What a time to be alive! These days, just staying alive feels like an accomplishment. As of late January 2021, at least two million people have died worldwide from COVID-19 (the disease caused by the virus SARS-CoV-2). A little more than a year after it was first recognized in Wuhan, China, we have the first vaccines being distributed; a scientific feat brought to you by the study of evolution. Yes, evolution. If you learned anything during this pandemic, I hope it is a healthy dose of the ‘forbidden science’ (no one calls it that).

‘Herd immunity’, ‘mRNA vaccines’, ‘mutations’, ‘phylogeny’, what a great resource for our evolution lectures! Evolutionary biologists will no longer be relegated to being the bantering wit at cocktail parties (remember those) yapping about birds being dinosaurs, or how extinct Neanderthals live on in our DNA; no, now is a time for us evolutionary biologists to roll up our sleeves and explain to others what the people actually saving humanity are doing. Sure, we weren’t those fabulous front-line workers actually risking their lives for the greater good, or the microbiologists, immuno-engineers, and Faucis heroically working to find an end to the scourge. Instead, we evolutionary biologists worked mostly behind the scenes, but you could say we’ve seen this play before and could help set the stage. Evolutionary biologists include those figuring out what this disease is and where it came from in the first place. We are used to thinking in geological time, so forgive our stumbling acceleration from our typical glacial pace; all this “evolution-in-action” data that came pouring out during this pandemic was hellishly exciting and horrifying at the same time.

Starting in late February and March 2020 many of us were drooling over the data coming off the science website NextStrain (https://nextstrain.org/) which proudly exclaims on its homepage to show ‘real time tracking of pathogen evolution’ (1) (and it doesn’t disappoint). On that site you can actually play (and replay, over and over) a day-by-day phylogeny (an evolutionary diagram depicting relatedness) and a corresponding world map showing the spread and growth of SARS-CoV-2 as it moved and mutated into new forms. Recently we learned of new even more virulent variants of SARS-CoV-2 first appearing in the United Kingdom, Brazil and South Africa (2,3). These variants are a result of mutations; mutations are errors in the copying of the genetic code of the virus as it is replicated, and are the raw material of evolution. Coronaviruses, like SARS-CoV-2, use the host cells to replicate and copying errors arise from this process (4). They are called “coronaviruses” because they look spiky, like an evil monarch’s crown (“corona” means “crown” in Latin); fun fact: several viruses that cause the ‘common cold’ are coronaviruses. The virus uses the crown to latch on to host cells; the vaccines being produced help your immune system recognize the proteins that make the spiky crown (via a messenger(m)RNA, hence ‘mRNA vaccines’), thus priming you to fight off the real virus if you encounter it (5). As the virus mutates into new variants it becomes harder for your immune system to recognize the disease compared to what the vaccine originally primed it to fight. That is why there is evidence that some of the available vaccines may not be so effective against the new strains (6). That genetic variation caused by mutations is also why you need a different flu shot every year; the flu is evolving and changing so a different vaccine is needed each year to keep up. Expect getting updated shots each year for COVID too.

The more people that get the virus the more opportunities it has to reproduce and mutate resulting in new strains and new complications for scientists trying to stop it (which is why avoiding other people is so important right now)(7). Eventually, if enough people do receive protection from the vaccines we will achieve ‘herd immunity’. For the anti-vax crowd, herd immunity is when everyone gets the disease and those that survive will be part of a new immune population. While that is very Darwinian of them, survival of the fittest shouldn’t be used to “trim the herd” of our most vulnerable e.g., the elderly, the immunocompromised, and those exposed to the virus like front-line workers and fast-food employees and others forced to work. Natural selection is brutal, ‘applying’ natural selection to humans is really just eugenics (since you would really just be sparing the privileged who can afford to avoid the virus). It isn’t ‘survival of the richest’ you know.

In the ‘age of COVID’ we also learned about human variation; not all populations are impacted by the virus in the same way, revealing the biased nature of our healthcare system (8). Worse still is that the vaccine may not be as effective on Black and Asian populations due to our different histories and genetic makeup (9,10). We also see big geographic discrepancies in where COVID genetic samples come from (11) which will also hurt our chances for finding new variants before they spread around the globe.

When the virus first emerged we didn’t know what it was until it was included in an evolutionary tree and found to be a SARS (Severe Acute Respiratory Syndrome) coronavirus (12), then with further evolutionary detective work we learned it originated from pangolins or bats (13,14), and definitely was not man-made in a lab as some conspiracy theorist and past-presidents suggested (15). Learning the origin of this disease helped demonstrate another reason why natural history collections should be supported so they can help identify and detect these disease vectors as they emerge (16) (natural history and taxonomy being an important part of the study of evolution). New zoonoses (diseases coming from wild animal populations) can be better tracked if we have a good understanding of what organisms exist out there and what disease they carry (and how they live with those diseases, i.e., after they get herd immunity the hard way) and how those organisms and diseases relate to each other in the evolutionary Tree of Life (17,18).

So as we watch the virus evolve, and the vaccines do their work, let’s keep in mind the evolutionary biology that went into the study of both. And after we’ve thanked the real heroes of this pandemic, remember to keep learning a little bit of that evolutionary biology that can teach us the nature of these pandemics in the past, present and future.

Stay safe and wear a mask or two,

Your friendly neighborhood evolutionary biologist,

Prosanta Chakrabarty

1 Hadfield, J., Megill, C., Bell, S.M., Huddleston, J., Potter, B., Callender, C., Sagulenko, P., Bedford, T. and Neher, R.A., 2018. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 34(23), pp.4121-4123. https://academic.oup.com/bioinformatics/article/34/23/4121/5001388

2 Baric, R.S., 2020. Emergence of a Highly Fit SARS-CoV-2 Variant. New England Journal of Medicine https://www.nejm.org/doi/full/10.1056/NEJMcibr2032888

3 CDC. Emerging SARS-CoV-2 Variants. January 28 https://www.cdc.gov/coronavirus/2019-ncov/more/science-and-research/scientific-brief-emerging-variants.html

4 V’kovski, P., Kratzel, A., Steiner, S., Stalder, H. and Thiel, V., 2020. Coronavirus biology and replication: implications for SARS-CoV-2. Nature Reviews Microbiology, pp.1-16. https://www.nature.com/articles/s41579-020-00468-6

5 Zhang, N.N., Li, X.F., Deng, Y.Q., Zhao, H., Huang, Y.J., Yang, G., Huang, W.J., Gao, P., Zhou, C., Zhang, R.R. and Guo, Y., 2020. A thermostable mRNA vaccine against COVID-19. Cell, 182(5), pp.1271-1283. https://pubmed.ncbi.nlm.nih.gov/32795413/

6 Zimmer, C., Weiland, N., LaFraniere, S. 2021. Johnson & Johnson’s Vaccine Offers Strong Protection but Fuels Concern About Variants. New York Times. January 29, 2021 https://www.nytimes.com/2021/01/29/health/covid-vaccine-johnson-and-johnson-variants.html

7 Evolution goes viral. Nat Ecol Evol (2021). https://doi.org/10.1038/s41559-021-01395-2

8 Manning, K.D., 2020. The Art of Medicine: More than Medical Mistrusts. The Lancet, 396: 1481-1482. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)32286-8/fulltext

9 Ray, T. 2020. MIT machine learning models find gaps in coverage by Moderna, Pfizer, other Warp Speed COVID-19 vaccines https://www.zdnet.com/article/mit-machine-learning-models-find-gaps-in-coverage-by-moderna-pfizer-other-warp-speed-covid-19-vaccines/

10 Liu, G., Carter, B. and Gifford, D.K., 2020. Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and their Augmentation by Compact Peptide Sets. Cell systems. https://www.sciencedirect.com/science/article/pii/S2405471220304610

11 Centre for Genomic Pathogen Surveillance https://beta.microreact.org/project/pa7U6YScBKgFkEmk1sp1SX-cog-uk-2021-01-25-global-sars-cov-2

12 Eickmann, M., Becker, S., Klenk, H.D., Doerr, H.W., Stadler, K., Censini, S., Guidotti, S., Masignani, V., Scarselli, M., Mora, M. and Donati, C., 2003. Phylogeny of the SARS coronavirus. Science, 302(5650), pp.1504-1506. https://science.sciencemag.org/content/302/5650/1504.2

13 Zhang, T., Wu, Q. and Zhang, Z., 2020. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Current Biology (30) 1346-1351.e2 https://www.sciencedirect.com/science/article/pii/S0960982220303602

14 Flores-Alanis, A., Sandner-Miranda, L., Delgado, G., Cravioto, A. and Morales-Espinosa, R., 2020. The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789. BMC research notes, 13(1), pp.1-6. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7450963/

15 Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. 2020. The proximal origin of SARS-CoV-2. Nat Med 26, 450–452. https://doi.org/10.1038/s41591-020-0820-9

16 DiEuliis, D., Johnson, K. R., Morse, S. S., and Schindel, D. E. 2016. Opinion: Specimen collections should have a much bigger role in infectious disease research and response. Proceedings of the National Academy of Sciences, 113(1), 4–7. https://www.pnas.org/content/113/1/4

17 Quammen, D., 2012. Spillover: animal infections and the next human pandemic. WW Norton & Company.

18 Thompson, C.W., Phelps, K.L., Allard, M.W., Cook, J.A., Dunnum, J.L., Ferguson, A.W., Gelang, M., Khan, F.A.A., Paul, D.L., Reeder, D.M. and Simmons, N.B., 2021. Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies. Mbio, 12(1). https://mbio.asm.org/content/12/1/e02698-20

Thanks to Dr. Vicky Forster (@vickyyyf) for help and discussion about this post.

