A career pathway in protein folding: from model peptides to postreductionist protein science

This review discusses the inherent challenge of linking "reductionist" approaches to decipher the information encoded in protein sequences with burgeoning efforts to explore protein folding in native environments-"postreductionist" approaches. Because the invitation to write this article came as a result of my selection to receive the 2010 Dorothy Hodgkin Award of the Protein Society, I use examples from my own work to illustrate the evolution from the reductionist to the postreductionist perspective. I am incredibly honored to receive the Hodgkin Award, but I want to emphasize that it is the combined effort, creativity, and talent of many students, postdoctoral fellows, and collaborators over several years that has led to any accomplishments on which this selection is based. Moreover, I do not claim to have unique insight into the topics discussed here; but this writing opportunity allows me to illustrate some threads in the evolution of protein folding research with my own experiences and to point out to those embarking on careers how the twists and turns in anyone's scientific path are influenced and enriched by the scientific context of our research. The path my own career has taken thus far has been shaped by the timing of discoveries in the field of protein science; together with our contemporaries, we become part of a knowledge evolution. In my own case, this has been an epoch of great discovery in protein folding and I feel very fortunate to have participated in it.     

Gaia Pigino: Inside the cell

Gaia Pigino studies the molecular mechanisms and principles of self-organization in cilia using 3D cryo-EM.

Gaia Pigino was only 3 yr old when she became fascinated with nature in the beautiful countryside of Siena, Italy, where she grew up. The neighbor’s daughter showed her a hen in the chicken coop, and they caught it in the act of laying an egg. Gaia remembers, “This was for me almost a shock, as my experience about eggs was that they come directly out of paper boxes!” Her father was also an important part of awakening Gaia’s curiosity for the amazing things in nature. He used to bring home the award-winning magazine Airone, the Italian equivalent of National Geographic. Gaia never missed an issue; even before learning to read, she could spend hours looking at the captivating photos of the wildlife. She wanted to understand what she was seeing, and maybe because of that, she was determined to do science.Gaia Pigino. Photo courtesy of Human Technopole.Gaia took her first “scientific” steps with Professor Fabio Bernini and Professor Claudio Leonzio at the University of Siena, where she studied bioindicators of soil contamination and detoxification strategies of soil arthropods as part of her PhD project. But it was later, when she joined the laboratory of Professor Pietro Lupetti and met Professor Joel Rosenbaum, a pioneer of cilia research, that Gaia discovered the world of 3D EM and felt her place was “inside a single cell.” She solidified her interest in the structure of protein complexes of cilia and flagella and boosted her passion for cryo-electron tomography (ET) in the laboratory of Professor Takashi Ishikawa, first at the ETH Zurich and then at the Paul Scherrer Institut in Switzerland. In 2012, Gaia started her own laboratory at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, Germany, with the vision of creating a truly interdisciplinary laboratory. Her team combines techniques from different fields such as biophysics, cell biology, and structural biology to answer open questions in the cilia field. Gaia recently moved countries again—this time to take over the position of Associate Head of the Structural Biology Research Centre, at the Human Technopole, Milan, Italy.We reached out to Gaia to learn more about her scientific journey and future research directions.What interested you about cilia?The first thing that attracted me toward cilia and flagella were some EM micrographs, by Professor Romano Dallai in Siena, that showed the beautiful geometrical microtubular structures of sperm flagella. I was intrigued by the apparent perfection of these organelles that clearly showed me that a cell is a coordinated system of complex molecular machines, the mechanism of many of which we do not understand. Soon after, Professor Joel Rosenbaum introduced me to the bidirectional transport of components inside cilia, which, he explained to me, is required for both assembly and function of virtually all cilia and flagella, from the motile cilia in our lungs to the primary cilium in our kidneys. He called it intraflagellar transport (IFT) and compared it to a Paternoster elevator, where the individual cabins were what we now call IFT trains. I was completely fascinated by the IFT system, the structure, the function, the dynamics, and the mechanism of which were still largely unknown. Quickly, I realized that in addition to IFT, cilia represent a virtually infinite source of open biological questions waiting to be solved, from the mechanics and regulation of the beating to the sensory function of primary cilia, and their importance for human health.What are some of the scientific questions currently of interest in your laboratory?In the past few years, we have made substantial contributions to the current understanding of the structure and the mechanism of the IFT (1, 2, 3). Currently, we are investigating how the structure of IFT trains relates to their functions by looking, in cryo-electron tomography, at how anterograde trains transform into retrograde trains and at how different ciliary cargoes are loaded on the trains. Beside this more classical line of research, we are exploring other approaches to study IFT, for instance we have developed a method to reactivate IFT trains in vitro on reconstituted microtubules. We want to use this approach to investigate the behavior of IFT trains, and their motors, in experimentally controllable conditions, e.g., in the presence of only certain tubulin posttranslational modifications. We have also made interesting