Finding autophagy: It’s a question of how you look at it

To tell the truth, I find it difficult to work when flying, or even when sitting in an airport for an extended period of time. So, typically I take along a book to read. And when I truly cannot concentrate, for example when a flight is considerably delayed, I have even been known to resort to word puzzles. Depending on the type, they do not require much attention (that is, you can pick up right where you left off after you glance at the flight status screen for the twentieth or so time, even though you know nothing has changed), or effort (although you need to use a pen or pencil, not a keyboard), but nonetheless they can keep your mind somewhat occupied. I even rationalize doing them based on the assumption that they are sharpening my observational/pattern-finding skills. One type of word puzzle that is particularly mindless, but for that very reason I still enjoy in the above circumstances, is a word search; you are given a grid with letters and/or numbers, and a list of “hidden” terms, and you circle them within the grid, crossing them off the list as you go along. I do admit that the categories of terms used in the typical word searches can become rather mundane (breeds of dog, types of food, words that are followed by “stone,” words associated with a famous movie star, words from a particular television show, etc.). Therefore, on one of my last seminar trips I decided to generate my own word search, using the category of autophagy.     

Location,location, location? No. Catalog number

Once you start to read this Editor’s Corner, you might wonder why I have devoted an entire article, albeit a short one, to this topic. Let me assure you there are reasons. First, I want to announce a new policy for the journal that will affect all research papers. Starting with all papers that are not currently in press, we will no longer be asking for geographical locations of research companies that follow the listing of a reagent. In Materials and Methods the authors typically refer to a reagent and then list the company and its location parenthetically. For example, “…p-nitrophenyl phosphate (Sigma-Aldrich, St. Louis, MO).” Instead, we will require catalog numbers. The reason is that it is now quite easy to find a company using the internet, and in fact you rarely need to know the location because it is rare that you would send a written order. On the other hand, knowing the name of the reagent is not always sufficient to narrow down the precise item. For example, if you search for “p-nitrophenyl phosphate” at the Sigma-Aldrich site, you get seven primary choices and it is not at all obvious which one to choose. When my lab uses p-nitrophenyl phosphate for the Pho8?60 assay, we use item N9389, which narrows it down to a precise reagent. Thus, we will start requiring papers to write “…p-nitrophenyl phosphate (Sigma-Aldrich, N9389).

Second, I think this is actually a useful change, and one that many journals will start to institute once they see it being done here. The old style of listing the city and state is a relic that is no longer relevant. Furthermore, it is not even clear in the current global marketplace if this is particularly helpful. For example, if I am ordering an item from Roche Applied Science, why would anyone care where it is coming from? It is highly unlikely that a researcher in Germany or Japan is going to order from Roche Applied Science that happens to be based in Indianapolis, IN when there are much closer sites in Mannheim, Germany and Tokyo, Japan. So, do not be surprised when you start to see more and more journals adopting this approach, and remember that you saw it here first. Autophagy—the cutting edge.     

Aquaporin Water Channels

Thank you very much. I am humbled, I am delighted; I am honored. This is every scientist’s dream: to give the Nobel Lecture in Stockholm. But I would not be honest if I did not tell you that I am having a little anxiety being on this platform. I have lectured a number of times in Sweden, and I thought I would share with you some events preceding a special lecture that I gave here a few years ago. Arriving at Arlanda Airport, I waited in line at the Pass Control behind a group of businessmen in suits with briefcases. I heard the first in line asked by the control officer to state the purpose of his visit to Sweden. When the man replied “business,” the officer approved and stamped his passport. One at a time, each stepped forward and was asked the same thing; each answered “business” and was approved. Eventually it was my turn, and I was dressed in rumpled clothes after spending the night in the Economy Minus section of an SAS jetliner. The officer asked me the purpose of my visit, and I said “I am here to give the von Euler Lecture at Karolinska Institute.” The officer immediately looked up, stared at me, and asked, “Are you nervous?” At that point I became intensely nervous and said “Yes, I am a little nervous.” The officer looked up again and stated “Well, you should be!“ So if the lecturers look a little nervous, the problem is at Arlanda.     

Biological design — a neglected art

I ought now, perhaps, to offer a summary of what I have been trying to convey in this lecture — but I am haunted by the failure which attended an effort, by an eminent scholar of this city, to do something of the same kind many years ago. Sir John Sheppard, Provost of King's, once gave a public lecture during one of the University's ceremonial gatherings. His subject was the Trojan War. The large audience sat spellbound in admiration of his depth of insight, breadth of knowledge and grasp of detail. As he was leaving after the meeting, a young man came up to him and explained that he was a graduate studuent engaged in research on the economic consequences of the Trojan War. He had, however, been spellbound by the lecture and had been too engrossed to write anything down. Would Sir John be so kind as to lend him his notes so that he could make a summary of the lecture? “My dear chap”, said Sheppard, “I'd be delighted; here are my notes — use them as you wish and let me have them back whenever they have served your purpose”. So saying he handed the young man a postcard on which was written: Agamemnon — Achilles — Agamemnon.I hope that members of the audience won't mind if I leave them to make their own summary of my remarks to which they have listened so patiently this evening.     

Response to William Domhoff's comments on "Meteorite or gemstone?…".