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Prosanta Chakrabarty

November 5, 2017

In the South Pacific for some Ichthyology

Prosanta Chakrabarty

November 5, 2017

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In late September my PhD student Bill Ludt and I traveled to the beautiful island of Tahiti to attend the 10th Indo Pacific Fish Conference. This meeting takes place every four years and I have been anticipating this trip since Bill and I went to the last meeting in Okinawa in 2013. I also knew that I couldn’t go all this way not to collect fishes. As with other conferences in remote locales, and most field trips, it took a while to get permits; we were lucky to get them a day before our planned travel began (even though Bill had been working on them for more than a year).

Also joining us for part of the trip was LSU Biology professor Brant Faircloth. Brant and I submitted a proposal to run a symposium on fish systematics focusing on ultraconserved elements. Our session ultimately became part of a half day symposium called ‘Genes to Genomes: Forging ahead in the study of marine evolution” which we were happy to help organize. (Special thanks to Dr. Michelle Gaither who was the lead organizer and did all the heavy lifting.)

Soon after arriving we knew we were in paradise - an expensive French paradise. My French is passable, but most of the locals we met also spoke English as well their local Polynesian dialects. I always wanted to come to Tahiti, not so much for its fishes or the beautiful teal-colored water, but because I loved the history of Captains Cook and Bligh in this region; and because of films like Marlon Brando’s Mutiny on the Bounty.

We went to the central fish market in Papeete around 5am the first few mornings to see what we could get. We made nice collections of local wrasses, goatfish, and unicornfish among other colorful, if odd-looking, species. At the local grocery store we did come across a large specimen of an Opah, or “Moonfish” which gained some notoriety recently as being “warm blooded” – although some ichthyologists remain unconvinced. Sadly the specimen was too big to collect, and already had it’s gills removed.

Opah at market (left), butterflyfish (top), and unicornfish.

We also traveled to the island of Moorea, which is about a 45min ferry ride from Tahiti. This island is home to, among other things, the Gump Research Station run by UC Berkeley. The Gump helped us get our permits but we were unfortunately unable to collect on Moorea. We had to settle for a lovely day snorkeling in crystal clear water surrounded by lush green mountains.

The conference started a few days after our arrival, and it had about 500 attendees from around the world. Bill, Brant and I all spoke in the first session of the first day after the plenaries. The Indo Pacific Fish Conference is one of my favorites because I get to see many of the European, Asian and African colleagues I often don’t see at conferences in North or South America. Bill and I started several important collaborations that hopefully will make for some fruitful publications over the next few months and years.

Bill, Brant and I in Cook Bay, Moorea; Bill on stage presenting his talk.

Although we didn’t hit the markets again during the meeting, I did get to collect some introduced guppies. The extent of my freshwater fieldwork was putting a bag down into a sewer off the main road in Tahiti and letting it fill with water then pulling the bag out of the water to find that 50 individual guppies had swam into the bag. Many of these specimens were mailed off to a colleague studying the introduction of guppies around the world. He was very happy to get individuals from this distant and isolated population.

I’ll spare you more details about the fish conference and swimming with humpbacks (as I did) and tiger sharks (as Bill did) and such, but rest assured this was no vacation (although it obviously wasn’t all work either). The conference was a great opportunity to talk about our work, including one collaboration that recently yielded the cover of Systematic Biology (Chakrabarty & Faircloth et al. 2017; left). That publication created some great opportunities to work with other scientists interested in using genomic fragments like ultraconserved elements in their phylogenetic studies of fishes.

Prosanta Chakrabarty

August 31, 2017

On Terry Wheeler

Prosanta Chakrabarty

August 31, 2017

Dr. Terry Wheeler had an enormous influence on my life. He was the first to tell me about the fields of Biogeography and Systematics when I was an undergraduate and the first professor to invite me to take a course at the graduate level with him. (I didn’t know that was possible as an undergrad back then.) I went on to get a Ph.D in Evolutionary Biology and I am now myself a tenured professor studying biogeography and phylogenetic systematics. I still have my notes from my courses with Dr. Wheeler and have never forgotten the foundation of knowledge he helped me build – but he also transferred his passion for the science. From him I learned of strange lands and connections between places that seemed distant and unexplainable. I learned to sketch the world map from memory on a chalkboard from him – and I do it for the same reason: showmanship – the students eat it up. From Terry I learned about Darwin, Wallace, Lamarck, Cuvier and many others; he was a great storyteller and he made the classes interesting by making them personal. I learned that he used an undergraduate project I did as an example in his classes while I was still a student at McGill: I remember being absolutely floored and touched by the honor. By chance he was presented the “McGill Teacher of the Year” honor at my Mac graduation ceremony in which I happened to be valedictorian – he would joke with me after that he was only at that graduation to hear my speech. He helped me understand not just science but scientists. He continues to influence how I teach undergraduates and graduate students of my own. I am not sure where I would be without Terry’s influence on my life – but I would certainly not be where I am. I am glad I got to keep in touch with him after I graduated from McGill in 2000, it took me about twelve more years before I had the guts to call him “Terry”: he will always the wonderful Dr. Wheeler to me.

Prosanta Chakrabarty

February 5, 2016

#ParsimonyGate: The Perspective of a Reformed ‘Hardcore’ Cladist

Prosanta Chakrabarty

February 5, 2016

If you are reading this article you have probably read the now infamous editorial in the journal Cladistics http://onlinelibrary.wiley.com/doi/10.1111/cla.12148/full . Although signed “The Editors,” it isn’t clear if this was approved by anyone besides the current Head Editor who is most certainly a “hardcore cladist” (someone who thinks parsimony is the most reasonable, if not only, tool for inferring the historical relationships of organisms through phylogenetics). I distinguish between “hardcore cladists” and just “cladists,” because I think I am a cladist and that most other systematic biologists are too. A cladist in my personal definition is anyone who is distinguishing between pleisiomorphic (“primitive” features shared with a designated outgroup) versus apomorphic (derived characters distinct from the outgroup condition). Under my broader definition, basically everyone doing morphological or molecular work to discover the relationships of organisms is a cladist, and it doesn't matter if you are using parsimony, likelihood, or Bayesian approaches. The only exception are folks that are using overall similarity (e.g., bats and birds are close relatives because they both have warm blood and wings) which doesn’t distinguish analogy (convergence of characters) versus homology (characters derived from common ancestry) because it doesn’t follow the Henningian, or cladistic principal, of distinguishing between pleisiomorphic versus apomorphic characters.

This view of cladistics I outline above are basically the foundation of Willi Hennig’s 1966 book “Phylogenetic Systematics” that is the bible of the Willi Hennig Society (publisher of Cladistics) and the foundation of modern systematic theory. At the time the idea of distinguishing between pleisiomorphy versus apomorphy was radical. Famed evolutionary biologist Ernst Mayr was the first to call those following Hennig’s principles “cladists” - as a pejorative by the way. Mayr preferred doing “evolutionary taxonomy” - basically where the expert on a group makes a hypothesis about the relationships of organisms based on characters they think are most important for supporting those relationships (e.g., owls, eagles and hawks are all each other’s closest relatives because these “raptors” all kill with their feet). The other alternative method in systematics in those early days were the numerical pheneticists that used overall similarity to group organisms as I explain above. (Read more about this interesting time in history in David Hull’s, “Science as a Process.”) The original cladists weren’t fighting for parsimony, they were fighting to only use derived characters in phylogenetics. Parsimony came around a little later with the work of several groups mainly from the University of Michigan and American Museum of Natural History. Parsimony was the only game in town to the early cladists, which was mainly for understanding the transition of morphological characters from primitive to derived. Then with the rise of molecular tools for obtaining DNA characters came new methods for inferring trees: model-based approaches including maximum likelihood and eventually Bayesian inference. Systematists of all sorts would meet at the annual Systematic Zoology/Biology meetings every year until the “hardcore cladists” decided to break away and have their own meeting, the meeting of the Willi Hennig Society founded in 1980.

Now I should mention I trained as a systematist at both the University of Michigan and the American Museum of Natural History, the hot bed of cladistics and Hennig worship, albeit late in the game in the early 2000s. I was a hardcore cladist most of my early graduate career. I thought parsimony was the only reasonable way to infer relationships because it wasn’t a model-based approach like maximum likelihood or Bayesian inference. Those models made too many assumptions I thought and was taught. Alternatively, parsimony wasn’t a model because the foundation of that idea is to “minimize ad hoc assumptions about homoplasy” (i.e., reduce noise in the tree from characters moving around). Using parsimony, the shortest tree with the fewest steps (or evolutionary transitions) is the best tree – period. The other methods were using models to guesstimate from DNA sequences too much about how often an A (adenine) turns to a C (cytosine) or a T (thymine) to a G (guanine). It was crazy how much assuming those crazy-assuming people were doing. If they just did some morphology they would better understand how all this stuff really worked and that there is only one true religion, I mean method, parsimony. We were the Jedi knights that stuck to our principles; those other folks just weren’t thinking it through. Then something happened: I saw the light.

I realized at one point that there isn’t a right way to study historical relationships. We can’t actually know the truth about who is related to whom when discussing organisms that diverged millions of years ago. We are also using methods that are extremely computationally intensive. They are all models, even the heuristic we use to run parsimony. No computer on Earth can fully resolve a phylogeny of more than a dozen or so species using any heuristic of parsimony or likelihood: there are just too many possible answers. When we study a historical science using morphological characters or DNA we will never be sure we are right. As I started using DNA methods more I realized I wanted to start better understanding when these lineages started to diverge. I needed to put a rough age on a group and to do that I needed to use likelihood and Bayes because only those use evolutionary models from which you can understand how DNA sequences change over time. I slowly found myself using these other methods more and more. Did I still use parsimony, sure sometimes, but it gave me the same answer as those other methods, just less information (e.g., a tree without branch lengths or information about time). The relationships themselves are interesting but I also wanted to know about evolution and biogeography beyond the tree.