discoveries about the distribution of tubulin posttranslational modifications on the microtubule doublets of the axoneme and how this spatially defined tubulin code affects the function of different ciliary components. We hope we will be able to share these new “stories” with the structural and cell biology community very soon!What kind of approach do you bring to your work?I believe that the main reason for why science became an integral, and dominant, part of my life is because it provides infinite riddles and continuous challenges. I have always been curious about how things work in nature, but I quickly realized that learning from books didn’t satisfy me. My desire was to be at the frontline, to be among the ones that see things happening in front of their eyes, at the microscope, for the first time. I wanted to be among the ones that make the discoveries that students read about in textbooks. Thus, what I bring to my work is an endless desire of solving biological riddles, curiosity, creativity, determination, and energy, with which I hope to inspire the members of my team. My laboratory uses an interdisciplinary approach; we use whatever method, technique or technology is needed to reach our goal, from the most basic tool to the most sophisticated cryo-electron microscope. And if the method we need does not yet exist, we try to invent it.A young Gaia Pigino (3 yr old) the day she discovered how eggs are made. Photo courtesy of Giancarlo Pigino.Could you tell us a bit about the Structural Biology Research Centre at the Human Technopole (HT)?At the HT Structural Biology Centre, we are working to create a vibrant and interdisciplinary scientific environment that will attract molecular, structural, cell, and computational biologists from all over the world. We are creating fantastic facilities, including one of the most well equipped and advanced electron microscopy facilities in Europe—and likely the world—headed by Paolo Swuec. My team, together with the teams of my colleague Alessandro Vannini and the research group leaders Ana Casañal, Francesca Coscia, and Philipp Erdmann, already cover a vast range of competences and know-how from classical molecular and structural biology approaches, such as crystallography and protein biophysics, to cryo-CLEM, cryo-FIB SEM and cryo-ET, all of which allow us to address questions in cell biology. Our goal is to create a scientific infrastructure and culture that will enable biologists to obtain a continuum of structural and functional information across scales.What did you learn during your PhD and postdoc that helped prepare you for being a group leader? What were you unprepared for?I learned that everyday research is mostly made of failures, but that with the right amount of obsession, persistence, curiosity, and creativity, it is always possible to succeed and discover new things. Being given the freedom to develop your own ideas and your own project very early in your career is a treat; science is not only about having good ideas! One needs to follow up on these ideas with intense work and troubleshooting to make them reality. In addition, I realized that being fearless and attempting what is considered too difficult by others, despite challenges, can turn into a worthy learning experience. Also, how you present your work to the scientific community matters for swinging the odds of success in your favor. Different places might work in very different ways, and conducting good science does not only depend on you, but also on the possibilities given to you by your environment.What was I unprepared for?—I guess several things, but one comes immediately to mind: I underestimated how much being responsible not only for my own life and career, but also the career of students, postdocs, and others in the laboratory, would affect me personally.Structure of the 96-nm axonemal repeat reconstructed by cryo-ET and subtomogram averaging. Image courtesy of Gonzalo Alvarez Viar, Pigino Lab.What has been the biggest accomplishment in your career so far?This is a tricky question for me... I tend to look into the future more than celebrating the past. I fight to succeed in something, but as soon as I conquer it, I find it less of an achievement than the thing I could conquer next. Nevertheless, I am happy about the discoveries and the papers published together with my students and postdocs (1, 2, 3, 4, 5). I am extremely excited about the fact that after many years of work I am now leading an interdisciplinary laboratory, where we combine techniques from different fields. I am also happy that three times my husband and I were able to move from one world class academic institution to the another to start exciting and fitting jobs and could still live together in the same place. We worked hard for this, but we also got lucky.What has been the biggest challenge in your career so far?I studied French in school; I had almost no exposure to spoken English until the end of my PhD. To avoid having to show my English insufficiencies, I did hide beside the board of my poster at the first international conference I attended in 2004! It took me a while to overcome this barrier and feel confident to express my thoughts and ideas in English.What do you think you would be if you were not a scientist?I had been a good fencer during my youth. I was a member of the Italian National Team between ages 14 and 19 and saw quite a bit of the world, which was cool! When my sporting career failed, due to diabetes, I was torn between art and science. I guess that in a parallel universe, I am a wildlife photographer and a potter specialized in wood kiln firing. [Gaia confesses that she misses “the amazing and addictive adrenaline rush of a good fencing match!”]Any tips for a successful research career?Do not compare your performances to the ones of the people at your career stage; compare yourself with people that are already successful one level higher than you currently are at. For example, if you are a PhD student, ask yourself what in your current performance separates you from being a good postdoc—once a postdoc, what is missing to be a good PI.     

