Science & sun in Lausanne

Along with co-organizers from Sweden, Germany, and the States, I was thrilled to take part this week in an inspiring workshop at the Lausanne headquarters for the Centre Européen de Calcul Atomique et Moléculaire (CECAM). Founded 47 years ago to promote fundamental research and applications of computational methods in science, CECAM joined the Swedish e-Science Research CentreBioExcelJournal of General Physiology and Nature Structural & Molecular Biology in sponsoring our three-day program—Ion Transport from Physics to Physiology: the Missing Rungs in the Ladder—on the campus of the École Polytechnique Fédérale de Lausanne (EPFL) in the south of Switzerland.

Our thirty participating scientists—representing 22 institutions in 11 countries—discussed recent successes and (often more interesting) challenges in studying ion channels and transporters at the molecular level. Among other things, an emergent theme was the need for a public database of molecular dynamics simulations, analogous to the Protein Data Bank or—perhaps less obvious, but with likewise important parallels—biomaterial repositories.

Alongside the stimulating science, I was moved by my virgin visit to Lausanne. The EPFL campus was populated by industrious sheep as well as students enjoying the spring sun; downtown, the Olympic Museum gardens offered idyllic views of the French Alps from the north banks of Lake Geneva. Evening at Chalet Suisse was equally memorable for fondue, raclette, and a breathtaking hilltop sunset.

Many thanks to Ignacio, Marianne, Bogdan, and the entire CECAM staff for making our Swiss sojourn so productive and enjoyable.

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Sabbatical’s end, and a new start

Skidmore College held commencement, as usual, on a sunny late-May morning in the glorious open-air Saratoga Performing Arts Center. I celebrated with new graduates I’ve grown to care for and respect over the past four years, including several from my first Skidmore course back in 2012.

It was a potent ceremony for me, as it also marked my own departure from Skidmore, at least for the next few years. As our personal and professional communities End - 8will know, I move this week to a research position with Stockholm University, funded by a Wallenberg Foundation grant to work for my long-time collaborator Erik at the Swedish SciLife Lab.

This has been a surprise ending to my sabbatical story. I set out to disrupt some habits of mind, reconnect with my research, and engage with new technologies and developments in my field; I did not anticipate concluding the year with a change in employment. And though it feels a natural transition, it’s been a weighty decision to step (at least for now) off a linear academic path, away from the undergraduate liberal arts environment I’ve long idealized. There has been lots to love about Skidmore: students effusing creative aspirations; hardworking faculty pouring themselves, term after term, into a rarefied curriculum; and an administration diligently navigating the complex social, political, and technological landscape of higher education today.

A major and indefinite move like this has also involved careful personal calculus for Oliver and me. On the down side, we are leaving behind historically beautiful Saratoga Springs—its plethora of entertainment, including the oldest sporting venue in the States; its natural wonders, among them a State Park and the city’s eponymous carbonated springs; and our own small, but hugely supportive, community of friends and colleagues. We will miss easy visits to Oliver’s northeastern family, and the dramatic seasonal beauty of the Adirondack region.

On the up side, we are eager to make a new home in Stockholm, however long we stay. Traveling over the past year has reinforced how much we enjoy learning new spaces and and communities, and how we’ve missed the energy and diversity of urban life. We both felt surprisingly at home by the end of last year’s Swedish semester, End - 18and look forward to digging deeper into the Capital of Scandinavia. For Oliver, this move also brings proximity to his Irish and German relatives, and the professional opportunities of Europe’s premier tech hub.

For my part, trading some of the autonomy of professorship for participation in a more research- and resource-intensive team seems the right next move. And in taking a break from the classroom, I am eager to engage more actively in the mentoring of trainees at various levels. As for many of my colleagues, serving on the Skidmore faculty has highlighted major challenges facing higher education and research science in the States. Much as I continue to value small-scale liberal arts training in my own experience and our students’, the soaring costs alone—on track with its peers, a Skidmore education today approaches $250k—make it hard to see sustainability in our current system. Among other things, I hope that inhabiting an alternative academic environment abroad may provide some new perspective.

To be clear, I retain good relations with, and great respect for, my Skidmore colleagues and students. To minimize the impact of my departure on my department, I informed them of my intentions as soon as my new position opened last January—prior, in fact, to receiving an offer letter. I served on the search committee for a visiting professor to cover the coursework I would have taught next year, and I was open with my students about my pending exit, enabling them to find new lab homes for the coming semester(s).