Now I’m still a cladist, and I hope I can count many friends among those in the Willi Hennig Society. (I named my dog Willi.) The folks in that society helped me think more clearly about methods and the philosophy of systematics, and also about the limits of what we can know in general (epistemology). They have invited me for talks at their annual Hennig meetings and I always learn a lot at this conference. Many people are intimidated by these meetings because many senior members do yell at each other, but they are friends in the end - trying to improve each others work. They do sometimes pick on folks that aren’t their friends, and that isn’t cool. You do have to bring your “A” game to Hennig because there are no concurrent sessions and there is an unlimited time for questions. You always have to explain why you picked a certain method over another, it isn’t about using the newest method it is about justifying your choice. (Much like the Cladistics editorial was trying to say. I think.) Compared to other meetings where there is often few, if any, questions - even after a terrible talk - I actually think Hennig is doing it right. They have many fewer members than other major systematic societies so they have the luxury of having just one session at a time and an open-ended question period. The Hennig conference is also strongly skewed male, which is a problem they really need to fix. Many senior members of the society need to tone it down a bit too. They can be crass and pedantic and use jargon as a weapon to make semantic arguments over relatively mundane things (“how can you test a model with a model”; “is there such a thing as an order-quantifiable metric of similarity”). I still publish in Cladistics (as recently as last year) and it even had a Bayesian analysis in it. Although I let my membership lapse a few years ago I’m not opposed to going to another meeting in the future. I think the editorial they published is a step backwards only because it sounds so uninviting: “If alternative methods give different results and the author prefers an unparsimonious topology, he or she is welcome to present that result, but should be prepared to defend it on philosophical grounds.” Many read that as, “You can submit non-parsimony things but you need to explain why, and even if you explain why, we still might not like it because parsimony.”

I think the editorial was a mistake because it sounded like they will only accept the parsimony answer if you get alternatives from other sources. And that makes the journal “Hardcore Cladistics” and it was, at least recently, just “Cladistics.” I do hope they reconsider their stance, or at least clarify. I still consider Cladistics a great journal, one that I enjoy reading because of its organismal focus on systematics. I haven’t had issues with editors or reviewers telling me I need to do a parsimony analysis or remove a likelihood or Bayesian analysis, but I’ve heard that other may have. Time will tell if the journal and the society can right the ship, unfortunately, it was a storm of their own creation that has it teetering.

Prosanta Chakrabarty

January 26, 2016

Learning “R” in Spain

Prosanta Chakrabarty

January 26, 2016

Studying turtles with R. Julien Claude in the background.

The sun rising from Montserrat.

From January 17-23 my new PhD student A.J. Turner and I went to a small town near Barcelona in Cataluña, Spain. We were there to take a morphometrics course in R (more info here:Transmitting Science) . For the uninitiated, R is a programming language and environment that can used to manipulate data, conduct analyses, and make beautiful figures - among other things. We would like to use R to measure and compare shapes of various fish species to better understand how body shapes change over the life of an organism; how these shapes evolve among/between groups; and how to use information about shape to better understand the changing forms of of fishes over time. A.J. is quite clever and smart and he will one day be able to use this tool to make his cutting-edge dissertation even more cutting-edge. I was once clever and smart too but I’ve felt a little dumb post-tenure. I saw this class as an opportunity to retool, and to reshape (pun intended) some old projects and to think of new ones. It didn’t hurt that the course took place in beautiful Spain. The course was taught by Julien Claude, who is the author of a book “Morphometrics in R,” and he also wrote an R package called “ape” that has been cited thousands of times. There were about twenty other students from around the world there, some were studying shapes of dinosaur bones, or fruits, or flowers - among countless other projects. Almost all brought data to play with and manipulate. From 9am to 7pm for five days we were on our computers going through dozens of examples and exercises. It was rather intense, especially for me – not having been a student since I got my PhD almost 10 years ago. Except for some short breaks and meals, we were engrossed in R all day. The group of students and instructors were a disparate mix of international students, postdocs and PIs. Luckily everyone was very nice and A.J. and I ended up with twenty or so new friends and maybe some future co-authors. I particularly liked Julien. He and I share a rather silly and nerdy sense of humor. A running joke about one of the students being from the future and taking this class to destroy R like the Terminator had us giggling for days for some strange reason. (It might be that writing ten hours of computer code a day makes almost everything else hilarious.) Speaking of bad jokes: Do you know the favorite coding language of pirates? … R! ) By Day 4 my brain was full and I needed to take a bit of a break from the dark classroom and spend some time outdoors. A.J. and I got up at 5am and took a cab to the top of beautiful Montserrat and watched the sun rise over Cataluña. A.J. and I found ourselves walking around the grounds of a rather breathtaking Basilica at the top of Montserrat. There were monks chanting, bells ringing, and beautiful rows of multicolored candles lit for prayer. The sun rising over the mountains was stunningly beautiful as were the paintings and décor inside the monastery. The monastery has a famous dark skinned Virgin Mary statue that reminded us of this part of Spain’s rich African history. Cataluña houses an interesting mix of cultures, something that is notably distinct from the rest of Spain. We were often greeted with ‘Bom dia” in the morning (similar to the Portuguese “Bon dia”), and with “merci” in place of “gracias.” But alas we only had time to learn one new language, and we were back learning the grammar and culture of R in our classroom that same morning. In R we say hello like this setwd("/Users/Prosanta/Desktop/MorphometricswithR2016/datasets"). Our visit to Montserrat was just a few hours but luckily we also had a few free hours when we landed in Barcelona. My postdoc Fernando Alda is from Spain and I wouldn’t have been able to look him in the eyes if I didn’t tell him we saw at least some sites while we were in his home country. Luckily we were able to also see the Sagrada Familia on our way to the course on the day we landed. The Sagrada Familia is the infamously beautiful/hideous giant church designed by Spain’s most influential architect Antoni Gaudi. Inspired by biological shapes (apparently all biological shapes all at once), Gaudi initiated construction of this building in 1882 and it won’t be finished until 2020 (maybe). The building is impossible to describe with words, but let’s just say I don’t think Gaudi would have been good at R. Although I think our instructor Julien Claude can probably make anyone good at R.
Julien is a patient and kind instructor who made sure every student was getting the current set of skills being taught before moving on; and he also understood that we each had different goals, projects, and kinds of data. For me learning elegant new tests of hypotheses for modularity (the independent changing of shape in one body part versus another) or fluctuating asymmetry (the unbalanced growth across a body’s axis of symmetry) were worth the price of admission. I already have new projects in mind and hope to help some students learn new morphometric techniques. A.J. and I are extremely grateful to our Department of Biological Sciences and Office of Research and Economic Development for the opportunity to attend the R class in morphometrics.

A.J.Turner at La Sagrada Familia

Prosanta Chakrabarty

November 4, 2015

Survey Your Society to Gather Demographic Data

Prosanta Chakrabarty

November 4, 2015

If you have been to a scientific conference and looked around a bit you see students, postdocs, faculty and other professionals. We care mostly about the scientific abilities of these folks - how well they present their findings, the significance of their work, the ambition of the young, and the impact of the senior members. But we should also care about the demographic make-up of the members of these academic societies. (If I have to explain why diversity is good stop reading here.) Each society should know: What is the ratio of the sexes: 50/50? How may folks are internationals/locals? Are there members with disabilities? What about the make-up of different races and ethnicities? Does your academic society look like the general population? Does it even look like your academic institution?

I would like each member of a society to ask their governing body to send out a simple demographic survey to all its members to gather these data anonymously. The survey below is crude and oversimplified and based on the one from the National Science Foundation, but it is better than nothing. Keeping this anonymous ensures that no members should feel uncomfortable revealing this information. The results of the survey should be presented as simple pie charts of the metadata presented on a groups public website.

So why do this survey? For starters you can learn how well your society is doing recruiting and retaining a diverse membership? You won't know without a baseline survey. Doing the survey annually will tell you if you have a problem with retention and recruiting. It can help you improve your groups diversity. Does your society have few female members - have you thought about having more female members as part of the governing body, balancing the gender ratio of invited speakers, and perhaps having some parental care options for young parents attending your conferences? Does your society have few African Americans - have you thought of sending some members to recruit and visit at HBCUs?

I hope that every scientific society starts keeping track of this kind of information. We can compare across groups that way. Those comparisons will help us know if there is a general problem across academic societies, or if it is just an issue in some sub-disciplines.

As the Chair of Diversity Committee in my college I know we try to get a diverse pool of candidates to apply to open positions in my university. Part of the way we do that is by contacting groups with a diverse membership. If your scientific society lacks a diverse membership, you won't be helping with our goal. A simple survey like the one below can help you identify potential issues and help you begin the process of trying to solve them.

Please try to convince your academic societies that this survey of membership demographics is important.

EXAMPLE SURVEY
send out an email to members and then send out an anonymous survey monkey questionnaire.

Dear XXXX Members,

We want to collect diversity data from our membership. You will get an invitation to participate in a survey monkey questionaire from zzz@yyy.com

Please complete the survey by xx/xx/xx.

As a society we want to be aware of our ability to recruit a diverse group of scholars from different backgrounds, this survey will help us better understand how well we reflect the general population and compare to other scientific and academic societies and organizations. Please help by taking a few minutes to fill out this survey.