My paper, “Meteorite or Gemstone…” is not trying to divide dream theories into two categories as Dr. Domhoff appears to believe. Rather, it is an effort to nudge dream theory and dream work into new directions. I review many reasons why we often consider dreams “totally different” from daydreams, fantasies, etc. (the meteorite position). For each reason, I show that there is actually considerable overlap, and that the forms of mental functioning are best considered as a continuum. I point out that many dream researchers, from different perspectives, are taking the “totally different” (meteorite position) even though they may not explicitly endorse it. For instance those who insist that dreams are meaningless are taking the meteorite position since they obviously do not consider daydreams and fantasies meaningless. Very different researchers, including Dr. Domhoff's group, spend thousands of hours doing detailed analyses of dreams, counting number of words, number of characters, number of interactions, etc. I consider them too to be taking the meteorite position since they almost never analyze daydreams, fantasies, etc. in this way. I compare their efforts to spectroanalysis, which is worthwhile when studying a meteorite (but not a gemstone), since it may yield secrets about the world the meteorite came from. I am not criticizing these researchers, who have made some important discoveries, but rather trying to nudge them toward noticing the continuum, and perhaps broadening their studies to include daydreams, fantasies, and other forms of mental functioning. (PsycINFO Database Record (c) 2011 APA, all rights reserved)     

Génie musical et bipolarité, le cas Robert Schumann

The troubled poetic and musical genius confides, “However torn from the roots of my existence... I must create as long as there is light of day” [10]. And battle against depressive darkness and its somnolence, before the deep night of the organic. Battle against melancholy and despair, far from the splendor of everyday life, where wakefulness and sleep flow in the primary rhythm of life. Depression draws upon creativity and genius. A frightful lucidity, it reveals that the end is the beginning and feeds the idea of bringing the beginning to an end, to eliminate time. Beyond words, there is music, a place of love and death, the language of affect and value. Music, “supreme expression of poesy”, the word of the angels. When the cadential structure disconnects from temporality, you cruelly get its tonal relationship to the binary and ternary forms of vegetative vitality, the beating of the heart, the movement of the breath, the contraction of muscle, and the shifting of the eyes. Depression is this temporal vacuum, this remoteness from finiteness, the mark of depressivity in the service of the hollowness of existence, each time like a special opportunity to realize the potentials that remained silent. It is human genius in its most common meaning that is solicited, that which allows us to live our lives. There is a good side of depression.     

Towards theoretical formalisms

This article deals with the relationship between vocabulary (total number of distinct oligomers or “words”) and text-length (total number of oligomers or “words”) for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical formula known as Heaps’ law, which relates vocabulary to text-length. Our analysis shows that Heaps’ law fails to model this relationship for CDSs. Here we develop a mathematical model to establish the relationship between the number of type of words (vocabulary) and the number of words sampled (text-length) for CDSs, when non-overlapping nucleotide strings with the same length are treated as words. We use tangent-hyperbolic function, which captures the saturation property of vocabulary. Based on the parameters of the model, we formulate a mathematical equation, known as “equation of word organization”, whose parameters essentially indicate that nucleotide organization of coding sequences are different from one another. We also compare the word organization of CDSs with the random word distribution and conclude that a CDS is neither similar to a natural human language nor to a random one. Moreover, these sequences have their unique nucleotide organization and it is completely structured for specific biological functioning.     

Primate origins,human origins,and the end of higher taxa

When people learn that I study human evolution and we start talking about it, they sometimes ask me, “How long ago did the first humans live?” My answer is usually another question: “What do you mean by 'humans'?” That response seems as baffling and wrong‐headed to them as their question seems to me, and it usually takes us a while to straighten things out. © 2012 Wiley Periodicals, Inc.     

Receptivity to sexual invitations from strangers of the opposite gender

This study investigated the primary conclusion from Clark and Hatfield's often cited field experiment “Consent to Sex with a Stranger” that men agree to sexual invitations from moderately attractive strangers of the opposite gender more readily than women do. In addition, this study investigated whether rates of consent are influenced by a subject's age, relationship status, rating of confederate attractiveness, and type of sexual invitation. A number of moderately attractive confederates of the opposite gender individually approached 173 men and 216 women. After a standard introduction, the confederates asked each participant one of the following three questions: “Would you go on a date with me tonight or during the week/weekend?”, “Would you come to my place tonight or during the week/weekend?”, or “Would you go to bed with me tonight or during the week/weekend?” Significantly more men than women consented to a sexual invitation. Specifically, significantly more men than women consented to the “come to my place” and “go to bed with me” conditions. For female subjects, higher ratings of confederate attractiveness were found to significantly increase the odds of consenting to a sexual invitation, whereas for men, confederate attractiveness was found not to significantly influence consent rates. Finally, relationship status was found to be a significant and strong moderating variable of consent for both men and women. Thus, men and women who are not in a relationship are significantly more likely to agree to a sexual invitation than those who are in a relationship.     

Why do we need autophagy? A cartoon depiction

In my role as an instructor I am constantly looking for ways to more effectively convey information to my audience, which is typically the students in my class. However, the same concerns apply to most of the people who attend a seminar. The approach you take to making the material easier to understand is likely to be influenced by the course you teach. That is, the same instructor may use different examples when teaching an upper division vs. a lower division course. I teach introductory biology, and my students may have little familiarity with cell biology, let alone autophagy. Accordingly, I have tried to consider how to illustrate the importance of autophagy in a way that can be comprehended by people who may not even be familiar with the term.     