Kinship vis-à-vis Myth Contrasts in Lévi-Strauss' Approaches to Cross-Cultural Comparison

The enormous secondary literature which relates Lévi-Strauss' comparative studies to different schools of thought has failed sufficiently to emphasize the major discontinuity within his own work. This paper characterizes the basic methodological differences in his approaches to "kinship" and to "myth." It then suggests how, by concentrating on the kinship/myth distinction, we might constructively refine various structuralist concepts, such as distinctive feature analysis and the logical foundations of the "elementary" kinship structures. Only by concentrating on the few inconsistencies in Lévi-Strauss' remarkably coherent corpus of work can an adequate critique of his theories of comparison be commenced.     

A year since George Floyd

The murder of George Floyd sparked an awakening, long overdue, which reverberated throughout society. As science begins to acknowledge its role in perpetuating systematic racism, the voices of Black scientists, which have largely been absent, are now being called on. As we rightly begin to make space for diverse voices and perspectives in science, we all must think about what it is we are asking minoritized individuals to do.

It has been roughly 1 year since the murder of George Floyd, an unarmed Black man, who was killed over an alleged counterfeit 20 dollar bill in Minneapolis, Minnesota (Hill et al. 2020; Kaul, 2020; Levenson, 2021). In many ways, his murder was no different than the murders of thousands of other murders of Black people in this country (Thompson, 2020; Lett et al., 2021; Tate et al., 2021). However, what distinguishes George Floyd’s murder from many other high profile cases is that it was unambiguously captured on video (Alexander, 1994), an act of bravery by Darnella Frazier, a 17-year-old Black woman (Izadi, 2021), at a time when the world was mostly housebound by a raging global pandemic. As a result, his murder reverberated through society in a way that has not happened in my lifetime. While there have been other high profile cases of murders carried out by police (Treyvon Martin, Walter Scott, Breonna Taylor, and Philando Castile, among many others), these cases failed to fully sustain the attention of a national and international audience (Chan et al., 2020; Chughtai, 2021). The murder of George Floyd was fundamentally different, and for once, more than just Black people were paying attention. His murder sparked protests across the nation led by the Black Lives Matter (BLM) movement (Day, 2015; Taylor, 2016; Banks, 2018; Taylor, 2021), and the demands for change were so loud people could not help but hear.As a Black, gay man who is also a scientist, I was thrown into despair. All of my life I have thought if I just worked hard enough, if I am kind and unthreatening, if I play the game and keep my head down, maybe I can make it in academia. Maybe then I will be seen and accepted, not just by society, but by the scientific community. George Floyd’s murder reminded me, and many of my Black colleagues, that our degrees can’t protect us, that our privileged middle-class upbringing (if we had one) was not a shield. Our lives were not worth more than a counterfeit 20 dollar bill.Science, which has always been a product of society, was not impervious to these reverberations. By late June my inbox began to slowly fill with invitations to speak at several institutions for their seminar series, retreats, or special symposia. It felt as if the scientific community, for the first time, realized that there were Black scientists among them. In the throes of my own despair, and the feeling that I needed to be doing something for my community, I began to say “yes.” I was not going to participate in the nightly protests that occurred in my newly adopted hometown of Portland, Oregon. Aside from fearing I could be next to lose my life at the hands of the police (Edwards et al., 2019), these protests were happening in the backdrop of a global pandemic. I came to the conclusion that by accepting these invitations to speak, this could be my activism, my way of sparking change, increasing visibility, and being seen not only for my own sake but also for other Black scientists.Before I write anything else, I want to be clear: I am extremely thankful to all the institutions and organizations that invited me and gave me a platform. I am extremely proud of my students’ work and of the research we produce. I am sharing my experiences with the hope that they can be instructive to the greater scientific community, but if I am being frank, there is a bit of anger.I received over 15 invitations and gave an additional three or four interviews over the course of the year. Most of these came with the expectation that I would also talk about my work in Diversity, Equity, and Inclusion. But here’s the lowdown: prior to this year, I did not view myself as someone who did Diversity, Equity, and Inclusion work. I am co-chair of the LGBTQ+ committee of the American Society of Cell Biology and a member of the Diversity, Equity, and Inclusion committee of the Genetics Society of America. I volunteer for both of these committees because they speak to something I care deeply about, the advocacy for minoritized ¹ scientists. I also embody both of these axes of diversity; so, in some way, I am only looking out for myself. This is far from being a scholar or doing “Diversity work.” I fully recognize that there are individuals who have dedicated their lives to this type of work with entire academic fields populated with accomplished scholars. So, I started this year of talks being invited because I am a Black, gay scientist at a time when science was grappling with its own systematic racism, under the guise of my nonexistent Diversity, Equity, and Inclusion work.What has this year actually taught me? The first thing it taught me is that I have been missing out. Prior to George Floyd’s murder, I had only received three seminar invitations from major research institutions and unfortunately all within a year of being posttenure. That is after nearly 6 years in my current position.In giving these talks I got the opportunity to meet with some of the giants in my field, people I have looked up to for years. I received reagents, offers to collaborate, and a litany of great ideas that will help drive my research program for years to come. I left some of these meetings truly inspired and excited to start experiments. These opportunities would have been invaluable to me, pretenure. One could argue, I did not need it. I made it even without this networking and the advantages these visits bring. Before you applaud my ability to persist and be resilient, we should take a deep look at the systems that have forced people who look like me to be doubly resilient. If George Floyd had not been murdered, would any of these invitations have happened? If the previous 6 years are any indication of a trend, I would have to say most certainly not. Why did it take a murder and the reignition of a Civil Rights movement for me to have the type of interactions I now know many of my straight, white counterparts have had from the very beginning of their independent careers? Let me be clear: this is a form of systematic racism, plain and simple.As I began to make the rounds, I was often asked to either share a bit of my journey or include my Diversity, Equity, and Inclusion work in my talks. This sometimes came at the expense of sharing my lab’s work. While I was very happy to do so, this was very much implicit in the invitations I received. At times it did feel that my inclusion was only checking a box, placating the graduate students so that they could see that their department or institution was responding to their demands. This also had the consequence of making me feel as though my science was merely performative. I was being invited to do the Diversity work institutions did not want to do. This is the tension I, and many other minoritized scientists, face. I want to share my experiences with the hopes that the next generation will have it better; but, my scholarly work is not in Diversity, Equity, and Inclusion. I fully recognize that it is my embodied diversity that is bringing me to the table; but, it is the science I want to share.On the first invitation to give a seminar, I promised myself that I was going to be honest. This meant that I would tell the truth about my experience and bare my soul over and over again. What I had not counted on was the emotional toll this would take on me. Reliving my own trauma, on a regular basis, left me emotionally drained after these visits. In one of my “stops” (I use quotes here because these “visits” were all virtual), I met with the queer, person of color (POC), graduate students. This session quickly turned into an emotional support group where I heard stories of mistreatment, racism, and discrimination. It was nearly impossible to maintain my composure. Diversity, Equity, and Inclusion work is clearly extremely important, but, maybe, we could just start by listening to the needs of the students and having a bit of humanity.The trial of Derek Chauvin has come and passed, and much to my surprise, and to the surprise of many other Black people nationwide, he was found guilty and was sentenced to prison (Arango, 2021; Cooper and Fiegel, 2021). This, of course, is not justice, not even close. Justice would mean that George Floyd is still alive and would get to live out his life in the way he chose. We are also at the beginning of the end of the pandemic. In 6 months or less, we may all be returning to life, more or less, as it was before George Floyd, before COVID-19. Does this mean we stop fighting? Does this mean that I, and many other Black scientists, suddenly disappear? For George Floyd, for countless other faceless Black people before him, I sincerely hope not. We need to continue to give Black scientists a platform. We need to ensure that they, too, are given the opportunity to network, collaborate, and interact with the larger scientific community. This means the invitations cannot stop. To further this, we need to ensure that Black scientists are included in every grant review panel, are included on speaker lists at every national and international meeting, are funded, and are in the room where funding, tenure, and other critical decisions are being made. We need to recognize that systematic racism has not gone away with Derek Chauvin’s conviction and sentencing. We need to continue to push forward. And, for all of you young, minoritized scientists (and allies) reading this, demand change and do not take "no" for an answer. I am truly sorry this has fallen on your shoulders, but enough is enough. The next generation of minoritized scientists should be recognized for their science without the additional burden of creating their own space.About the AuthorI am currently an Associate Professor of Biology at Reed College (https://www.reed.edu/biology/applewhite/index.html), which is located in Portland, Oregon. I arrived at Reed in 2014; prior to that, I was a postdoctoral fellow at the University of North Carolina, Chapel Hill. I received my PhD from Northwestern University in Cellular and Molecular Biology and a BS in Biology from the University of Michigan where I was also a 4-year letter winner in track and field. My research focuses on the cytoskeleton where I study cell motility and morphogenesis using Drosophila and Drosophila derived in tissue culture cells to explore actin, microtubules, and molecular motors. My current lab is composed of fierce, determined undergraduate students. I am a member of the American Society of Cell Biology (ASCB) and the current chair of the LGBTQ+ Committee (https://www.ascb.org/committee/lgbtq/). I am also a member of the Diversity, Equity, and Inclusion Committee for the Genetics Society of America (https://genetics-gsa.org/committees/). I also serve as an editor for MBoC’s Voices series.     