End - 20
Architect plans, Skidmore CIS

If one thing might have altered my decision, it could have been more rapid progress on the Center for Integrated Sciences (CIS), a longstanding plan to unite and improve Skidmore’s STEM facilities. It’s become increasingly clear over my four years on campus that our existing buildings are variously outdated, run down, or otherwise inadequate for our growing science programs. For many reasons the CIS has been difficult to fund; so I was delighted last week when Skidmore’s Board of Trustees approved a new plan to combine cost-cutting, revenue-boosting, and borrowing to complete the project within the next ~5 years. Although this progress comes too late to benefit my own lab, I believe it will prove a crucial investment for the entire campus.

My new position will bring its own challenges. Our Stockholm team aims to address major questions in neurophysiology and pharmacology, optimize and integrate classical and novel methods, and build partnerships between diverse investigators. We have the privilege of some powerful resources, but the problems are complex: to paraphrase one of my earliest mentors, most paths in science are series of failures, End - 25punctuated by tantalizing moments of insight. I believe our project will provide a strong return-on-investment, but am realistic about its limitations, and the unavoidable risk of unknown unknowns.

As our ollibatical has ended, we will no longer post regularly in this space. However, we have enjoyed archiving images and reflections here, and plan to keep it live for our own recollections and, as appropriate, new discoveries. We hope to preserve the traveler’s mindset our sabbatical rekindled as we begin our next adventure. Vi ses!

Top photo credit: Yosemite Basecamp, Jan 2016 by Maya Bisineer

Recapturing credibility

Another guest post for the 60th Annual Meeting of the Biophysical Society. These and other posts can also be found on the Biophysical Society Blog.

economistScience’s Reproducibility ProblemThe Cost of Science ErrorsScience, Now Under Scrutiny Itself. Recent headlines communicate a crisis in credibility for researchers. And with stories like the 2009 retraction of a dozen crystal structures from a single author, biophysics is no exception.

Implications of this broad problem for our field were the subject of Sunday’s afternoon panel, Transparency, Reproducibility and the Progress of Science, cosponsored by the Biophysical Society Public Affairs and Publications Committees. Part of the Professional Development and Networking series at this year’s Biophysical Society Annual Meeting, the 90-minute program was moderated by Publications Committee Chair Olaf Andersen (Weill Cornell Medical College), and featured three speakers with similarly substantial authority in both research and administration.

Yamamoto-portraitKeith Yamamoto from the University of California, San Francisco opened the program with a breakdown of four major challenges to reproducibility in bioscience. Although difficult to quantify, he estimated the contribution of willful misconduct to be relatively minor; more substantial in his view are experimental errors, statistical insignificance, and the inherent complexity of biology. As Vice Dean for Research and Vice Chancellor for Science Policy and Strategy at his institution, it is perhaps unsurprising Yamamoto collapses the majority of these problems into an education deficit: a gap in scientific training, particularly at the graduate level.

Yamamoto envisions doctoral curriculum reform that takes responsibility for broad scientific literacy, with a rigorous regard for quantification, statistics, exposition of known variables—and acknowledgement of the Rumsfeld factor, the plethora of unknown unknowns in our discipline. As a goalpost, he quoted a seminal paper on the genetic code—now over fifty years old—in which Nobel laureate Marshall Nirenberg admitted with brutal honesty his own challenges reproducing critical findings. Along with tackling correctable sources of error, Yamamoto called on scientists to restore a more open humility about the complexity and variability of biology itself. Easy as it is to identify sources of external pressure and regulation from publishing and funding agencies, he emphasized the responsibility lies with scientists to change our own culture.

unknowns2

Credit: Alicia Haag

Emilie Marcus, Editor-in-Chief of Cell and CEO of Cell Press, echoed much of Yamamoto’s message from the perspective of the publishing industry. She implicated an even longer catalog of causes in irreproducibility, and identified five major ways publishers can contribute to restoring credibility. The first of these, methodological transparency, has motivated the recent creation of repositorites like Nature Protocol Exchange and Elsevier MethodsX; marcusother priorities for Marcus include data sharing, ethical evaluation, accountability in the review and retraction process, and training efforts—like this panel. In 2014, Cell endorsed the NIH Principles and Guidelines for Reporting Preclinical Research, with the mission of identifying the common opportunities in the scientific publishing arena to enhance rigor and further support research that is reproducible, robust, and transparent.

Responding to audience concerns about the limited incentive to report negative results, Marcus pointed out that Cell Press regularly publishes carefully executed findings that challenge previous data; a greater concern, she said, is that many failed experiments tell us less about biology than about the inherent challenges of research. This issue is likely exacerbated for the life sciences: in contrast to some mathematical fields, a biology reviewer can rarely reproduce another author’s experiments in their entirety. While acknowledging the roles publishers can play, Marcus insisted pressure for funding, publication, or tenure cannot become an excuse for unethical conduct among practicing scientists; again, culture change should primarily come from within.

