is not an acceptable answer. This type of nuance happens repeatedly throughout the test.
Those conflicting instructions and confusing answers are alarming because the test is administered by a person, orally, which opens the door to discrimination. The instructions state, “The civics test is an oral test … The USCIS Officer will not accept an incorrect answer. Although USCIS is aware that there may be additional correct answers to the 100 civics questions, applicants are encouraged to respond to the civics questions using the answers provided below.” For the vice president question, would “Joe R. Biden” be accepted? This is unclear; the judgement of correctness is subjective, decided by the test-administering officer. That leaves test-takers at the mercy of the test administrators, opening the door for implicit bias and discrimination to decide who ultimately passes.
How would I do on the test? I used a program to randomly generate 10 numbers between 1 and 100 and gave myself the test. Try it yourself. I would have passed if I could be sure that Q.2 (“What does the Constitution do?”) would accept “established powers of the federal government.” To be fair, if I needed to take the test officially, I would study beforehand. But even then, if I were assigned an officer who was in a bad mood today, or if that officer just didn’t like my look, name, accent, makeup, clothes, or tone of voice, I would not be assured a fair shot.
The Bigger Picture
Besides these social issues, a more general complaint from an educational assessment point of view is that the test assesses rote memorization of simple facts, not more general concepts and critical thinking which are more important for citizenship. I’d rather someone be able to write a letter to the editor of a newspaper stating their opinion on federal rights pertaining to marriage than recite the number of voting members in the House of Representatives (Q.21) or list the current Supreme Court Chief justice (Q.40).
Before deciding whether to adopt the test as part of high school completion requirements, the test needs to do its homework, including open commentary and review by assessment experts, similar to how other education initiatives (Common Core, NGSS) are organized. Sorry, U.S. Naturalization Test, you failed this one.
For more, check out the official test. Some of my minor complaints:
Should all biology classes include evolution? Lately I have been thinking about "evolution across the curriculum," the initiative promoting evolution as a core concept of biology that should exist in class of every subdiscipline -- from ecology to microbiology to physiology and biochemistry (Wei, Beardsley, & Labov, 2012). Working on a project to move evolutionary thinking into a microbial genetics course here at MSU, I am learning that transplanting concepts from one field into another is not so simple. In this post, I discuss how language can impede learning when terms have multiple definitions and non-scientific meaning for students.
Mead and Scott (Mead & Scott, 2010a) discuss how evolutionary biology language use differs between students and scientists, specifically discussing the ambiguous meanings of terms “design” and “purpose.” Language ambiguity is problematic when words have more than one meaning (Rector, Nehm, & Pearl, 2012). For example, the word “purpose” in a biological sense often refers to a structure’s function, but non-experts may associate “purpose” with non-scientific existential meaning. Without explicitly discussing the meaning of “purpose” in a given context, use of the word could inadvertently lead to student confusion about the content. Mead and Scott suggest one way to avoid confusion is for teacher's to use alternative words that don't have teleological connotations. For example, a teacher might substitute in "function" where "purpose" was previously used. Mead and Scott give an example:
How can I stay clear of potential teleological thinking in microbiology? One way is to focus on structure-function reasoning, similar to the aardvark example above. Rather than asking a vague “why” question, I could ask "What structures and functions are involved with the E. coli colony color turning blue?" I could then explicitly contrast methodological practices with natural phenomena by following with, "In this experimental setup, the E. coli are blue. Are they blue in nature? Would this trait be adaptive in nature?" Finally, I could explicitly disambiguate the "design" we do as human researchers from the adaptive emergence of functions produced by evolution by natural selection.
The classroom is not the only place facing confusion due to language ambiguity. I commonly find this problem in non-evolutionary biology writing and discourse, such as in microbiology seminars and biomedical literature. Here's an example from the CDC (Antibiotic Resistance Questions & Answers, 2013)
What do you think? Where is there room to incorporate evolutionary thinking across the curricula? How do different biology disciplines have unique challenges when it comes to making those changes?
Antibiotic Resistance Questions & Answers. (2013). Antibiotic Resistance Questions & Answers. Center for Disease Control. Retrieved June 1, 2014, from http://www.cdc.gov/getsmart/antibiotic-use/antibiotic-resistance-faqs.html#why-bacteria-resist
Mead, L. S., & Scott, E. C. (2010a). Problem Concepts in Evolution Part I: Purpose and Design. Evolution: Education and Outreach, 3(1), 78–81. doi:10.1007/s12052-010-0210-8
Mead, L. S., & Scott, E. C. (2010b). Problem Concepts in Evolution Part II: Cause and Chance. Evolution: Education and Outreach, 3(2), 261–264. doi:10.1007/s12052-010-0231-3
Rector, M. A., Nehm, R. H., & Pearl, D. (2012). Learning the Language of Evolution: Lexical Ambiguity and Word Meaning in Student Explanations. Research in Science Education, 43(3), 1107–1133. doi:10.1007/s11165-012-9296-z
Wei, C. A., Beardsley, P. M., & Labov, J. B. (2012). Evolution Education across the Life Sciences: Making Biology Education Make Sense. Cell Biology Education, 11(1), 10–16. doi:10.1187/cbe.11-12-0111
I came across two startling headlines this morning while working on a manuscript about evolution acceptance and knowledge:
"Poll: Big Bang a Big Question for Most Americans"
"More people believe in bacterial evolution than human evolution..."