Stepping Stones：A New Future for Zoological Research

正This past year has been an auspicious one for Chinese science.With the recent lunar landing and the advances and the Chinese Academy of Sciences’growing reputation as the leader of scientific publishing in Asia,the media is now constantly reporting the"great leaps"that Chinese researchers have made.But we would do well to remember an old Chinese proverb:"It is better to take many small steps in the right direction than to make a great leap forward only to stumble backward."None of the recent advances of this year are great leaps in the sense that they occurred from     

假说检验和科学方法

本文的意图是让研究者审视研究方法,并在研究设计中充分使用假说检验,并在选择模式物种时充分理解其自然史.我们的总前提是,按照"强推论"(指假定拒绝某一假说而不是支持某一偏爱假说)的逻辑,科学能够进展得更快、更可观、更有确定性.我们强调并提供了符合逻辑的一系列步骤,即确定科学问题或确定具有未知生物学意义的问题;列出所有可靠的、能解释所观察现象的假说,每个假说列出其可检验的、可证明其无根据的预测;然后是符合预测检验的实验或研究设计.我们也强调,模式物种对于解决科学的理论问题以及得出推论是很重要的.本文所展示的不是新思想,只是提醒研究者要注意遵循的基本研究途径.     

Human evolution in Polynesia

The number of eastern Polynesian females required to found the Maori population of Aotearoa (New Zealand) has been recalculated. Our estimates use computer simulations that incorporate realistic sigmoid population growth models and include previously published and new mitochondrial DNA (mtDNA) 3' hypervariable region 1 sequences from M?ori (N = 109) and other eastern Polynesian (N = 125) volunteers. Approximately 190 (170-230) women are estimated to have been present in the founding waka (canoes). This new figure is more than double the previous estimate (Murray-McIntosh et al. 1998). Our claim for a large Maori founding population fits well with M?ori oral history and has additional support from M?ori paleodemography studies based on fertility estimates (Brewis et al. 1990; Pool 1991). An increasing body of data, including our own, supports the concept of planned multiple settlement voyages to Aotearoa by Polynesian navigators, leading us to suggest that theories for an "accidental discovery" of Aotearoa can now be completely disregarded. Four rare and novel M?ori mtDNA haplotypes have been identified in the present study, but we are unable to assign the immediate origin of M?ori to an exact Pacific island "homeland" because these haplotypes are not currently known elsewhere in Polynesia. We also discuss briefly the ultimate origin of all Polynesians (including M?ori) in a wider context. In general, we support the emerging consensus for Pacific origins most closely encapsulated by the "slow boat" model (Oppenheimer and Richards 2001a). Previously "competing" models for the settlement of Oceania are seen as extremes in a continuum of possibilities with the slow boat representing an "intermediate" model. We suggest that a complete account is now close, incorporating data from all relevant interdisciplinary fields to provide a "synthetic total evidence theory."     