ETHNICITY (choose one)

_____Hispanic or Latino

_____Not Hispanic or Latino

_____Do not wish to Provide

RACE (choose one or more)

_____American Indian or Alaskan Native

_____Asian

_____Black or African Amerian

_____Native Hawaiian or Other Pacific Islanders

_____White

_____Other (describe)

_____Do not wish to Provide

DIABILITY (choose one or more)

_____Hearing Impairment

_____Visual Impairment

_____Mobility/Orthopedic Impairment

_____Other (describe)

_____None

_____Do not wish to Provide

GENDER IDENTITY(choose one or more)*

_____Female
_____Male
_____Transgender
_____Other (describe)
_____Do not wish to provide

And then adding

SEXUAL ORIENTATION (choose one or more)*
_____Straight
_____Lesbian
_____Gay
_____Bisexual
_____Queer
_____Other (describe)
_____Do not wish to provide

*UPDATED - thanks to Jeremy Yoder (@JBYoder) and Allison Mattheis for providing these categories from their Queer in STEM survey

Prosanta Chakrabarty

March 3, 2015

So you want a recommendation letter…

Prosanta Chakrabarty

March 3, 2015

‘Tis the season for writing recommendation letters for medical and dental school applicants. Many of these requests are from undergraduates who took my large (nearly 100 student) Evolution course. Unfortunately, I don’t have the time to interview all of the students individually, and I usually only get to know a handful of students well enough to write a proper letter. I typically reply to a request for a letter with a request for more information. I ask the students for the following:

(1) What is your overall GPA?

(2) Why do you want to go to Dental/Med School?

(3) Where did you grow up?

(4) What were the topics of your assignments in my class?

(5) What was your final grade (numerical) in the class?

(6) Why did you choose LSU?

(7) What volunteer opportunities have you taken advantage of as an undergrad?

(8) Do you have research/internship experience?

(9) Please send along a CV/resume if you have one.

(10) Please provide any additional information you think would help me write your letter…

(11) What are your preferred pronouns?

Once I get the answers to those 10 questions/inquiries I usually have plenty of information to write a more personal and useful recommendation. Question 1, overall GPA, usually gives me a clue what the chances are that this student will actually get into medical or dental school. Q2, tells me why they want to go to one of these schools – if they don’t have a good answer to why they want to be a doctor - they are unlikely to become one. Questions 3-6 basically tell me (a) are they truthful (because I already know their grades and assignment scores) and (b) their level of ambition and undergrad background. Question 7 and 8 tell me if they are just trying to do well in classes or if they actually tried to accomplish something outside of class. Why would you come to an R1 (Research 1) university and not try to work in one of your professor’s labs? If you haven’t done any research or volunteer work then all you have are your grades, and that isn’t enough. Those students with lots of volunteer hours or research experience have taken advantage of their time as a student and are the most likely to succeed. Q9 and Q10 help me round out the letter and make it as personal as possible.

Not only do these questions make me write the best letter possible for the students, it also helps me write the letter more easily. Rather than struggling to remember how the student stood out in my class, I can have more direct answers that tell me what kind of person they are and how they compare to my other students (because they all answered the same questions). Also with these answers I can plug in big chunks of text into a letter already formatted for medical and dental school applications. Most professors are modifying the same letter over and over again (we often get dozens of requests a year), at least with these questions I can still make my “standard" letter pretty specific to the individual student.

Prosanta Chakrabarty

January 29, 2015

On Academic Peaks

Prosanta Chakrabarty

January 29, 2015

I like to use the metaphor of peaking when talking about highly productive times at different stages of your academic career. Think of these peaks as the high-water marks (i.e., year your most high profile papers came out any you get a new grant). These peaks are preceded by periods of high data gathering and much writing; and followed by periods of transition, where new methods are being learned, and the finishing touches are put on loose ends of major projects. I think these peaks should come every three to five years and they are important milestones in your academic career. The first major peak should be around the 3^rd year of your PhD program, another sometime during your postdoc, and your highest peak should be during the midpoint of your time as an assistant professor (3^rd year pre-tenure or so). There are other peaks (e.g. just before going up for associate and full professor) but let’s talk about the three majors ones in more detail.

When you are starting off in grad school (let’s assume a PhD program), you want to be a sponge learning new techniques and gathering data over the first couple of years. As you learn to write during these years it usually takes until at least your 3^rd year until the publications from those early works start coming out. That’s a good thing because that’s usually the time you go up for your qualifying exams (to be a PhD candidate in good standing). The students that have some pubs coming around this time are usually on the fast track. Those pubs will be some thesis chapters, but also collaborative side projects with others. Once you reach this peak, the thesis committee usually is okay with passing you for these qualifying exams making you a PhD candidate. After that peak, students typically focus on the meatier sections of their thesis and getting them ready for publication.

Another peak should come at some point during a postdoc. You’ve learned some new skills as a graduate student, and those techniques will make you marketable to others. After you get a postdoc, you won’t need to worry about the constraints you had in graduate school like classes, or friendships (just kidding here, but usually postdocs are kind of in limbo in their new short-term work environment, so friends are harder to come by for sure). Without these constraints you should hit the ground running and publish like mad, collaborating with your new lab, finishing up old projects, getting your last thesis chapters published. This peak should push you out onto the job market.

So you got a job, time to finish your own personal Mount Everest climb of academic peaks. As you get your new desk tidy, turn on your new computer for the first time, and figure out how to order everything from pens to major lab equipment, you should also be setting yourself up for big peak around the midpoint of your time before you go up for tenure (again around the 3^rd year). Your pubs from your postdoc should be coming out (always include your new and old address on these pubs) but also the new cool things you started on at your new position; those things you always wanted to try but didn’t have the independence to attempt. It is all those ideas you put together for your “future plans” slides in your job talk that are coming to fruition. During your first and second year of your job you should have a good bit of start-up to spend and hopefully you have been applying for grants at this time. If you get that grant before your start-up runs out you are in good shape. This time should be the most productive period of your career, you still have postdoc skills, but you also have your own lab, and those people are being productive as well feeding off your ideas and plans.

These peaks aren’t set in stone at these different time periods but I like to think of them as goals you are trying to reach. Of course you can have a brilliant career peaking at very different times but you don’t want to have your highest peak as a postdoc, or in grad school and Peter out at your new job. And of course these recommendations are just based on personal observations of people’s work and career paths that I’ve generalized here. Sometimes new graduate students get impatient and discouraged about the pace at which publications are coming out, so I always tell them it is important to be patient and that it really isn’t until their 3^rd year that we expect them to really be getting those pubs coming out at a regular clip. Likewise, a postdoc with no pubs for a few years certainly isn’t peaking, and almost certainly isn’t getting a tenure-track job anytime soon. A new faculty member in his/her 4^th year without a grant and with few pubs might have quite a few things come out in Year 5 but by then the voting faculty will already be thinking of that person with whispers of them not having the stuff to get tenure. That person might still get tenure with the last minute drive but that late peek will be remembered and sometimes considered a negative (e.g. they might say, "This person couldn’t get their stuff together in time for their 3^rd year pre-tenure review. Will they be a good scientist with tenure?"). So yes these peaks are generalizations but they are good things to keep in mind as you move up the academic landscape with all its peaks and valleys.

Prosanta Chakrabarty

August 25, 2014

Guest Post for Wiley - The Top Dos and Don’ts for your First Month of Grad School in a Research Lab

Prosanta Chakrabarty

August 25, 2014

I wrote a guest blog post for Wiley:

The Top Dos and Don’ts for your First Month of Grad School in a Research Lab

http://exchanges.wiley.com/blog/2014/08/22/the-top-dos-and-donts-for-your-first-month-of-grad-school-in-a-research-lab/

Prosanta Chakrabarty

July 16, 2014

A Terrible Cover of Science Magazine & An Example of The Power of Today's Social Media

Prosanta Chakrabarty

July 16, 2014

I checked my mailbox this afternoon, and looked at the cover of my Science magazine and thought: “Whoa, this should have been in a brown paper covering like they had for dirty magazines.” I saw an image on the cover of provocatively clothed women, the title being “Staying a Step Ahead of HIV/AIDS.” Why did this picture need to be on the cover for that story I thought? The image made me think that Science was trying to be incendiary, hip or edgy or something. I put the magazine and my thoughts about it aside; then just before I was about to have a meeting in my office, I decided I needed to put the journal face down and out of view.

I tweeted the joke about the brown paper covering but then decided the cover was still bugging me and tweeted. “When we said we wanted more women in Science this is not what we meant.” and tagged @AAASmember

I thought that would be the end of it, but then Jim Austin (@SciCareerEditor) the Editor of Science Careers (from Science) quoted my tweet and sarcastically replied “Good one.” Shortly after he tweeted, “Am I the only one who finds moral indignation really boring?” I was off Twitter, but Jacquelyn Gill (@JacquelynGill) and others were luckily paying attention. They called him out and the twitterverse went after him and the stupidity of that cover pretty strongly. A few hours later we got a response from Marcia McNutt (@Marcia4Science) Editor-in-Chief of Science magazine, “From us at Science, we apologize to those offended by recent cover. Intent was to highlight solutions to HIV, and it badly missed the mark.”