Spinning plates and juggling balls

A PhD thesis is a project with an established goal and a deadline. As such, the tools, strategies and insight of professional project management can be used effectively to improve both research success and personal well-being.A project is a “temporary endeavour undertaken to create a unique product, service or result” [1]. Although this is a generic definition, it pretty much describes any PhD research project. There are many ways to manage a project effectively and efficiently. Unfortunately, most of us are so busy with our science that we forget about the importance of planning and management to our own success, sanity and health. Instead, we approach our first three years of genuine scientific endeavour wide-eyed and unprepared to juggle the hundreds of tiny balls that make up a PhD. Several techniques from the realm of ‘project management'' might therefore be helpful for PhD students who need to plan and manage the many competing demands that doctoral research can place on them.A PhD comprises both the research itself and the acquisition of skills and knowledge that will facilitate your future career. As such, it is of paramount importance to establish your own objectives early on. For example, alongside dividing your project into work packages—smaller projects that might be discrete or might build on each other—it is also essential to define which so-called transferable skills—additional knowledge and experience that might improve your job prospects—you feel will be of greatest use to you, depending on what you want to do after your PhD. The importance of these skills is becoming more widely recognized and taken far more seriously, and you should find that your supervisor is willing to give you the time to pursue them—your institute or university usually requires that he or she does so. More importantly, you should give yourself the time to invest in these skills, as they are going to be vital to everything you do once your PhD project is over.Doctoral research requires a multitude of skills, most of which you will inevitably lack when you commence your PhD programme. The first step is to identify the gaps in your knowledge to plan what skills on which to focus. This will allow you to acquire them in good time, either through professional activities—shadowing a postdoc, teaching undergraduates, joining journal clubs and blogging—or through both internal and external courses and workshops to improve communication, presentation, writing, networking and other skills. In addition to your planned skills acquisitions, you will also have situations arise, in which you need to acquire new skills quickly. The more you plan training activities and skills acquisition in advance, however, the smoother this aspect will be of your PhD. By way of example, part of my own PhD project relates to statistical analysis of data. An early analysis highlighted several areas in which I had to improve my skills, including hierarchical cluster analysis, principal component analysis and χ² testing against standard distributions. Having identified these gaps in knowledge early on in my doctoral programme, I could plan ahead accordingly when and how to acquire these skills.The full scope of your PhD project is usually unknown at the outset, and even the direction of your research might well change before you are finished. ‘Rolling wave planning'' is a technique that allows you to take these facts into account and plan the short-term future in detail, with a high-level provision for medium- to long-term activities. For those new to developing project schedules, I advocate a simple five-step approach. First, make an ordered list of high-level activities needed to achieve your goal. Second, expand this list by adding lower-level activities for which you have a detailed understanding of the scope, for example work to be performed in the next six months. You now have a work breakdown structure. Third, turn this work breakdown structure into a dependency-driven list by adding associations between the activities, for example by adding links to precursor activities that need to be completed before another activity can be started. Fourth, estimate the duration of each activity and extrapolate the start and end dates beginning with the first scheduled activity. Finally, as you progress through your research, and the scope of future activities becomes clearer, update the project schedule with these low-level activities as they become known. This approach of generating a hybrid-level project schedule, and updating with detailed activities as the scope becomes clearer, is known as ‘rolling wave planning''.…we approach our first three years of genuine scientific endeavour wide-eyed and unprepared to juggle the hundreds of tiny balls that make up a PhDThere is a range of professional software to help develop project schedules, but there are also various freeware tools available. Alternatively, you can use one of the many word processing or spreadsheet applications to make a simple Gantt chart. Along with the technical scope of your doctoral research, it would also be useful to include milestones that your institution enforces; for example literature review submission, formal progress reports and thesis chapter outlines. Including these in your rolling wave planning will allow you to keep in mind the bigger picture and the formal aspects that must be completed for your PhD, in parallel with the progress you are making towards your specific research subject.It is of course a cliché, but it is true that ‘failing to plan is planning to fail''. Of course the fluid nature of research makes it difficult to estimate accurately the time that it will take to complete various experiments, especially as a novice researcher. I therefore believe that although experiments do overrun and PhD projects can change, developing a project schedule is not a futile activity. By having a plan, even if it is made up of ‘guesstimates'', you can forecast roughly how much time you have left for your research and roughly what you can realistically hope to achieve. After all, without a plan, how can you predict when you will complete your research, submit your thesis and ultimately gain your PhD?Doctoral research requires a multitude of skills, most of which you will inevitably lack when you commence your PhD programmeThe serious consideration of scope is necessary in any project, but even more when you are simultaneously project manager, research scientist and key stakeholder. This raises various crucial questions regarding scope management: what is my doctoral research all about (the goal), and what work do I need to do to meet this goal? Once this has been agreed between you and your supervisor(s), it is essential to manage the scope of your project—the breadth and number of experiments you will perform—and how this will achieve your goal(s). Furthermore, be specific—knowing exactly what you want to achieve will keep you motivated until you get there.Project managers often use the concept of the triple constraint to manage work: scope, time and cost are intricately linked in a project and the different level of focus that each is given affects the perceived quality (by others) of project deliverables (Fig 1). Project managers understand that any deviation in one of the triple constraints changes one or both of the others. This is where the project schedule really comes into its own by allowing you to forecast when you will complete the agreed goals of your PhD project. For example, is your doctoral programme for a fixed-term period? If so, then once a project schedule has been agreed that uses all of the time available, any project overruns will cause an overrun to the overall PhD. The two main possibilities for a PhD student to manage this situation and bring the projected completion back into acceptable timescales are either to work longer or to reduce the scope or goals of the project, either by conducting fewer experiments to answer the same question or by modifying the depth of the question being asked. This leads to the issue of whether there is a minimum set of goals that need to be achieved, or whether several agreed activities are ‘nice to haves'', but are not crucial for the overall PhD. I believe that your supervisor(s) are best suited to answer questions about the minimum goals and the scope needed to achieve them.Open in a separate windowFigure 1The project management triangle as applied to a PhD. Three competing constraints influence project management: time, scope and cost. The time constraint reinforces that projects are temporary endeavours, and that in most cases have defined timescales (absolute deadlines). The cost constraint refers to the budgeted amount allocated to the project that, from the perspective of doctoral research students, will predominantly be focused on the amount and duration of the stipend awarded, but might also incorporate various expenses such as bench fees, conference fees and consumables. For those changing career, the cost might also comprise an element of salary sacrifice. The scope constraint refers to what must be done, produced or developed to meet the objective of the project, which in the case of a PhD generally comprises the actual doctoral research to be performed, development (and submission) of the thesis, publication of one or more journal articles, presentation at conferences and potentially teaching. The triple constraint principle highlights that any change to one of the constraints will have an impact on one or both of the other constraints. For example, increased scope typically leads to increased time and cost; tight time constraints usually mean that an overrun in activities (such as experimentation) might have a knock-on effect of requiring the scope to be reduced to submit your thesis on time, or increasing the overall amount of time required to complete your PhD. Similarly, a tight budget could mean you cannot gain access to various resources, resulting in either