Borrowed robes

Should scientists indulge their fantasies by writing fiction? Subject Categories: Careers, Economics, Law & Politics, History & Philosophy of Science

Like a substantial fraction of the literate population, I have a collection of unpublished novels in the drawer. Six of them in fact. Some of them were composed in barely more than a week, and others I have been struggling to complete for over 10 years: so maybe it is more accurate to say five and a half. Anyhow, most of them are good to go, give or take a bit of editorial redlining. Or, as my helpful EMBO editor would say, the removal of thousands of unnecessary adverbs and dubiously positioned commas.What do I write about and why? My style is not unique but rather particular. I write fiction in the style of non‐fiction. My subject matter is somewhere in the general realms of science fiction, alternate history and political drama. Putting these ingredients together, and taking account of my purported day job as a serious scientist, it is easy to see why my fictional work is potentially subversive—which is one reason why I have been rather reluctant thus far to let it out of the drawer. At the very least, I should take pains to conceal my identity, lest it corrupts perceptions of my scientific work. Even if I regularly tell my students not to believe everything they read, it would impose far too great a burden on them if they came to question my peer‐reviewed articles purely on the basis of untrue statements published in my name, spoken by jaded politicians, washed‐up academics or over‐credulous journalists. Even if they are imaginary. Real journalists are theoretically bound by strict rules of conduct. But imaginary ones can do whatever they like.Today, I noticed a passage in one of these unpublished works that is clearly written in the style of a young William Shakespeare, dealing with a subject matter that fits neatly into one of his most famous plays. In fact, the illusion was such that I was sure I must have lifted the passage from the play in question and set about searching for the quote, which I then could and should cite. Yet, all Internet searches failed to find any match. The character in whose mouth I placed the words was depicted as being in a delirious state where the boundaries of fact and fiction in his life were already blurred; borrowed identities being one of the themes of the entire novel and arguably of my entire oeuvre. But am I guilty here of plagiarism or poetry, in adopting the borrowed identity of my national playwright?In another work, I lay great emphasis on the damaging role of mitochondrial reactive oxygen species (ROS) as the cause of biological ageing. I have even grafted this explanation onto a thinly disguised version of one of my most valued colleagues. Although there is some support for such a hypothesis from real science, including some papers that I have myself co‐authored, it is also a dangerously broad generalization that leads easily into wrong turnings and misconstructions—let alone questionable policies and diet advice. But, by advancing this misleading and overly simplistic idea in print, have I potentially damaged not only my own reputation, but that of other scientists whom I respect? Even if the author’s identity remains hidden.In one novel, I fantasize that nuclear weapons, whilst they do undoubtedly exist, have in fact been engineered by their inventors so as never actually to work, thus preventing their possible misuse by vainglorious or lunatic politicians unconcerned with the loss of millions of lives and planetary ruin. But if any insane national leader—of which there are unfortunately far too many—would actually come to believe that my fiction in the style of non‐fiction were true, they might indeed risk the outbreak of nuclear war by starting a conventional one in order to secure their strategic goals.Elsewhere, I vindicate one author of published claims that were manifestly based on falsified data, asserting him to have instead been the victim of a conspiracy launched to protect the family of an otherwise much respected American President. None of which is remotely true. Or at least there is no actual evidence supporting my ridiculous account.I have great fun writing fiction of this kind. It is both liberating and relaxing to be able to ignore facts and the results of real experiments and just invent or distort them to suit an imaginary scenario. In an age when the media and real politicians have no qualms about propagating equally outrageous “alternative facts”, I can at least plead innocent by pointing out that my lies are deliberate and labelled as such, even if people might choose to believe them.In a further twist, the blurb I have written to describe my latest work characterizes it as the “semi‐fictionalized” biography of a real person, who was, in fact, a distant relative of mine. But if it is semi‐fictionalized, which bits are true and which are made up? Maybe almost the whole thing is invented? Or maybe 99% of it is based on demonstrable facts? Maybe the subject himself concocted his own life story and somehow planted it in falsified documents and newspaper articles to give it an air of truth. Or maybe the assertion that the story is semi‐fictionalized is itself a fictional device, that is, a lie. Perhaps the central character never existed at all.It is true (sic) that the most powerful fiction is grounded in fact—if something is plausible, it is all the more demanding of our attention. And, it can point the way to truths that are not revealed by a simple catalogue of factual information, such as in a scientific report.But I have already said too much: if any of my novels ever do find their way into print, and should you chance to read them, I will be instantly unmasked. So maybe I’ll have to slot in something else in place of my pseudo‐Shakespearean verse, mitochondrial ROS hypothesis, defunct weapons of mass destruction and manipulated data manipulation.     

Alcodemia: are we training our students to be great thinkers or great drinkers?

Academia has fostered an unhealthy relationship with alcohol that has an undeniable impact on the health and behaviour of students and staff. Subject Categories: S&S: History & Philosophy of Science, Chemical Biology, S&S: Ethics