After reading the actual questions used in the Associated Press-GfK poll, I disagree.
Respondents were given a variety of statements which they rated from 'Extremely confident' to 'Not at all confident.' The topics included human evolution, the cause of cancer, vaccine safety, climate change, etc. But a closer look at the statements and responses indicates some big flaws.
For example, one statement reads "The universe began 13.8 billion years ago with a big bang." Fewer than 50% of those polled were highly or somewhat confident in the statement. It seems this statement was meant to assess American's confidence in the Big Bang. However, another interpretation of the statement is that it isn't so much about whether the Big Bang happened as it is about whether someone remembers when it happened. Personally, I'm not that confident I'd remember whether 13.8 myr is the best estimate produced by science, even though I've been watching the new Cosmos! I'd rate that as "Not too confident."
For evolution there are two questions: 1) "Life on Earth, including human beings, evolved through a process of natural selection." and 2) "Overusing antibiotics causes the development of drug-resistant bacteria." Respondents were more often at least somewhat confident in the statement about antibiotic resistance (>90%) than the one about human evolution (<50%), leading to the inference that people more highly 'believed' in microbial evolution than human evolution.
The major problem with this 'comparison of evolutions' is that the antibiotic resistant statement is incorrect. Applying selection pressure (in this case, antibiotics) does not cause drug resistant bacteria. Mutations and horizontal gene transfer cause drug-resistant bacteria. We've known that since 1943, when Luria and Delbruck showed that mutations happen first, then selection acts on that variation. The mutation timing misconception* is a frequent thorn we try to address in evolutionary biology and microbiology education, and it's too bad it's shown up in a national poll gaining a lot of headlines. The other problem is that 'evolution' wasn't used in the antibiotic resistant statement, and the word itself may influence how some people respond because they have different notions about what evolution is and isn't.
How would I score the evolution questions? I'd give the human evolution statement "Extremely confident" and the antibiotic question "Not at all confident."
How to improve the poll?
1) Pose the antibiotic resistant statement in a manner similar to the human evolution statement, perhaps "Antibiotic resistant bacteria, including MRSA, evolved through a process of natural selection."
2) Take out specific qualifiers that many people would be uncertain about, simply stating "Antibiotic resistant bacteria evolved through a process of natural selection." And "The universe began with a big bang."
3) Run the statements by some experts. A physicist might see the Big Bang statement differently than a biologist. Other microbiologists and evolutionary biologists will see the statements I came up with in a different way and have further qualifications.
* 'naive conception,' if you prefer
It doesn’t. It’s E. coli.
Today we began Day 1 of the Microbial Genetics Lab for Undergrads here at Michigan State – we’re lucky this year with small class sizes of 32 and 28 students, with three instructors per section! Students arrive, usually without the pre-lab completed, hear a short technical lecture on the day’s tasks, and then set out to do the tasks. I find the entire thing to be a crazy fun bustle of confusion as we teachers tumble about the room correcting flaws in sterile technique, quizzing students about their conceptual understanding of the experiments, encouraging the especially curious. (Will there be any Martin Arrowsmiths this semester?) This is my second semester of teaching, so I'm still learning how to organize a classroom.
Today we spent an hour covering all the things micro students “should” know already: how to flame sterilize an inoculating loop until red hot, how to ethanol and flame a`hockey stick, how to put out an ethanol fire… (On this last point, we demonstrated and then had each student repeat this process: 1. Purposely lighting our ethanol containers on fire, and then 2. Calmly placing the container lid over the blaze, which extinguishes the fire.) The students seemed to get a kick out of this. No, lab safety doesn’t have to be boring. <<That said, you should read safety instructions like this and have someone experienced demo the technique before you before trying it out yourself.>>
Next I asked the students what they would be observing in the next lab period. Most said, “Whether or not the strains grow.” This answer, I think, is a residual response from the intro micro lab, where the students spend the semester streaking unknown isolates on various media, using growth to help identify species and strains – it’s typical flowchart work that doesn’t require much thinking. So, I next got to explain that we’ll be observing gene expression using color indicators and that we’ll be thinking a lot about genes and operons this semester, and welcome to microbial genetics. Today we used x-gal to indicate expression of the gene coding for B-galactosidase, which results in blue colonies.
Sometimes I ask my students questions like, “Why does E. coli want to produce blue pigments?” That gets them to think and provides a teaching moment that a) E. coli doesn’t really want or not want to do anything; it's E. coli, and b) In the natural environment B-galactosidase metabolizes the sugar lactose, not x-gal, which is a convenient substrate we use in the lab to produce blue colonies.
If everything makes more sense from an evolutionary perspective, we might ask, “Why did E. coli evolve to produce blue pigments?” It didn’t. The E. coli lac operon evolved as an efficient way to regulate expression of lactose metabolism. (Not everything is an adaptation, after all.)
... read the punchline and more in my post for the BEACON "RESEARCHERS AT WORK series.
See my new "Evolution 101" guest blog for BEACON: Host-Parasite Interactions, Of Mice and Cheese and Men and Zombies
Side Projects, The Blog!
A blog for all things non-dissertation.