It was nice of them to apologize especially after Jim Austin’s comments. Read more about the entire exchange from the tweets I highlighted on Storify https://storify.com/LSU_FISH/sexist-and-transphobic-cover-of-science

The cover is still up on-line, and the magazine is still on my desk face down. I was disappointed in Science for publishing a cover that I thought objectified the people in the image, and I was more disappointed by the initial response from Jim Austin. I’m glad the head editor apologized but I was most moved by the quick response from Twitter. In the old days (when they really did put brown paper over dirty magazines) we’d see something like this, maybe shake our fists, maybe even write a letter (like actually write a letter) to the offending party and maybe in 3-6 weeks something would come of it (usually nothing). We might have thought, “well just another example of sexism” and let it slide. Thanks to social media I’m glad at least we all got to vent and share our collective impressions and opinions. I found out I was not alone in being offended, and we all shared a common message that the image was inappropriate. We even got a rapid apology from the editor. And maybe, just maybe, I think the people behind that cover of Science will think twice next time they consider a cover that might be sexist, homophobic, or otherwise just wrong.

Prosanta Chakrabarty

May 1, 2014

The Funding Cycle Wheel of Feels

Prosanta Chakrabarty

May 1, 2014

I'm already on Kermit, two days after hearing about my grant.

Prosanta Chakrabarty

April 23, 2014

I “made it” in academia, and that means you can too!

Prosanta Chakrabarty

April 23, 2014

I’ve seen many posts recently about people quitting academia (check out hashtag, #QuitLit on Twitter if you don’t believe me, or this post, or this one) but I don’t see that many positive alternatives. (There are a few, I still love “The Awesomest 7-Year Postdoc”) I want to tell my positive story because I don’t think it is all that unusual or special, and that isn’t because I’m special or different. I don’t want to call it a success story because success is defined by how you reach the goals you set, it doesn’t matter if you change them along the way. I hate when people look down on someone who dropped out of a Ph.D. program, or didn’t land a postdoc, or didn’t get a tenure-track position. Those people didn’t fail, they ran into a roadblock or had a change of heart that took them on a new career path: they found success elsewhere.

I think luck had a lot to do with my version of success, as did having a loving and understanding partner. I also think I had something to do with my version of success. I’m still relatively young (35) and I am one final step from tenure (positive faculty vote, Dean and President all give the thumbs up – waiting on the Board of Regents). Most of the people I went to grad school with at the University of Michigan are happy and I’d consider them successful (some are on the tenure track, others are still postdocs, some are teaching at liberal arts schools, others are doing soft money research, some are working in policy). I think most of these people initially envisioned eventually landing a tenure-track position – probably because you are essentially taught this is the only option. We all know this goal is not realistic for everyone. One of the much discussed graphics that came out recently shows less than 10% of PhD students get a faculty position (link here). There aren’t enough academic jobs for everyone in the graduate pool, a combination of talent, luck and support gets you there. But some of the people in the training pool decide this wasn’t the place for them after all.

Rather than be discouraged by all the negativity out there, I say – enjoy the process. Being in graduate school or a postdoctoral fellowship can be an amazing and fulfilling experience. Don’t waste your time being cynical about future prospects before you’ve given yourself a chance. I remember when my in-laws asked me what my future plans were early on in my graduate career. I said, “I want to be a professor but I’m still trying to find out if I’m good enough or not.” Around my third year of my PhD when my publications started to finally come out I started to feel like a scientist and I loved that feeling. I melted with joy when there was a proof of my new publication in my inbox and I treasured the smell of fresh new reprints in the mail (this was way back in the mid-2000s when we still used paper). I loved knowing the fruits of my labwork and fieldwork were going to get published. I loved every second of being a graduate student and my postdoc was even better: I travelled throughout Asia collecting fishes and would come back in between trips to write a paper. It was such awesomeness. If you don’t feel that joy, academia might not be for you. If you do love your “job” then stick with it and don’t worry so much about the next step. It’ll work out, trust me, I’m a scientist.

Of course there is more to it. I’m in a niche discipline, ichthyology. I’m also an evolutionary biologist and systematists but all my papers are on fish. I wanted to be a curator of fishes like my undergrad, Ph.D and postdoc advisors. I did everything I could to get a curator position in ichthyology. There aren’t many of these (very few actually) but I tried not to think of the few job prospects and just rolled with whatever happened. Except I did think ahead enough to put myself in contention when a job did become available. I went to meetings, especially the big ichthyology meetings every year so that I could get to be part of the community that would eventually hire me. I volunteered for everything, and I built a good network. I also made lots of mistakes and tried to learn from them. As I went through the process I steadily learned to write papers and do science and I got enough pubs that I landed a great postdoc at the American Museum of Natural History. Luckily for me a few curator positions in ichthyology opened up around that time. I interviewed at three places and had some heartache, but I got a great gig here at LSU. I’ve had many more failed attempts at grants than positive ones but I’ve had just enough to be doing okay. I’ve trained grad students and postdocs and they’ve helped me build a career, as have my many mentors and collaborators.

The point is I think that there isn’t enough voices saying “I made it, so can you - I know the road can be tough - but you can still make it if you still want it and if you are enjoying the process.” The toughest times in academia are when you don’t know your next gig: when you are a finishing Ph.D. student looking for a postdoc, or a postdoc running out of time waiting for a job. Maybe if I didn’t get the LSU job I wouldn’t have gotten another offer. I don’t know what would have happened then, I’ll try not to think about it. So yes circumstances have to be in your favor. If you stay positive, chances are the right opportunity will come your way.

I certainly feel like I’m living the dream. I’ve got great colleagues, a lab of students that are more productive and smarter than me, and a job that I real love. I get to write papers on stuff that interest me and write grants that help me fund that research. I’ve got enough flexibility to have plenty of time to hang with my twin daughters (my actual favorite thing to do). Yes, some days are tougher than others but I can’t imagine being in another profession. If your dream is still to be an academic, don’t give up on that dream if you are enjoying the process. Work hard and stay positive and there will plenty of room for you in academia.

Prosanta Chakrabarty

February 11, 2014

A Proposal for a New #Altmetric, the Influence Score, to Accompany the H-Index and to Help Evaluate a Scientist’s Impact on Society

Prosanta Chakrabarty

February 11, 2014

The H-index is among the most widely used metrics for evaluating the quality and quantity of a scientist’s publications; but what about their influence on society? Here I introduce the Influence Score that can help an outside reviewer better understand a person’s impact not just among other scientists but among the general public and those outside of academia. If the ultimate goal is to evaluate a person’s true overall role as a scientist, I think we should be considering how they communicate with all people not just other scientists (which is the case with the H-index). The new index can be used to accompany the H-index, but also incorporates it. All elements of the Influence Score can be looked up through simple Google and Twitter/Facebook searches.

The H-index can be easily calculated in Google Scholar, I prefer it to the Web of Science or Scopus because Google Scholar counts books and other

Fig.1. Google Scholar Profile Page Showing H-Index in Red Box.

non-traditional peer-reviewed publications: and it is free! To calculate the H-index you essentially count down the number of publications and their citations until the numbers no longer overlap. A person with an H-index of 5, has at least 5 papers with 5 citations. Read more HERE to learn how to calculate the H-index.) Because a scientist’s main role is still to communicate their science among peers (via peer review), the Influence Score multiples their H-index by 100, and down weights the other elements, which are a little easier to accumulate (e.g., # of twitter followers). I chose the H-index over say, total number of citations (which might be more similar to # of followers), because it is easier to calculate for a given researcher, especially one without a Google Scholar profile (Fig.1).

The other measures of the Influence score includes a measure of their visibility with the press (i.e, the Press Index or P-Index for short). Using Google News, one simple puts the person’s name in the search box and counts the number of articles that are found, which Google also does for you (Fig.2). Because


Fig 2. Red box shows Google News P-index.

Google News is only searching through a relatively recent window of time, few scientists will have much more than a few articles about them. Sometimes it is worth googling the person with “science” following their name, as I did for James Watson (e.g., “James Watson science”), to distinguish him from other news articles about people with the same name. This measure largely is to bump up those scientists truly making a social impact as newsmakers. That is without bumping them up too much, I’m trying to avoid giving too much influence to “celebrity scientists” that don’t do much science of their own. Therefore, I suggest that you divide the total number of search results of the Press Index by 100 so that this score is not completely overweighing the person’s academic accomplishments represented by the (albeit crude) measure of the H-index. Folks like James Cameron that are great promoters of science, but are best known for other things, are intentionally excluded here. If someone could separate press about science related activities from all others, they obviously could still be included. This is also the most dynamic element of the score because it can change so rapidly. Jane Goodall can skyrocket to the top of the list with the publication of a new book.

Fig.3. Twitter and Facebook Fan pages showing # of followers.

The third part of the Influence Score considers your sway in social media (i.e, the Social Media Index or SM-index for short), specifically Twitter or Facebook. For someone on Twitter you get 1pt for every follower. For someone not on Twitter but that has either a Facebook “Fan” Page or Facebook “followers,” you get 1pt per fan or follower. You don’t get points for regular old Facebook “friends” because that isn’t necessarily measuring your scientific influence. If they have both a Facebook Fan page and a Twitter handle you only get points for whichever is the higher value. To learn more about the role of twitter for outreach read David Shiffman’s @whysharksmatter excellent article HERE). As with the Press-Index you divide the total number by 100; again this is to allow the more academic H-index to still have some weight. The reason being that someone with 40,000 Twitter followers and an H-index of 0 might not really be more influential than a scientist with an H-index of 40 and only 4000 twitter followers.

The Influence Score is then the total of your (H-Index X 100) + (Press index/100) + (Social Media-Index/100). I would round this to the nearest integer. All three can be discovered relatively easily through searches (e.g. GoogleScholar, GoogleNews, and a Facebook/Twitter search). Below I’ve compiled a list of some of the most well known scientists and have calculated their Influence Score. I’ve also added folks randomly that I admire that might not be the most famous folks but that I hope will be one day, I think adopting the Influence Score might help them get the recognition they deserve for the impact they have in society. This metric is imperfect: but I hope it is a good start.