increased time or a reduction in scope. Recently, a fourth component of the project management triangle has been introduced highlighting that along with the three constraints competing with each other, they also interact to form a fourth dimension of quality.If you need to complete your doctoral programme within a specified time frame, then you need to manage your goals and scope mercilessly—do not allow additional research questions or extra experiments to take away precious time. This does not mean that you cannot deviate, but any deviations need to be managed. Remember, whether you wish to remain in scientific research or not, the PhD is a stepping-stone to your future career and not the end goal in itself. Once you have achieved the goals agreed with your supervisor, it is more beneficial for you to write-up your doctoral thesis and move on [2].Good communication is essential in every area of work, but even more so for a PhD as you are simultaneously learning how to research along with doing the research. Often, access to your supervisor is limited by constraints on his/her or your time, which means that clear communication is vital. Do not assume that your supervisor knows every intricate detail of what you are doing; he or she might have a large group in which each member is looking at complementary aspects of a more general topic. It is, therefore, your responsibility to ensure that all your stakeholders—supervisors, postdoc leads and any others involved—know what you are doing and, more importantly, why you are doing it.This is another area in which the apt use of technology can maximize efficiency. Subject to institutional licensing, collaboration tools such as SkillsForge or Evernote can improve communication between stakeholders. For example, meeting minutes, action points to be followed and research results can be uploaded for sharing. Supervisors can then review the material at a convenient time to ensure that they stay up to date with the progress of each student within their research group.As PhD students usually aspire to become research scientists, it is of paramount importance that you learn the correct application of the scientific method and the context in which your work is being done. Before jumping into practical work—wet-lab experiments or computational modelling—it is important to understand the meaning and relevance of your project in relation to existing knowledge and the underlying science. For example, the hypothesis-driven research life cycle in systems biology [3,4]—my own field—advises that computational models should be developed on the basis of wet-lab data relating to the underlying biological system. Almeida-Souza and Baets state that a PhD in science is an opportunity to learn how to tackle problems scientifically and, as such, requires the development of skills in critical thinking, hypothesis formulation and experimental design [5]. I believe that the requirement for these skills is universal across the sciences, and that molecular biosciences and computational systems biology are no different.The serious consideration of scope is necessary in any project, but even more when you are simultaneously project manager, research scientist and key stakeholderTherefore, before the first wet-lab experiment is performed, or the first line of code is written, it is essential that we understand why the experiment is important and what results we might expect to support our initial hypotheses. Furthermore, regarding computational systems biology, I believe that it is also essential for wet-lab and computational researchers to collaborate to ensure both have a consistent understanding of the data and the purpose of the computational model. After all, for the most part, computational models are developed for their predictive capacities and to allow hypothesis generation for subsequent wet-lab experimentation. Baxter et al have extensively covered this area and advocate not only designing the project up-front, but also the need for quality control [6].You need to manage the scope and goals of your PhD mercilessly and, at the same time, be flexible enough to grasp new opportunities. Conversations at conferences, for instance, can open up opportunities for collaboration and take your research in a direction that you had not considered previously. In my case, I was invited to turn a conference paper relating to my masters degree into a full paper for a special issue of a well-known bioinformatics journal. Although it was not related to my doctoral research, the prospect was too good to turn down. I therefore discussed the idea with my PhD supervisor, and once we were in agreement, I updated the project schedule to incorporate this new activity, trying to mitigate as much as possible the resulting slippages to my doctoral research. In essence, I had performed an impromptu risk–reward analysis and decided that the reward that would be gained from publishing this work outweighed the risk of a slight overrun of my PhD thesis. It must be noted that I was lucky in this instance, as my PhD supervisor also supervised the research project during my master''s degree, so a full paper would be beneficial for both of us.A project risk is “an uncertain event or condition, that if it occurs, has an effect on at least one project objective” [1]. The positive side to risks is that the likelihood of their future occurrence can be mitigated by planning in the present. Once a risk is realized, however, and its effects begin to be felt, it has turned into a project issue. The first step in trying to manage risks is their identification. Risk identification in this context is the process of determining which events, if they occurred, would affect your research. In the context of a molecular biosciences PhD, I believe that general risks relate to access to resources, such as people—postdocs and collaborators, for example—reagents, cell lines and shared equipment. For example, if your work uses fluorescent proteins within single cell analysis, how would you be affected if the fluorescence microscope was booked out by another research lab? Similarly, in computational systems biology, if the design process for your computational model requires access to wet-lab data, what would the effect(s) be if this was not available?Once risks are identified, it is important to develop risk response plans. By using the above example of access to a microscope, what should your response be if you cannot gain access? The initial risk response would be to liaise with the other research lab to understand their requirements and ascertain whether you could gain access at a mutually convenient time. Alternatively, another approach might be to work outside normal office hours, either throughout the evenings or on the weekend, subject to health and safety procedures at your institution and your own health and well-being. I believe that a degree of creativity is often required when developing effective risk response plans.A PhD thesis is a hefty document that might run to many hundreds of pages. They are generally not written as a single large document from start to finish, but as chapters. In the molecular biosciences, a thesis consists of an initial literature review early in the doctoral programme, work-in-progress documents for materials and methods, experimental results throughout the middle section, which is followed by analysis and critical evaluation towards the end of your experimental work. Whether through software tools or through your own manual methods, such as keeping a configuration log and keeping a copy of each version of your working documents, it is essential that you maintain an up-to-date repository of all your notes. I have found through experience that it is beneficial to save not only the final versions, but also each of the working drafts of documents generated throughout your PhD. Ideas previously discounted, and thus removed from more recent versions of documents, might once again take centre stage at a later date.The positive side to risks is that the likelihood of their future occurrence can be mitigated by planning in the presentThis can be aided through the development and use of a project library with a logical folder structure to facilitate easy access to documentation. Noble [7] provides an in-depth discussion of organizing your computational biology project—in particular the value of version control—but the concepts are transferable across disciplines. Furthermore, do not forget to back-up your work, and without seeming too pessimistic, back-up your back-up!Finally, look after the most important resource: you. Exercise, diet, alcohol, caffeine and holidays all affect your well-being. Holidays and time away from the lab or office allow you to take a step back from the detail and reflect on your experiences and progress. Sometimes, time off allows you to process issues subconsciously and develop new approaches to overcome problems that you have been tackling for extended periods of time without success. Finally, holidays also help you recharge your batteries and enthusiasm to return to your project with fresh vigour. If you have sensibly and reasonably planned time off alongside your work, you will be able to enjoy it.Although a PhD requires consistent commitment, you simply cannot—and should not—work at full capacity all of the time. Issues arise periodically throughout any project, and if you have no reserves of energy—either mental or physical—you will be unable to tackle them head on with the step change of performance that is required. Furthermore, doctoral research is a marathon and not a sprint; we all experience the symptoms of burnout from time to time, and sometimes it is better to walk away for a short period to recharge than to carry on, become stale, and ultimately slow down.To conclude, I wish you good luck with your doctoral research, and I hope these techniques help you to manage your PhD project through to successful completion.? Open in a separate windowRichard Alun Williams     