University life has a lot to offer. And, for better or worse, much of it goes hand in hand with a bottle. Believe it or not, I was a bit of teetotaler in my undergraduate days but quickly made up for it in graduate school, where each celebration included inebriation. Indeed, my initial tour of the laboratory I eventually worked in included a refreshing visit to the grad club. Orientation week ended with a marathon beer blitz at a nightclub. The semester’s first invited seminar speaker was welcomed with the sounds of loose change, ice buckets and the clickity‐clack of organic microbrews being opened. Our inaugural genome evolution journal club was such a success that we vowed to spill even more red wine onto our notebooks the following week. In hindsight, I should have realized at this early stage in my studies that I was fostering an unhealthy and unsustainable relationship between biology and booze. Unfortunately, my post‐graduate education in alcohol didn’t stop there.Like many keen students, I arrived at my first scientific conference with a belly full of nerves and a fistful of drink tickets, which I quickly put to good use at the poster session. The successful completion of my PhD proposal assessment was met with pats on the back as I was swiftly marched off to a local pub with no chance of escape. My first peer‐reviewed paper literally arrived with a pop as Champagne was generously poured into plastic cups for the entire laboratory group. My failures, too, were greeted with a liberal dose of ethanol. “Sorry you came up short on that scholarship application, Smitty. It’s nothing a little weapons‐grade Chianti won’t cure.” “That experiment failed again! Come on, let me buy you a lunchtime martini to make up for it.” Soon I learnt that every academic event, achievement or ailment, no matter how big or small, could be appropriately paired with beer, wine or spirit. Missing from the menu were two crucial ingredients for any burgeoning researcher: moderation and mindfulness.But it was the older vintages that really inspired me – the legendary drinking escapades of my scientific mentors, advisors and idols. The tale of professor so‐and‐so who at that epic meeting in 1993 polished off an entire magnum of rosé at dinner and then went on to deliver among the greatest keynote lectures on record at 9 am the following morning. That celebrated chaired researcher who kept the single malt next to the pipette tips for quick and easy access. The grizzled evolutionary ecologist who never went into the field without half a dozen cans of high‐end smoked oysters and two hip flaks, which didn’t contain water. And so, when I was told by someone in the know of how the most famous geneticist on campus wrote that monumental Nature paper (the one I’d read ten times!) while locked in his office for twelve hours with a six‐pack, I bought into the romance hook, line and sinker. The result: I’ve been nursing a recurring headache for nearly two decades and I’m still waiting on that Nature paper. Most importantly, I now realize the various dangers of romanticizing the bottle, especially for individuals in mentorship positions.Like my idols before me, I’ve accrued a cask full of well‐oaked academic drinking stories, except that they haven’t aged well. There is that heroic evening of intense scotch‐fueled scientific discussion, which led to me forfeiting two front teeth to the concrete sidewalk (my mother still thinks it was a squash accident). Or that time I commemorated the end of a great conference in Barcelona by throwing up on the front window of a café while the most prominent minds in my field sipped aperitifs inside (thank god this was before Twitter). Even more romantic: me buying a bottle of Cotes de Nuits Burgundy at Calgary airport on route to a job interview, discreetly opening the bottle in‐flight because economy class wine sucks, and then being met by airport security upon landing. Let’s just say I didn’t get the job. To some, these anecdotes might seem light‐hearted or silly, but they are actually rather sad and underscore the seriousness of substance abuse. Many readers will have their own complicated experiences with alcohol in academia and, I believe, will agree that it is high time we asked ourselves: are we training our graduate students to be great thinkers or great drinkers? Moreover, this question does not address the equally if not more serious issue of excessive drinking among undergraduate students.As I sit at my desk writing this, I think to myself: is it normal that within a two‐minute walk of my university office there are three different places on campus that I can have a beer before lunch, not including the minifridge behind my desk? Is it normal that in my department the first thing we do after a student defends their thesis is go to the grad club where they can have any alcoholic drink of their choosing for free from the goblet of knowledge, which is kept on a pedestal behind the bar? Is it normal that before the COVID pandemic when I was visiting a prominent university for an invited talk, one of the professors I met with offered me a glass of expensive Japanese gin at 11 am in the morning? (And, yes, I accepted the drink.)Of course, if you don’t want to drink you can just say no. But we are learning more and more how institutional cultures – “the deeply embedded patterns of organisational behaviour and the shared values, assumptions, beliefs or ideologies that members have about their organisation or its work” (Peterson & Spencer, 1991) – can have powerful effects on behaviour. Excessive alcohol consumption is undeniably an aspect of collegial culture, one that is having major impacts on the health and behaviour of students and staff, and one that I’ve been an active participant in for far too long. I’ll be turning forty in a few months and I have to face the fact that I’ve already drunk enough alcohol for two lifetimes, and not one drop of it has made me a better scientist, teacher or mentor. The question remains: how much more juice can I squeeze into this forty‐year‐old pickled lemon? Well, cheers to that.     

Ye Tian: Surveilling stress to live longer

Ye Tian investigates how mitochondrial stress signaling pathways regulate longevity using C. elegans as a model system.