I would like to thank Paige Brown @FromTheLabBench and her class #manship4002 for helping me figure out a more user-friendly way to compile this Influence Score. Also would like to thank Joshua Drew (@Drew_Lab) and David Shiffman (@WhySharksMatter) for their comments and advice.

Scientist	H-Index x 100	Press Index /100 (total articles according to GoogleNews)	Social Media Index /100 (Twitter/or Facebook followers)	Influence Score
Stephen Hawking	8400	781	9,591	18,772
Neil deGrasse Tyson	600	14	16,100	16,714
Richard Dawkins	4000	36	8,870	12,906
Bill Nye	100	140	11,500	11,740
Jared Diamond	10800	104	208	11,112
J. Craig Venter	9600	20	186	9,806
E.O. Wilson	8800	64	12	8,876
Steven Chu	8200	17	212	8,429
Buzz Aldrin	0	10	8,150	8,160
Sean B. Carroll	7500	.01	0	7,500
Jane Goodall	4500	21	1,650	6,171
Ed Yong	0	.12	4,660	4,660
Jane Lubchenco	4600	.71	0	4,601
Jack Horner	3600	.16	18	3,618
Carl Zimmer	1700	3.83	1700	3,404
Amanda Vincent	3200	0	3	3,203
Neil Shubin	3100	3.94	9	3,113
David Attenborough	1500	45	1,423	2,968
James Watson	2600	18	0	2,618
Hope Jahren	2200	0.01	24	2,224
Eugenie Clark	2200	0.01	0	2,200
Eugenie Scott	1800	0.06	71	1,871
David Shiffman	200	0.04	1,470	1,670
Sylvia Earle	1400	1	213	1,614

Note: As always I would like feedback on this post and if people have suggestions for changes or additions to the metric. Please e-mail me at prosanta@lsu.edu

Prosanta Chakrabarty

January 12, 2014

On being cool and calm for your presentation

Prosanta Chakrabarty

January 12, 2014

You have to give a public talk and you are crapping your pants thinking about it. Good. If you aren’t a little nervous then you’re a robot and dead inside. But you don’t want to be too nervous. So how can you shake your fear of public speaking? Here are some tips.

(1) Even if you are nervous, try not to let it show

Have you ever watched a regular schlub get interviewed by Oprah and wondered - how come they look so calm? Well most people will not appear nervous unless they are shaking with fear, stammering, or saying “um….um” a lot. So be comforted by the thought that most people won’t notice your nervousness, they are just there to listen to your presentation. Most people will look at the screen while you talk, not you; even more reason not to let your nerves get to you.

(2) You’ve done scarier things than talk to a room full of quiet people

That time you asked a girl you liked out. That time you had that operation. That time you jumped out of a plane. If you haven’t done anything scarier than talk to a bunch of attentive scholars than you aren’t living life the right way. This talk isn’t a big deal in the grand scheme of things. Calm down knucklehead. Save the nerves for when you go deep-sea diving in a leaky bathysphere.

Alternatively, take on an alternative persona. Act like someone more confident than you who has nerves of steal, soon enough the act will become the real deal.

(3) Be chatty pre-presentation

Before you go up to give your talk, strike up a conversation with someone near you. If you are just sitting there thinking about your talk you will risk getting more and more nervous. Talking to someone will distract you. However, if you are at a conference and someone else is speaking it would be rude to talk. In that case think about what question you might ask about the talk you are watching. Go ahead and ask it during the question period. This too will get your mind off your own presentation. Any distraction that will keep you from working yourself up into a tizzy is fine.

(4) Think about the first line you are going to say

Don’t psyche yourself out. If you must think about your talk just focus on the first line you are going to say: “Thank you for coming today, I’ll be talking about frog AIDS.” The rest will come easy after that.

If you are going to be nervous for your talk don’t start the talk with a joke. These almost never work. If you tell it and it bombs you will be even more nervous. If you have a joke for later in the talk fine, just don’t lead with it, unless you are sure you can pull it off. If you are confident enough to do that you probably don’t need to read this post.

(5) Did you just mess up?

Don’t sweat it. If you blanked for a second, or you said something that was meant for another slide, don’t say, “I’m really sorry everyone” or “shoot, damn it Bobby, get it together” or anything that will accentuate your error. Don’t apologize or chastise yourself, just move on, believe me, no one noticed. If you need to stop for a second, take a sip of water and move on.

(6) End with a thank you

If you end your talk, as many people do with “and I’ll take any question you might have,” you aren’t giving your audience an opportunity to clap for you. It’s awkward. Just end with “thank you” after your conclusions or acknowledgments. That “thank you” lets the audience know you are done, and you can have your applause.

(7) The question period

Time to get nervous again. Don’t panic. People are generally pretty kind during this period, they are here to help you and better understand the topic, not to make you look foolish. Call on someone, listen to the complete question, then answer as best you can. If you don’t know the answer or don’t understand the question, just say “I’m not sure about that, let me get back to you; perhaps we can chat more about it later.” It’s okay not to know everything. Just do your best.

(8) Practice. Practice. Practice.

Don’t want to be nervous? Then be prepared. If you know why you have each slide up there and what key points you want to make then you’re golden. If it helps you, have a printout of the slides (multiple per page so your not flipping every two seconds) with notes on the key points you want to deliver. (Or use the speaker notes in Powerpoint or KeyNote.) DO NOT READ FROM A SCRIPT! Nothing is more off putting than listening to someone read from a handout. You are not a politician, you are talking about your research, no one knows this stuff better than you. So be cool fool, and just do your best.

Prosanta Chakrabarty

November 28, 2013

On Diversity: a couple of suggestions for increasing ethnic and gender diversity in your department

Prosanta Chakrabarty

November 28, 2013

Over the last few years I’ve been chair of the Diversity Committee at the college level and I think we’ve come up with some innovative and cheap ideas to increase ethnic and gender diversity. We are mainly targeting increasing gender and ethnic diversity at the faculty level and I’d like to share two of the simplest of these changes that I think have the potential to work anywhere. These are (1) the appointment of a Diversity Advocate on every faculty search and student recruitment committee and (2) the creation of a hybrid postdoc/assistant professor position to bridge targeted hires to becoming stronger candidates for tenure track positions.

1. The Diversity Advocate position is simply appointing someone already on any faculty search or student recruitment committee as the person who will bring attention to diversity issues related to the search. This person should try their best to contact groups, clubs or individuals representing traditionally under-represented groups in the field related to the search. So for instance a member of the search committee for a position in Ecology could contact the Women and Minorities in Ecology (WAMIE) Committee to ask them to spread the word among their members about this search and to encourage their members to apply for this position. Too often the pool of applicants for a given search have few applicants that are women or members of underrepresented minorities. The reasons for the paucity of underrepresented candidates varies (follow @DNLee5 and @AtheneDonald for some answers). Having a Diversity Advocate ensures that someone is trying to make an honest effort to increase diversity among the pool of applicants. Likewise the Diversity Advocate could call attention to someone who didn’t make the shortlist but is the strongest candidate not to make it among those from traditionally underrepresented groups. It might be someone that the department decides to add to the shortlist because it is otherwise not very diverse. I’ve seriously seen several cases where this additionally invited candidate blows everyone away and has gotten the job. The beauty of the Diversity Advocate position is that you don’t need to add a new person onto a committee, you are just appointing someone already on it to help advocate for diversity. In our College we have a form that we ask each Diversity Advocate to fill out and send to our Dean once the search is done. This tells us what was done to increase diversity among the pool of applicants (http://science.lsu.edu/Faculty+Staff/Diversity%20in%20Science/item61566.html).

Examples of what the Diversity Advocate can do:

(1) On A Search Committee - encourage or seek out minority/female applicants from other institutions to apply for a particular job opening for an upcoming search

(2) On A Graduate Admissions Committee – ensure that applications from underrepresented groups are properly treated and perhaps act to connect potential faculty members with these applicants

(3) On A Search Committee - encourage the department to bring in a 3^rd or 4^th short-list candidate among the pool of job applicants if none of the top choices are female or part of an underrepresented minority

2. We also recommend the creation of a hybrid postdoc/assistant-professor position to target diversity hires for folks who are not quite ready to join the tenure track. This position is not a postdoctoral fellowship nor a tenure-track position but something in-between that is meant to be a bridge to a tenure-track faculty position. The position can be used to target postdoctoral students of underrepresented groups that don’t quite have a strong enough CV to compete for a faculty position. The intent is to create this position to allow the candidate to apply for grants and write papers in order to become more competitive in a faculty search in the future (hopefully at our institution but not necessarily).

(1) On paper to be titled a “Research Assistant Professorship” but is not initially a tenure-track position.

(2) The candidate can apply as a PI for external grant funding and is expected to apply

(3) The candidate will work in a fostering PI’s lab (mentor’s lab) as a post-doc would, but with greater independence. Some funds will be provided for equipment that would stay with the mentor’s lab and for disposables. Some funding may also be made available for the mentoring PI’s as incentive to take the fellow under their mentorship.

(4) Expected to write and publish scientific papers in order to become competitive for an R1 position.

(5) Will have a mentoring committee (composed of at least three senior faculty) just like assistant professors receive. This committee will provide feedback to the researcher on their progress and will prepare a report for the Chair of the department.

(6) Expected to build CV to eventually apply to, and join, the tenure track.

This hybrid position is meant to help seal the leaky postdoc pipeline where many underrepresented candidates drop out of science because of the lack of opportunities. Unlike the Diversity Advocate position this position actually costs money. However, it is a worthy investment if the result is someone who becomes a strong candidate for a faculty position that would have otherwise become another statistic.