A Tale of Mother and Daughter

Loving science and nature and being a scientist can be very different, yet the two are so intertwined in a scientist''s life that you will certainly experience both aspects. This essay presents my perspective on how, as one who loves science and nature, I came to fall in love with centrosome behavior in stem cells and how I came to run a lab as a scientist. When I started, there was a big gap between my love for science and my experience as a scientist. I filled this gap by learning a “laid-back confidence.”Before the beauty of cell biology (or whatever you love), who you are (i.e., your age, gender, or race) is immaterial. Yet history shows that the ease with which you can pursue science is influenced by who you are. This has certainly been my experience. The key is to find a way to fill in the gap between who you are and what you are (i.e., a scientist), a goal in which we must all support each other. It is my hope that this essay will convey something helpful to those who are at early stages of their career and might be encountering obstacles because of who they are.     

Pedagogy of the Black academic

I am just starting my career as a cancer biologist, but I have always been a Black man in America. This means that I have always inhabited a world that generally disregarded my existence in some form or another. It is June 17th, 2020 and protests have been happening for weeks since the killing of George Floyd in Minneapolis. The current state of America may be uneasy for some, but for many Americans, the looming threat of exclusion and violence has been an unwelcome companion since birth. This letter is not about a single person, but the Black academic’s experience of race inside and outside of the academy during a time of social upheaval. I have trained in a variety of institutions, big and small, and all the while acutely aware of the impact of my Blackness on my science. The intent of the following is to provoke the reader to reflect on how we as a nation can move toward radically positive change and not incremental adjustments to the status quo. The views expressed are my own and are the result of years of personal experience observing the anti-Black standard in America.