BermanHelen Berman brought many of these points home to biophysics, speaking both as a Distinguished Professor at Rutgers University, and as former director of the RCSB Protein Data Bank (PDB). The sensational Murthy retractions made not-so-welcome headlines for the PDB in 2009, and partly motivated the recent adoption of the more rigorous PDBx standards for macromolecular structure data deposition. More broadly, Berman cited the PDB as a touchstone for bottom-up collective action within the science community. She drew parallels to the ideas of Elinor Ostrom, a 2009 Nobel laureate in Economics, in emphasizing the sustainability of this approach over top-down enforcement; but she credited crystallographer JD Bernal with an even earlier insistence—articulated, among other places, in his 1939 text The Social Function of Science—that scientists work together to share practices and resources.

Following the panelists’ remarks, discussion opened to a range of questions—some emotionally charged—around what has changed in the credibility of science, and what needs to. Some contention surrounded the Biophysical Society’s own decision not to endorse the 2014 NIH Guidelines; the Biophysical Journal did develop its own Guidelines for the Reproducibility of Biophysics Research, reflecting similar principles as the NIH list, but dodging the murky preclinical label. A more general refrain was the evident deficiency in training of new scientists—though its causes and potential remedies were less clear. As Marcus reminded us, every manuscript published in Cell includes at least one senior, experienced author; the artisan-model of science training should provide infrastructure for younger authors to learn from these mentors. Still, several participants commented on the real-vs-movie-scientist2changing character of academic labs: as Yamamoto put it, we’re not really training students—we have a bunch of people doing our experiments. Others argued the culture of scientific discourse itself has changed: conferences (including this one) rarely feature true work-in-progress posters these days, nor forums to workshop experimental design.

Credit: The Upturned Microscope

It seemed appropriate, somehow, to tackle these topics in Los Angeles on Oscar Sunday, in the midst of a wider national debate over credibility and authority in the very different Hollywood entertainment industry. If definitive answers were not in evidence, the transparency of conversations like these still seems critical to navigating a brighter path through crises to come.

From pasta to pentamers

I am currently guest-blogging for the 60th Annual Meeting of the Biophysical Society. These and other posts can also be found on the Biophysical Society Blog.

cellsoupCells are often said to be filled with cytosolic soup, a chunky broth where organelles and macromolecules carry out the mechanics of life. According to Michaela Jansen, the proteins that inhabit this intracellular stew may be less like wet noodles than previously thought.

MJ_2015_NHsmallJansen was the penultimate speaker in Sunday’s early-morning Symposium on Pentameric Ligand-Gated Ion Channels, chaired by University of Wisconsin Professor Cynthia Czajkowski. The field has experienced substantial progress in the past decade, with structures of ten distinct family members (or substantial domains thereof) determined by crystallography, NMR, or cryo-electron microscopy since 2005. However, no structure yet published has included a complete intracellular domain: variable in sequence and poorly behaved in isolation, this region is thought by some to be intrinsically disordered—floppy pasta tethered loosely to the better-characterized transmembrane and extracellular domains.

ModelSo it was stirring news that Jansen’s team, based at Texas Tech, has succeeded in expressing and purifying a soluble construct containing the intracellular domain of the serotonin-3A receptor. This channel is a target for drug developers as well as neurophysiologists, and contains one of the longest cytosolic loops of any family member. Surprisingly, the protein’s intracellular domain—fused to a soluble expression partner, the identity of which Jansen declined to share due to pending patents—forms pentamers on its own, mirroring the stoichiometry of the full-length channel. As Jansen described it, this spaghetti conundrum indicates the presence of previously-unidentified assembly determinants in the region: after all, even well ordered pasta does not oligomerize. Given that the corresponding extracellular and transmembrane domains often form noncanonical states in isolation, intrinsic intracellular domain assembly could help explain the selective oligomerization of many pentameric ligand-gated ion channels.

Jansen’s talk was one of several in her session to leverage comparative structures in this increasingly well-characterized family: preceding talks by Pei Tang (University of Pittsburgh) and Claudio Grosman (University of Illinois at Urbana-Champaign) took alternative chimera approaches to elucidate mechanisms of modulation and selectivity, among other things. Session chair Czajkowski closed the session with new spectroscopic and fluorescence data revealing precise gating motions in bacterial homologs. Czajkowski’s final remarks also provided some poignant perspective: when she began attending Biophysical Society meetings, she remembers finding only a handful of posters on pentameric ligand-gated ion channels; img-czajkowski-labin contrast, this year’s meeting includes her own featured Symposium, a half-dozen additional subgroup and platform talks, and two dedicated poster sessions. Tantalizing data like Jansen’s further illustrate the potential of biophysics to open new lines of inquiry into such previously intractable proteins, including their most noodly domains.