I’ve been on three diversity committees: once as a graduate student, once in my department, and now as chair at the college level. Just having one of these committees in your department should be a must if the faculty are serious about dealing with issues of diversity. I’ve seen real progress being made by the suggestions of these committees.

Prosanta Chakrabarty

October 15, 2013

Where to publish?

Prosanta Chakrabarty

October 15, 2013

So you’ve begun writing a research paper and you are starting to think about where to send it. Sometimes picking the journal is easy: the subject matter is so specific that there are only a few places that will take it. Other times picking the journal to send your article feels like you are trying to find the right foster parents for your baby. (Okay, maybe not that hard.) Do you go for open access? Highest impact factor? Speed? Prestige? All these factors matter and yes your academic career can be defined by where, and where you don’t, publish.

What’s that you say, the journal doesn’t matter, only the content. Good luck with that. When you apply for an academic job the first thing (perhaps the only thing) that will be scrutinized is your list of pubs in your CV, not necessarily the pubs themselves. The person looking over your CV will look at your list of pubs and thinking thoughts like, “Hmmm…lots of first authored things, all of them are in low tier journals though….the best papers [the ones in high impact journals] were written by someone else.” Wouldn’t you think it was odd reading someone’s CV and seeing they have 15 publications all published in one journal? Unless that lone journal is Science, diversity is a good thing to have among the journals you’ve published in. I try not to submit different papers to the same journal even in the same year. Doing so may give the appearance that you have a friend on the inside that can fast track it or help out with negative reviews. Unlikely the case, but people think strange things when trying to read between the lines of someone’s resume.

I love open access (OA) journals like the PLoS group. Unfortunately even though this is one of the best run outlets for science, some people, especially the old guard, have stigmatized open access. Some think open access journals are “pay-to-play” even though you can get part or all of the publishing fees waived at PLoS very easily. (You should pay if you can to help out, remember PLoS isn’t your traditional publishing powerhouse http://www.plos.org/publish/pricing-policy/publication-fees/.) Other open access journals are far cheaper (e.g., PeerJ). Open access also takes a big hit from a stereotype caused by predatory OA journals that don’t actually put much effort into reviews but that do want your money (http://www.sciencemag.org/content/342/6154/60.full but also see rebuttal here http://neurodojo.blogspot.com/2013/10/open-access-or-vanity-press-science.html). No matter these concerns, open access is the future. Still most journals don’t have this option and in order to diversify you might need to look elsewhere.

The traditional line is to publish your paper in the best journal you can get it into. If you really have something good and want to go high impact you still have some decisions to make. You can go for the actual highest impact factor or the most prestigious. This is kind of like picking a college. If you are a zoology major you might pick a small public university because it actual has a zoology program over going to Harvard (which doesn’t), even though Harvard carries more prestige. Likewise, Molecular Ecology is a great journal with an impact factor of 6.25 but it doesn’t have nearly the prestige of Evolution (4.86) or American Naturalist (4.55). I picked Molecular Ecology for a paper that I could have easily sent to those other two journals because I wanted the paper to come out quickly and those other two journals are notoriously slow (would likely take more than a year). I almost always have picked speed over prestige in my career, mostly because I like to get things off my plate and I’m aiming to average about five pubs a year. I don’t think I sacrificed quality for quantity in doing so. Still, I do sometimes regret those decisions. Part of it is pride, when I’m introduced for a seminar it would be nice to hear, “he has published in Science, Nature, and Systematic Biology,” but I haven’t. My Molecular Ecology paper was published in 2011 and is one of my favorites. I was very happy with how it was handled at that journal and how it looks. The topic is bioluminescence and sexual selection and included phylogenetic analyses, and analyses of disparity and diversification (http://www.prosanta.net/docs/MolEcol.pdf); it was the culmination of my postdoctoral project and it has been cited exactly zero times. I can’t help but wonder if more people would have seen it if I sent it to one of the slower but more well known journals. This is a little counter intuitive since Molecular Ecology’s higher impact factor is due to its papers getting cited more on average than these other journals.

I recently went up for tenure and had a positive vote, I was told that one place to improve was having some papers in more prestigious journals. I agree, especially as I transition into this more stable academic period. These journals may be slow but they are traditionally the most selective with what they publish and so there is some honor associated with publishing there. However, I would recommend to students and pre-tenure folks that in general, it is definitely okay to go for speed, especially if (1) you might get scooped; (2) you need to maintain a relatively high and steady rate of publishing (> 3-5 pubs a yr). Keep in mind that one first authored paper in a very prestigious journal might be worth several in very low ranking journals. The sacrifice of prestige over speed often isn’t always that much. If you can maintain a steady rate of publishing and still have a few projects to send to big journals by all means go for prestige even if that means a few more months of waiting and perhaps an extra reviewer. I think in the near future the “best” journals will be fast, free, open access, prestigious and highest impact. Unfortunately, today those qualities are rarely found in one place so you have to pick what you want for each paper and calculate what you are willing to sacrifice to get it.

Prosanta Chakrabarty

August 12, 2013

Going up for Tenure

Prosanta Chakrabarty

August 12, 2013

So I’m like going up for tenure and stuff.

I just submitted my tenure package this morning and thought I’d share some thoughts and experiences. It all feels so odd, like I’m getting tested for a deadly disease. I obviously knew this was coming, I don’t really feel nervous, maybe anxious, it’s all a little strange. Not unlike gearing up to defend your Ph.D. thesis actually. I’ve never really liked the idea of people scrutinizing my scientific output - but that’s the process. In fact you can’t advance to any stage in academia without that happening. I have noticed that I’ve been a lot more forgiving when judging other people’s CVs in the last year. Perhaps I’m hoping people don’t look so harshly at mine. I mean, don’t get me wrong, I feel confident. I’ve done what I needed to do to earn tenure – but, you never know. People a lot smarter than me have failed the tenure process and the academic landscape is littered with the bones of more failed academics than successful ones. (Not that you can only be a successful academic if you get tenure.)

My actual hardcopy tenure package.

So what’s the big deal about tenure. Well for one, if I don’t get it, I don’t get to keep my job, i.e., I’m fired. If I do get it, I get to keep my job, potentially for as long as I want. The academic freedom of tenure is something worth coveting. I’ll give you an example of its power. If a paper company caused a forest fire I could write a scientific paper about that event that proved the company was at fault without having to worry about being fired by the university. Why would the university fire me? Well let’s say that paper company had promised to give ten-million dollars to help fund a new geology building at the university, they could pull that money if I published that paper. The university would want that money more than it wanted me, so I could be offed; unless that is, I had tenure. Tenure is academic freedom, it is permanent job security. Unlike any old employee at a business, a tenured professor can’t be fired just because they disagree with the administration or because they are publishing papers the Vice Chancellor disagrees with. Tenure is why you should listen to academics when they are being interviewed on the news. They speak from the evidence (so you hope) without being swayed by forces that might cost them their job (so you hope).

So back to me for a bit. My hope is this little post will help anyone else on the tenure-track, to demystify the process. Applying for tenure is very much like reapplying for your job. You hand in an application (with research and teaching statements, a CV), you give a departmental seminar and then you wait for people to give you a thumbs-up or down. (Every institution is obviously a little different, but tenure is generally the same at most Research 1’s. Harvard and Yale are special.) There are also big differences between applying for tenure and applying for a job, namely that you are already employed by the institution. Also you have five (seven in some places) years of being an Assistant Professor under your belt to prove your track record.

I’ve had a lot of support pre-tenure, I was assigned a mentoring committee made up of three colleagues in my department. These folks are there to give it to me straight. Once a year they tell me how I’m doing and if I’m on course for getting tenure. They submit a recommendation to the head of the department, and along with an annual report that I submit, an evaluation on my progress is made which I get to inspect and ponder. This is all set up to let me know if I am keeping up to speed with expectations. There was also a third-year review that basically is a intra-departmental review where the tenured faculty vote on your progress, a sort of mini-(in house) tenure review.

So what did the university expect from me pre-tenure. I was told basically that at LSU, like other R1 institutions I was expected to publish at least two papers a year in quality journals, get a grant of a sum that should be around my start-up package size, and have good teaching evaluations for the courses I teach. I’ve met all of these targets, but I still need to be fully vetted by both those at my institution and by my peers at other places. So I submit a tenure package.

What’s in My Tenure Package:

(1) Regular CV

(2) “LSU” Promotion and Tenure CV

(3) Research Statement

(4) Teaching Statement

(5) Curation Statement

(6) Syallabi from most recent courses (Evolution, Ichthyology)

(7) All Pubs as pdfs (Before and After LSU)

(8) Annual Reports/Teaching Evaluations

(9) Support Letters from Full Professors outside of LSU (between 5-10)

(10) Support Letter for LSUs fish collection from local government agent who uses collection regularly

(11) PDFs of a poster that we presented talking about the improvements to the collection

(12) Selected Press (BBC Radio, NPR radio link; Science, CNN links to articles, etc.)

(13) Support Letters (Editorial Service), Award Letters (LSU Rainmaker, McGill Alumni)

(14) Example lab and lecture slides as PDFs from classes

(15) Links to “A Guide to Academia,” including link to the review in Science

(16) Certificate from an NSF sponsored teaching workshop.

The items in red (1-7) are things I was asked to supply. Items in blue (8 & 9) are things supplied on my behalf by the department, and the remaining items (10-16) are things I’m throwing in there that I think will enhance my case.

There are two versions of my CV (items 1 & 2), the one with the layout I made myself and the LSU CV that has standard sections that I fill in. The LSU CV probably is the best one for upper administrators to look at and compare faculty from disparate backgrounds. Never-the-less most of the items in the different CVs are largely the same, just organized differently.