About the AuthorI am currently a cancer biologist at the University of Minnesota Medical School. My lab works to eliminate cancer health disparities in African Heritage communities and investigates the roles of lipids in modifying the immune response in tumors. This is what I do, but not all of who I am. I am also the eldest child of a mother, who managed to convince me that she had eyes in the back of her head (thank you, Mom; it kept me honest). I am a big brother, a husband, and a father. I also consider myself a fortunate Black man in America. I grew up in places where many of my friends did not live to adulthood. If they managed to survive past adolescence, it was usually their dreams that died prematurely. I was lucky to have survived and to continue chasing my dream of becoming a scientist. I never considered myself the fastest, strongest, or even smartest kid growing up, but I was the most determined. Determined, despite the lack of access to role models in science that looked like me or shared my life experience. Now my mission is to increase the number of dreams achieved and impact as many young minds as my time on this planet permits.As a Black scientist, I sometimes have to remind myself that I have never been immune to racism. Because as you spend thousands of hours delving into the microscopic world, the macroworld starts to fade into the background like white noise. And if you get good at it, you almost forget about the strange looks, the excessive questioning, or even the obligatory “tailing” in stores, on campus, or at home. But it is strange to realize how much you have grown accustomed to discrimination and the fact that you unconsciously prepare for it daily, before it ever shows its ugly head, like a prize fighter training months before a fight.This past month, amid the Coronavirus Disease 2019 (COVID-19) pandemic, the rest of the world has decided to say police are bad, and oh, by the way, Black lives matter too—as if the oppression of Black bodies was new, or as though the recent string of names added to the ever-growing list of innocent Black Americans killed by authorities is an atypical occurrence. Well sadly it is not, and it never has been in this country or any other place with colonial origins. That is the truth, and there is no other way to state it. America is a country built on and driven by racist ideology.So, as a Black American in an “essential” worker role (I am now working on COVID–19-related research), I have physically been at work daily during the pandemic, as the spirit of solidarity sweeps the globe. As much as I want to say this is progress, I find myself asking “why now, and not then?” Why didn’t this happen when Trayvon Martin was murdered; why didn’t this happen when Rodney King was beaten (Alvarez and Buckley, 2013; Mullen and Skitka, 2006)? Is it a sign of the end times, or is it just that racism/White supremacy has finally run its course?I have a theory about why we are now seeing a mass movement against discrimination and police brutality (a.k.a. state-sanctioned murder). My theory states that had it not been for COVID-19 and the nationwide shutdown of normal life, none of this protesting would even be feasible. Why do you ask? The simple answer is that some people with the financial means can normally find ways to distract themselves with various activities, some noble and some … not so much, whereas other folks are less able to disconnect from the drudgery of hand-to-mouth living. Leave it to a global health crisis to reprioritize everyone’s entire life in one fell swoop. Suddenly, people who had vacation plans are stuck at home, whereas people who were just making ends meet are now unable to make those ends meet anymore. The haves and the have-nots are now both in an altered reality. Does this make them equal now? No, but it does allow people to see who their real friends, allies, and enemies are. I suspect that it’s the pulling back of the curtain that has made many people ready to fight, not to mention it is also very likely that many folks, after experiencing weeks of cabin fever, just needed some way to let off all that pent-up energy.Before COVID-19 became a full-time concern, tensions in the United States were already high as the recent killings of unarmed Black Americans (Breonna Taylor and Ahmaud Arbery) had gone viral and cries for justice echoed from coast to coast (Lovan, 2020). Once the reality of the pandemic set in and shelter-in-place orders were issued nationally, the situation became a powder keg waiting for just the right moment. That moment happened in North Minneapolis on May 25, 2020. With the release of the video showing the killing of George Floyd, the entire country and much of the world had a reason to go on a “righteous rampage” that has seemed to get the results some thought impossible to achieve. It cannot be overstated how critical social media has been in displaying the oppression of Black Americans at the hands of authorities to the entire world.Now, several months into the protests, the possibility of a “new’’ new normal has people dreaming of singing Kumbaya in technicolor. Yet, as one of the few Black faculty on my campus, I still feel like people are watching me, but for a different reason now. As various reforms are broadcast across the university, the random wellness “check-ins” start creeping in, and the requests for feedback on “new initiatives’’ seem to be like a new flavor of spam in my inbox.Now, I do appreciate the fact that people are starting to notice the oppressive nature of not being White in today’s world (in particular being Black in America), but I have been doing this for a while now, and I am not sure if hashtagged initiatives are healthy for anyone. Plus, it’s kind of creepy watching all of these people jump on the social justice bandwagon, when they weren’t here 4 mo ago or 4 years ago. For many Black academics, it is not about being involved with something when it’s trending; it’s about being “about that life” when it is inconvenient as hell. Again, I do appreciate the fact that more people are willing to fight oppression, racism, and White supremacy (even if only digitally), but you will have to forgive me if I do not trust you just yet. I mean, you are just checking in during what could be the last leg of a marathon, and we’ve been running this whole damn time!Here is a short answer to every wellness check-in email that many of the Black academics I know have received in the last 2 mo: “we were never okay in the first place, but thanks for FINALLY asking!” We don’t need any more bias training, hashtags, or email check-ins. It was a nice start, but it too has become a part of the status quo. The work now and always has been the eradication of underrepresentation, hurtful socialization, and ridiculously skewed power dynamics, not just the awareness of the fact. I don’t have all the answers, but if real change is desired, I think we can first start by teaching history accurately to EVERYONE, no more whitewashing the reality of America’s story and ignoring the contributions of Black academics (and Black Americans in general). Second, stop being silent when you see or hear racism at work or home. If you do nothing when racism shows up, you ARE a racist! Third, the privileged class must relinquish their “privilege” once and for all. That means the powers that were inherited based on historical (and present day) theft and oppression have to dissipate, with the ultimate goal of power sharing. The country club atmosphere of academia and the “fit culture” must erode in favor of true meritocracy. The best person for the job and not “the person who won’t make me uncomfortable by making me see my own deeply held prejudices and fears.”Honestly, Black academics SHOULD not be charged with the task of fixing broken systems, along with protecting themselves and mentees, while working toward tenure. But if we (Black academics) are not driving the car, progress will likely go the wrong way again (getting rid of Uncle Ben and Aunt Jemima does not correct the underlying pathology). Paulo Freire’s Pedagogy of the Oppressed speaks to this in saying, “the violence of the oppressors prevents the oppressed from being fully human, the response of the latter to this violence is grounded in the desire to pursue the right to be human … the oppressed, fighting to be human, take away the oppressors’ power to dominate and suppress, they restore to the oppressors the humanity they had lost in the exercise of oppression.” (Friere, 1972, p. 56). This means that if we (Black academics) want to be treated as humans and as scholars, we must show you what that humanity looks like FIRST. Now the question is, are you willing to learn or are you going to co-opt this moment, this movement to make it into something that fits your preconceived notion of the acceptable levels of Blackness in the academy?     