An avid reader, Ye Tian used to save up her child allowance with the sole purpose of buying science fiction books. Reading and solving mathematical problems were her favorite hobbies; indeed, she liked mathematics so much that she was about to enroll herself as an architecture major but finally chose biotechnology. Ye moved from her hometown in the Northwest of China, Baoji—famous for housing the Zhou dynasty’s bronzeware and being close to the Terracotta Army—to Beijing for her college and graduate studies.Ye is proud of being among the earliest researchers working on Caenorhabditis elegans in her country; for her PhD studies, she joined the lab of Hong Zhang, who at that time has just established the first C. elegans lab in China at the National Institute of Biological Sciences in Beijing. Ye identified epg-2 as an adaptor for cargo recognition during autophagy. In 2010, she crossed the Pacific toward the U.S. West Coast for her postdoctoral training in the aging field with Andrew Dillin, first at the Salk Institute in San Diego and then at the University of California, Berkeley. There, she discovered that mild mitochondrial stress during development in worms rewires their chromatin landscape to establish specific gene expression patterns throughout the lifespan and promote longevity.Ye Tian. Photo courtesy of Ye Tian.Ye came back to China at the end of 2016 to start her own lab at the Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences. Her research team studies mitochondrial stress signaling pathways and their interplay with aging. We chatted with her to learn more about her next scientific plans.What interested you about the interplay between mitochondria and aging?I became interested in mitochondrial biology during my postdoc in Andrew Dillin’s lab. Since the origin of eukaryotic cells, mitochondria have been a driving force of evolution. During reproduction, mitochondria are passed from the mother to the offspring through egg cells and they exhibit a unique inheritance pattern. As essential hubs that dictate cellular metabolism, it is clear now that mitochondria and the nucleus maintain a bidirectional communication. Early life “stressed” mitochondria communicate with the nucleus to induce gene expression changes that are beneficial on longevity and persist throughout the lifespan. The fact that mitochondrial function is crucial to aging fascinated me; I wanted to continue exploring that topic further, and that’s why I established my lab around the question of how mitochondrial surveillance mechanisms regulate the aging process.What are you currently working on? What is up next for you?My research team focuses on the interplay between mitochondrial stress signaling pathways and aging. The first work that my lab published was a project that I started during my postdoc. The Dillin lab reported a phenomenon in which perturbations of mitochondria in neurons induced a mitochondrial stress response in the peripheral tissues and hypothesized that a secreted signal molecule, named after mitokine, is required for the cell non-autonomous regulation (1). The identity of this molecular signal remained elusive for almost ten years until we found that a secreted Wnt ligand, EGL-20, functions as the mitokine to coordinate mitochondrial stress signaling across tissues and promote longevity of the organism (2). We are also interested in how the crosstalk between mitochondria and the nucleus influences lifespan. We found that mitochondrial perturbations alter the nuclear epigenome to induce longevity via the histone deacetylation complex NuRD in response to cellular acetyl-CoA levels, the key metabolite at the entry point of the Krebs cycle (3).Lab group picture; current lab members (2021). Photo courtesy of Ye Tian.Our latest work stemmed from a serendipitous observation that neuronal mitochondrial stress is sensed by and transmitted through the mitochondria in the germline. Intergenerational, maternal inheritance of elevated levels of mitochondrial DNA via the mitokine Wnt/EGL-20, which causes the activation of the mitochondrial unfolded protein response (UPR^mt), provides descendants with a greater tolerance to environmental stress. This makes the offspring live longer (4).Among our short-term scientific plans, we’re determining how mitochondria functions during the aging process at both the genetic and biochemical levels and searching for ways to apply our findings from C. elegans to neurodegenerative disease models in mammals.What kind of approach do you bring to your work?The curiosity about how things work drives me; what I enjoy the most is when I see things happening in front of my eyes and when I figure out why they occur that way. That enthusiasm is what I try to spread to my team every day. In the lab, we rely on C. elegans as our model system and on genetics to dissect complex biological processes like aging. We have also adapted modern biochemical and imaging techniques as well as bioinformatics to complement our genetic studies. I’m a geneticist at heart, and I like to initiate a project with a well-designed genetic screen. The best part is that the screen often leads me to answers I was not expecting, and that’s genuinely inspiring!What did you learn during your PhD and postdoc that helped prepare you for being a group leader? What were you unprepared for?Like most scientists, my research career has gone through ups and downs. I had to change my research project in the last year of my graduate school; that was nerve-racking, but I eventually managed to redirect my thesis and get exciting results under time pressure, thanks in large to the support of my parents, mentors, and lab mates. That helped me prepare to become a principal investigator; I gained confidence in problem solving, and since I’ve experienced the stress of dealing with last-minute scope changes firsthand, I connect better with my students.I guess, as many other non-native English speakers, I wasn’t prepared for writing grants and papers fluently in English. This issue wasn’t obvious during my graduate and postdoctoral studies, as my mentors were always there for me and proofread and edited my writing. Now I have to stand up for myself. I spend most of my time writing; I’ve improved my writing skills but it’s still an ongoing process.Reconstruction of the nerve system of C. elegans by confocal microscopy. Green corresponds to YFP-labeled neuronal specific marker Q40, and red labels germline specific mitochondrial outer membrane protein TOMM-20::mkate2. Image courtesy of Ye Tian’s lab.What has been the biggest accomplishment in your career so far?My very first PhD student, Qian Zhang, graduated with two first-author papers and decided to pursue a research career in academia. Being responsible for someone else’s career is challenging but also rewarding.What has been the biggest challenge in your career so far?I use the model organism C. elegans for my research in aging, so from time to time, peers criticize the relevance of my work to human health. I’m used to justifying my scientific approach to funding agencies and peers in other fields, but sometimes it’s exhausting or not pleasant.Who were your key influences early in your career?My PhD mentor, Hong Zhang. He is very passionate about the science he does, and he is courageous to shift his research directions to answer new biological questions.What is the best advice you have been given?I think the best advice I’ve gotten is that “tomorrow is another day.” It reminds me to keep going and be optimistic.What hobbies do you have?I love art and music. When I was in San Diego, I used to play in the Chinese Music Band; I miss my musician friends over there. In my teens, I used to hike mountainside trails along the river with my parents. Now, running has become my new favorite hobby. I enjoy the tranquility and peace of mind while running; it’s soothing.     

XII. Something on Vision from Within

Earlier I attempted to show that Shpet was able to penetrate behind the external form of the word through its shell, which in itself is by no means simple, into its inner form, which proved to be immeasurably more complex than the external form. For me it still remains a mystery: How was he able to penetrate into the "living soul" of the word? Of course, he was helped in this by encyclopedic knowledge. He was, after all, a philosopher, a linguist, a psychologist, and an art cognoscente; he completed two years at the physics and mathematics and the history and philology departments of Kiev University. And Shpet also knew seventeen (!) languages. It seems to me that Shpet saw language (languages) and the word from within. He blended into the word rather than manipulated it. "Vision from within" is not a fantasy of my own. Goethe, who in the words of Ralph Waldo Emerson could see with his every pore, knew how to see from within. Ortega y Gasset in 1932 published a special article on this subject: "Goethe's vision from within." What Daniil Kharms saw from within was the absurd.     

His own private hospital

Dr. Brian Day had a simple solution when it became increasingly difficult to book operating room time in Vancouver. He built his own hospital. The Cambie Surgical Centre, which treats patients from BC and around the world, has 2 main operating rooms, 10 recovery beds and 5 private rooms for extended stays. "What I''ve done," says Day, "is say that if there are no operating rooms at UBC, I''ll build my own."     