The research, teaching, and curation statements (items 3-5) are all similar to what I would put into a job application. Most people don’t have to do a curation statement, but as a fish curator at the Museum of Natural Science it is part of my job (My appointment is 50% research, 25% curation and 25% teaching). The teaching syllabi (item 6) for the courses I taught provide an overview of the topics I teach, and I’ve supplemented this with an example lab handout and powerpoint slides from a lecture (item 14). The pubs (item 7) are perhaps the most important part of the package. I have a total of 35 peer-reviewed publications in journals, 20 since joining LSU. All of them are included in the package, numbered as they are in my CV, clearly showing which were published at LSU and which don’t have an LSU address. I also have to make clear which ones I am the corresponding author on. Along with the grant money generated, the quality and quantity of the publications can really make or break your tenure application.

The annual reports and evaluations I spoke of before are again supplied by the department, as are outside letters. To get a good non-biased look at a candidate the department asks about ten people not affiliated with the university to review a tenure package. These folks are established and well respected people in the candidates field. A few months ago I was asked to supply a list of five names of potential letter writers and short blurbs about each person’s credentials (e.g., H-index, # of pubs, area of expertise, awards). They had to be full professors (no associate and no pre-tenure folks), and they could not be my colleagues strictly at stand-alone museums. That last bit was a bummer for me, because as a curator I look up to people at the Smithsonian, Field Museum, American Museum of Natural History, etc. But they don’t have the same academic system as a university in terms of teaching and service so these institutions are not deemed peer academic institutions. The five full professors I named need to be at places like LSU or “better” (i.e., higher ranked, bigger reputation). The folks I picked also can’t have overlapped with me at any previous institution, even if they were in a different department. Obviously I couldn’t list anyone that would have a conflict of interest like my former advisors or co-authors. I can pick people I know, as long as they could still be trusted to be objective. The chair of my mentoring committee also had to come up with five to ten people to ask for evaluations, again all full professors that could independently evaluate my work. The chair of the department then picks between seven and ten of these people to formally ask. The department hopes to get at least five letters of evaluation to be included in my review. These letters are part of the reason it takes about a year to find out about your tenure decision.

I also included some extra items (#10-16) that I thought would help complement the core items (#1-9) of my package. For instance, I didn’t know if everyone reading my tenure package would understand what I had to do as a curator. I inherited a collection in disrepair and made it into something better and so I included a PDF of a poster that explains the renovations and changes to the collections over the last five years (#10). I also added a letter from a local Fish and Wildlife agent that regularly uses our collection to verify and compare his identifications (#11).

I wanted to strengthen the teaching section of the package as well by showing that I wrote a book about academia, so I included a link to the Amazon and Wiley pages that sell and discuss the book (#15). I also included links to the reviews of that book including one that was in Science. I also had some training through a teaching workshop so I included the certificate I got there because I figured it couldn’t hurt to include it (#16).

I’ve been lucky to get my share of press and research awards so I tried to put some links to letters and example press. These I think show that I’m a good communicator of my research and that some people think highly enough of my research to give me an award or to call me to discuss a topic for a newspaper or radio story. I also threw in some of the acknowledgments I got from my editorial work. You don’t generally end up with much tangible to show for your efforts with service; which is unfortunate because service is an important part of your academic life.

After I put in this package I will give a research talk to the department. Then in a few months someone will present a summary of my package in powerpoint form at a department faculty meeting (it will also be available in full for anyone to see) and then the tenured professors will vote in favor (or against) me becoming a tenured professor. The tally from this vote and my package will be sent up through different levels of university administration all the way up to the very top. Then, hopefully around this time next year, I will get a little letter in my mailbox that tells me I get to keep my job - or so I hope! Wish me luck.

After-thoughts:

I highly recommend you also read:

The Awesomest 7-Year Postdoc or: How I Learned to Stop Worrying and Love the Tenure-Track Faculty Life

You can find examples of research, teaching, and curation statements in my book along with other items related to going up for tenure. http://www.amazon.com/Guide-Academia-Surviving-Postdocs-Research/dp/0470960418

Prosanta Chakrabarty

May 28, 2013

Intro to Blog

Prosanta Chakrabarty

May 28, 2013

This is "A Guide to Academia" The Blog by Prosanta Chakrabarty, author of the book by the same name. This blog will serve to provide additional information and opinions on matters that I hope will help graduate students, undergraduates and other academics on the path to success.

Learn more about the book here: http://www.amazon.com/Guide-Academia-Surviving-Postdocs-Research/dp/0470960418

Learn more about the author here: www.prosanta.net

Prosanta Chakrabarty

May 28, 2013

On why graduate students need to ask questions during seminars.

Prosanta Chakrabarty

May 28, 2013

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One of my pet peeves as a professor is seeing that it is largely just us professors asking questions after a seminar. It isn’t that the graduate students don’t have questions: it’s just that they are not inclined to ask. Here I’d like to address why I think it is important that grad students speak up for the betterment of their own maturation as an academic and also for the good of science in general.

As a young student at the University of Michigan we were regaled with tales of the “good old days” when the systematics world was being turned on its head by the faculty (e.g., Arnold Kluge, Bill Fink) and especially the graduate students (e.g., Steve Farris). There was an atmosphere of scholarship and clear thinking because of the competitive environment among the young scholars there at the time. I’ve heard from people who gave talks at Michigan in those days about how scary it was to give a seminar there back then. If you had any insecurities the question period would really bring it out. As a graduate student I saw the reputation being upheld and I was proud to be part of it. Students and faculty asked difficult probing questions to get to the heart of an issue or problem. You might be picturing an angry audience full of people frothing at the mouth waiting to ask a “gotcha question” that makes the speaker look like a fool. To the contrary most questions were basically variations on “why did you do it like this, and not this other way?” or “what is the basic thing you are trying to discover?”

The result of a department’s reputation for asking tough questions is usually hearing lots of good talks. People who gave seminars were better prepared to answer questions and explain the fundamentals of their research. The American Museum of Natural History is another place where I also see the audience’s reputation for asking probing questions change the nature of the style of talks being presented. Seminar speakers are more nervous before their talk but those that come prepared generally do well. This environment may not be the best place to present preliminary work and that is certainly a drawback. Can audience members sometimes go too far and ask questions that are sometimes aimed more to embarrass the speaker, unfortunately that too can be the case. (That only serves to make the person asking the question look like a jerk.) However, in my opinion it is more respectful to ask a speaker a difficult but fair question than to ask no question at all. I think it is terribly embarrassing not to be asked a question during a seminar, both for the speaker and the audience. The speaker is thinking, “geez, I guess they didn’t get it or they didn’t care” and the audience might be thinking “damn it, why doesn’t somebody think of something to ask so we don’t look dumb.” It is the kind of palpable awkward silence you usually only get during a bad blind date. In my life as an academic I think I’ve learned more during the question periods of talks than I have during the talks themselves. That is because the questions and answers can bring out the fundamentals of what was being said over the entirety of the talk, and they sometimes reveal what was missing during the prepared speech. A question can give the speaker a chance to say, “what I meant was….”

So why does a graduate student need to ask questions during seminars? For one thing it is practice for public speaking. Even though you may be seated seemingly safely among your peers, everyone is listening to you. You may only say one sentence, but you are being judged on the quality of that sentence. (By the way the adage, “There are no stupid questions” may be true, but there are certainly 'stupidly worded questions.') A good question that reveals something new to the audience and speaker will highlight your intellect or at least knowledge of a subject, just as a badly worded question will leave people wondering what was the last grade of elementary school you completed. Because of the consequences of asking a good or bad question, it is only natural to get nervous before asking one. Everyone asks both good and bad questions in their life but the people who generally ask the best questions have asked the most. I know I’ve gotten a few collaborations out of projects that were born out of a question I asked or heard someone ask at a seminar.

Graduate students also need to ask questions because they need practice thinking on their feet. You don’t generally have much time to think about how you will be articulating your brief question. The quickest thinkers often ask the best questions, and thinking quickly comes with practice. People who ask good questions often give good seminars; they also typically give good answers to questions. These folks can anticipate the kinds of questions they may be asked. In a graduate school qualifying exam you will be asked many rapid-fire questions by faculty members with a lot more experience than you. If you can’t think on your feet, or anticipate what's coming, you will be in big trouble.

So what if you are just too shy to ask a question. That’s okay - lots of people are shy and many of those people are now not as shy because they forced themselves to be a little bit more outgoing. They did so perhaps by asking a short simple question during seminars until they got more comfortable with public speaking. I personally broke my shyness by taking notes during seminars. I write interesting things that I have heard and to try to formulate a good question to ask. I don’t always ask my question but I always try to write at least one. These notes and questions generally help me think about my own research more clearly. It certainly helps me articulate a good question and synthesize what I’ve learned or didn’t understand.

I’ve heard lots of excuses from graduate students about why they don’t ask questions: “I don’t want to show-up the speaker,” “I don’t know enough about the topic,” etc. I never hear “I couldn’t think of anything.” Usually I hear a great deal of talk about the presentation in little conversations away from the speaker. “I wonder why she ran that analysis?,” or “that was great, but I didn’t understand the part about…..”, or “that was awful, doesn’t he know about statistics?” If you think of a question or didn’t understand something a speaker says it is disrespectful not to ask something. Private conversations behind the speaker’s back don’t help anybody. Talking to the speaker privately after a seminar is fine too, although you do lose the practice of public speaking and thinking on your feet.

So grad students, go forth and ask some friggin’ question, for your sake and for the sake of promoting good science.