Reply to Rosenberg

I respond to two of the main arguments in Rosenberg’s commentary on “Mind, Matter, and Metabolism.” Rosenberg’s claim that metabolic activities are “modularized” in a way that sets them apart from cognitive processes is not true given the broad sense of the “metabolic” employed in my paper, and contemporary neuroscience, including the work on navigation cited by Rosenberg, has begun to yield an understanding of subjectivity and “point of view.”     

Welcome by the Dean Henrik Jeppesen at the 8th International Symposium on Tardigrada

Mr. Chairman. Distinguished ladies and gentlemen. As Dean of Science it is a great honour on behalf of the University of Copenhagen and the Faculty of Science to welcome all of you here to the 8th International Symposium on Tardigrada. We are especially happy to have you here at the August Krogh Institute (named after our well-known Nobel Prize winner in Physiology), because on September 1st we celebrate the establishment of the Faculty. So coming here and honouring our 150 year anniversary jubilee help us to promote the importance of science in our society. The University was founded in 1479 as a theological catholic school. It broke down in 1530 and was reestablished in 1537 after the reformation. Right from the start in 1479 there was science thought of at the university. Mathematics and Astronomy. And Zoology became a subject over the centuries together with other subjects which are today regarded as science. But only in 1850 did we become an independent Faculty thanks to the effort and progress done by the Danish Chemist H.C. Ørsted.The animals, which you study, are marvellous in the sense that they can survive under severe conditions for centuries. Under extreme dry conditions in Sahara, in extreme cold conditions (they can survive minus 273 °C, or survive in vacuum). This has practical implications for people who need to excuse their scientific interest, for medicine if we can freeze human tissue, or for space study how to survive under extreme conditions. The study of Tardigrada is an important field here at the Institute of Zoology, at the Zoological Museum, and at the University of Roskilde, 30 km west of Copenhagen. Some of our most distinguished zoologists take part in this research. That might be the reason why you have chosen to have the symposium here in Copenhagen. They are doing research on tardigrades in marine areas, and in Greenland on the ice cap. Especially interesting are the studies done in the Ikka Fjord in Greenland, where the unique Ikkaite Tufa columns made of calcium carbonate hexahydrate originating from alkaline cold springs at the bottom of the fjord create very specific environments with nearly brackish conditions in the center and sea water salinity on the outside. And this creates varied conditions for different species of Tardigrada.We also celebrate this year the 50th anniversary of the 2. Galathea expedition which went round the world and specifically looked for deep sea fauna. There are Tardigrades here. It has been interesting to look through the 54 abstracts in the programme and read the names and work places for the 65 participants listed. In English tardigrades are called water bears, in Danish “bjørnedyr” meaning bear animals. I prefer the Danish version, this sounds more like pet bears.The symposium is followed by a field trip to the faculty's research station on Disko in Greenland. In 1994 I arrived on the new research vessel “Porsild” to Disko to deliver the new boat some of you will sail in during the workshop up there. I stayed there some days, and there was this man Professor Reinhardt Møbjerg Kristensen, looking into his microscope. It was fascinating to see the joy which he expressed explaining his animals. His engagement was so impressive and his talk so marvellous. It was really his pet animals he caressed all day and night. If all of you are looking on the water bears with the same fascination and engagement, then this will be one of the most entertaining symposiums ever held. One can fear that you are so engaged that you will forget everything around you, even to listen to the contributions of the others, and to be careful that maybe a new group will be announced.I wish you some very good days here at the Faculty of Science and some very fruitful days. I should like to thank the sponsors of the meeting, The Danish Science Foundation, The Carlsberg Foundation and Dr. Bøje Benzon Foundation. I would like to express my gratitude to the organizing committee for attracting the conference here and making the programme so wide and interesting. I can promise the committee will do all their best to help you all way through. And for those going to Disko — you will have a most splendid experience.I shall ask my colleagues at my own institute, Geography, to arrange some bad weather except on Thursday where you join the excursion. This to prevent you from sneaking away and enjoy the wonders of Copenhagen.By this once again welcome and a wish for a fruitfulconference.     

After 2 years of a pandemic,students are struggling to find strong reference letters

Writing and receiving reference letters in the time of COVID. Subject Categories: Careers

“People influence people. Nothing influences people more than a recommendation from a trusted friend. A trusted referral influences people more than the best broadcast message.” —Mark Zuckerberg.