Specific effects and biofeedback versus biofeedback-assisted self-regulation training

In any field, clear and logical conceptualizations are the basis of accurate models----correct research design----correct results----correct conclusions----advancement in the field. Faulty conceptualizations----faulty models----faulty research design----faulty results----faulty conclusions----confusion. In analyzing the conceptualizations of "biofeedback" as expressed by John Furedy (1987) in, "Specific versus Placebo Effects in Biofeedback Training: A Critical Lay Perspective," we focus on two issues: Does biofeedback have a treatment effect? Is biofeedback necessary for the training effect? In discussing issue (1) we describe the multiple meanings of "biofeedback" and raise the fundamental question: Is biofeedback a treatment? We argue that faulty conceptualizations of clinical biofeedback (1) assume that the treatment in clinical biofeedback is "biofeedback" with specific effects, (2) assume that the scientific basis of biofeedback is dependent upon demonstrations of these specific effects through double-blind design that distinguish "specific" from "placebo effects," and (3) trivialize clinical research by attempting to determine the usefulness of biofeedback information--usefulness that is already understood logically by professionals and consumers and demonstrated by clinical studies in the laboratory and in the clinic. We further argue that accurate conceptualizations of clinical biofeedback (1) identify self-regulation skills as the treatment with specific effects of physiological change and symptom reduction, and (2) describe the use of information from biofeedback instruments as scientific verification of self-regulation skills. Finally, the scientific basis of clinical biofeedback is based on (1) evidence from experimental and clinical control studies that have demonstrated the effectiveness of self-regulation skills for symptom alleviation, and (2) the use of biofeedback instruments to verify the acquisition of self-regulatory skills, thus fulfilling the scientific dictum of verifiability.     

"Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits

Although mathematical relationships can be proven by deductive logic, biological relationships can only be inferred from empirical observations. This is a distinct disadvantage for those of us who strive to identify the genes involved in complex diseases and quantitative traits. If causation cannot be proven, however, what does constitute sufficient evidence for causation? The philosopher Karl Popper said, "Our belief in a hypothesis can have no stronger basis than our repeated unsuccessful critical attempts to refute it." We believe that to establish causation, as scientists, we must make a serious attempt to refute our own hypotheses and to eliminate all known sources of bias before association becomes causation. In addition, we suggest that investigators must provide sufficient data and evidence of their unsuccessful efforts to find any confounding biases. In this editorial, we discuss what "causation" means in the context of complex diseases and quantitative traits, and we suggest guidelines for steps that may be taken to address possible confounders of association before polymorphisms may be called "causative."     

Applied orienting response research: some examples

The development of orienting response (OR) theory has not been accompanied by many applications of the concept--most research still appears to be lab-based and "pure," rather than "applied." We present some examples from our own work in which the OR perspective has been applied in a wider context. These cover the exploration of processing deficits in autistic children, aspects of the "repression" of anxiety in elite athletes, and the locus of alcohol effects. Such applications of the OR concept in real-life situations seem a logical and, indeed, necessary step in the evolution of this area of psychophysiology.     

A Neo-Boasian Conception of Cultural Boundaries

For the past 30 years, anthropology's critics have repeatedly questioned the notion of "cultural boundaries," arguing that concepts of culture inappropriately posit stable and bounded "islands" of cultural distinctiveness in an ever-changing world of transnational cultural "flows." This issue remains an Achilles' heel—or at least a recurring inflamed tendon—of anthropology. However, in the conception of boundaries, we still have much to learn from Boasian anthropologists, who conceived of boundaries not as barriers to outside influence or to historical change, but as cultural distinctions that were irreducibly plural, perspectival, and permeable. In this article, I retheorize and extend the Boasians' open concept of cultural boundaries, emphasizing how people's own ideas of "the foreign"—and the "own" versus the "other" distinction—give us a way out of the old conundrum in which the boundedness of culture, as conceived in spatial terms, seems to contradict the open-ended nature of cultural experience.     

A different kind of quarterback

I am not big on celebrations, nor do I accept many invitations to receive awards. There is much work to be done, and the reward is in the doing. I learned this lesson early from my parents, Martha and Robert Guyden. However, I am humbled that anyone would even mention my name in association with E. E. Just. I, like he, was born into a segregated America, and somehow we both found biology. I think Just's life story instigates a discussion on diversity in science, as well it should. However, after reading Tyrone Hayes' (2010 E. E. Just Award recipient) essay from last year, "Diversifying the Biological Sciences: Past Efforts and Future Challenges" (Hayes, 2010), I have little to add on the subject. His words gave voice to my thoughts. That being said, I would like to use these pages to describe my journey into the "Cell" and the people who "hoed the row ahead of me."     

A path to the powerhouse: systems‐to‐structure approaches for studying mitochondrial proteins

The young investigator award from the Protein Society was a special honor for me because, at its essence, the goal of my laboratory is to define what obscure proteins do. Years ago, I stumbled into mitochondria as a venue for this work, and these organelles continue to define the biological theme of my laboratory. Our approaches are fairly broad, reflecting my own somewhat unorthodox training among diverse scientific fields spanning organic synthesis, chemical biology, mechanistic biochemistry, signal transduction, and systems biology. Yet, whatever the theme or the discipline, we aim to understand how proteins work—especially those that hide in the dark corners of mitochondria. Below, I recount my own path into this arena of protein science, and describe how my experiences along the way have shaped our current multi‐disciplinary efforts to define the inner workings of this complex biological system.