I regularly teach undergraduate courses in genetics and genomics. Sure enough, at the end of each semester, after the final marks have been submitted, my inbox is bombarded with reference letter requests. “Dear Dr. Smith, I was a student in your Advanced Genetics course this past term and would be forever grateful if you would write me a reference for medical school…” I understand how hard it can be to find references, but I have a general rule that I will only write letters of support for individuals that I have interacted with face‐to‐face on at least a few occasions. This could include, for example, research volunteers in my laboratory, honors thesis students that I have supervised, and students who have gone out of their way to attend office hours and/or been regularly engaged in class discussions. I am selective about who I will write references for, not because I am unkind or lazy, but because I know from experience that a strong letter should include concrete examples of my professional interactions with the individual and should speak to their character and their academic abilities. In today''s highly competitive educational system, a letter that merely states that a student did well on the midterm and final exams will not suffice to get into medical or graduate school.However, over the past 2 years many, if not most, students have been attending university remotely with little opportunity to foster meaningful relationships with their instructors, peers, and mentors, especially for those in programs with large enrollments. Indeed, during the peak of Covid‐19, I stopped taking on undergraduate volunteers and greatly reduced the number of honors students in my laboratory. Similarly, my undergraduate lectures have been predominantly delivered online via Zoom, meaning I did not see or speak with most of the students in my courses. It did not help that nearly all of them kept their cameras and microphones turned off and rarely attended online office hours. Consequently, students are desperately struggling to identify individuals who can write them strong letters of reference. In fact, this past spring, I have had more requests for reference letters than ever before, and the same is true for many of my colleagues. Some of the emails I have received have been heartfelt and underscore how taxing the pandemic has been on young adults. With permission, I have included an excerpt from a message I received in early May:Hi Dr. Smith. You may not remember me, but I was in Genome Evolution this year. I enjoyed the class despite being absent for most of your live Zoom lectures because of the poor internet connection where I live. Believe it or not, my mark from your course was the highest of all my classes this term! Last summer, I moved back home to rural Northern Ontario to be closer to my family. My mom is a frontline worker and so I''ve been helping care for my elderly grandmother who has dementia as well as working part‐time as a tutor at the local high school to help pay tuition. All of this means that I''ve not paid as much attention to my studies as I should have. I''m hoping to go to graduate school this coming fall, but I have yet to find a professor who will write a reference for me. Would you please, please consider writing me a letter?I am sympathetic to the challenges students faced and continue to face during Covid‐19 and, therefore, I have gone out of my way to provide as many as I can with letters of support. But, it is no easy feat writing a good reference for someone you only know via an empty Zoom box and a few online assignments. My strategy has been to focus on their scholarly achievements in my courses, providing clear, tangible examples from examinations and essays, and to highlight the notable aspects of their CVs. I also make a point to stress how hard online learning can be for students (and instructors), reiterating some of the themes touched upon above. This may sound unethical to some readers but, in certain circumstances, I have allowed students to draft their own reference letters, which I can then vet, edit, and rewrite as I see fit.But it is not just undergraduates. After months and months of lockdowns and social distancing, many graduate students, postdocs, and professors are also struggling to find suitable references. In April, I submitted my application for promotion to Full Professor, which included the names of 20 potential reviewers. Normally, I would have selected at least some of these names from individuals I met at recent conferences and invited to university seminars, except I have not been to a conference in over 30 months. Moreover, all my recent invited talks have been on Zoom and did not include any one‐on‐one meetings with faculty or students. Thus, I had to include the names of scientists that I met over 3 years ago, hoping that my research made a lasting impression on them. I have heard similar anecdotes from many of my peers both at home and at other universities. Given all of this, I would encourage academics to be more forthcoming than they may have traditionally been when students or colleagues approach them for letters of support. Moreover, I think we could all be a little more forgiving and understanding when assessing our students and peers, be it for admissions into graduate school, promotion, or grant evaluations.Although it seems like life on university campuses is returning to a certain degree of normality, many scholars are still learning and working remotely, and who knows what the future may hold with regard to lockdowns. With this uncertainty, we need to do all we can to engage with and have constructive and enduring relationships with our university communities. For undergraduate and graduate students, this could mean regularly attending online office hours, even if it is only to introduce yourself, as well as actively participating in class discussions, whether they are in‐person, over Zoom, or on digital message boards. Also, do not disregard the potential and possibilities of remote volunteer research positions, especially those related to bioinformatics. Nearly, every laboratory in my department has some aspect of their research that can be carried out from a laptop computer with an Internet connection. Although not necessarily as enticing as working at the bench or in the field, computer‐based projects can be rewarding and an excellent path to a reference letter.If you are actively soliciting references, try and make it as easy as possible on your potential letter writers. Clearly and succinctly outline why you want this person to be a reference, what the letter writing/application process entails, and the deadline. Think months ahead, giving your references ample time to complete the letter, and do not be shy about sending gentle reminders. It is great to attach a CV, but also briefly highlight your most significant achievements in bullet points in your email (e.g., Dean''s Honours List 2021–22). This will save time for your references as they will not have to sift through many pages of a CV. No matter the eventual result of the application or award, be sure to follow up with your letter writers. There is nothing worse than spending time crafting a quality support letter and never learning the ultimate outcome of that effort. And, do not be embarrassed if you are unsuccessful and need to reach out again for another round of references—as Winston Churchill said, “Success is stumbling from failure to failure with no loss of enthusiasm.”