Re-tallying transport

For the next few days I will be guest-blogging for the 60th Annual Meeting of the Biophysical Society. These and other posts can also be found on the Biophysical Society Blog.

Bert de Groot had a problem: too many ions.

bdgAs a molecular dynamics specialist at Göttingen’s Max Planck Institute for Biophysical Chemistry, de Groot has been probing the thorny problem of ion channel permeation: how proteins carry specific ions across cell membranes. He joined four other speakers in Saturday’s Permeation & Transport Subgroup session, one of the opening-day events of the 2016 Annual Meeting of the Biophysical Society. Sudha Chakrapani from Case Western Reserve University had kicked off the session with structural and spectroscopic data on pentameric ligand-gated ion channels; de Groot would be followed by talks on transporters by Nieng Yan (Tsinghua University) and Peter Hinterdorfer (Johannes Kepler University), and a broader treatment of membrane transport from the NIH’s Sergey Bezrukov.

poreionsIt’s been over a decade since Nobel laureate Rod MacKinnon used the simple bacterial protein KcsA to identify ions at four precise positions in the channel pore, specifically coordinated by backbone oxygens in the selectivity filter. And it’s long been assumed that charge repulsion would allow only two of these four positions to be occupied at a time, with alternating spots filled by water molecules. But de Groot’s simulations—using computational electrophysiology, a method to push ions through channels in silico—indicated something different. With both ions and water in the filter, what he saw was basically a dead channel: few ions passed through, even in the presence of a strong driving force. A transition occurred when water exited the filter, placing ions in adjacent positions: their repulsion switched the channel into a conducting state, with apparent currents approximating functional recordings. These results were replicated using multiple force fields, water models, and ion parameters—too many ions in the filter, at odds with what had always been proposed.

Credit: Köpfer et al., 2014: Six ion binding sites in the KcsA selectivity filter

By 2014, de Groot had some experimental evidence to back up his claims. He partnered with Tim Grüne and George Sheldrick at the University of Göttingen, experts in crystallographic structure refinement, to take a second look at previous X-ray data. TlWhen refined solely against anomalous diffraction data, the occupancies of four thallium ions—similar in size to potassium, but with a strong anomalous signal—were close to 0.9–1.0 each in the open KcsA filter, consistent with simultaneous occupancy at all four sites.

Credit: Nick Kim

In newer data presented Saturday, de Groot teamed up with Tom Baukrowitz of the University of Kiel to study a similar phenomenon in K2P channels, another family of potassium-conducting proteins. These channels are voltage-sensitive, despite lacking a canonical voltage-sensing domain. Baukrowitz and colleagues demonstrated that the inactive selectivity filter itself acts as a voltage sensor in K2P channels, carrying a gating charge of 2.2 elementary charge units. Assuming a linear voltage drop, this implies that at positive potentials (where the channel is open), 3–4 ions should be forced into the filter—likely occupying all four binding sites. As described in their paper, published last Thursday in Cell, “this represents the first direct electrophysiological measurement of the number of ions that can simultaneous occupy the filter in a K+ channel.” Through further computational electrophysiology experiments, k2psmde Groot demonstrated that mutations reducing ion binding at either end of the filter alter permeation and voltage-sensing: more evidence that four ions may not be too many for normal function, after all.

Credit: Schewe et al., 2016: Moving ions open the selectivity filter gate in K2P channels

More than a conference amuse-bouche, subgroups like Permeation & Transport help likeminded researchers focus and mingle before the distraction of posters and overlapping sessions begins the following day. This year, the number of Subgroup Saturday sessions was up to fourteen: newcomers Bioengineering and Cryo-EM held two-hour inaugural symposia, while longstanding participants Mechanobiology and Bioenergetics ran as long as ten hours. And although the ever-expanding Saturday schedule suggests specialization, LA - 1subgroups generally play well together—e.g. in cosponsoring Sunday evening’s SRAA student poster competition; in a nod to their inherently overlapping nature, each contestant enters in at least two categories. When the transport talks wrapped up for the subgroup business meeting, conference goers moved onto other sessions or into downtown LA with a few more ions in the filter, and a few more ideas for the meeting to come.

Sightly science

Three inventive museums.

Museum of Science & Industry, Chicago, IL

California Academy of Sciences, San Francisco, CA

Exploratorium, San Francisco, CA

Celestial spirits

This week’s news brought even more on the theme of alcohol research—this time in space!

Lead author Nicolas Biver
Lead author Biver (credit: EPSC, 2015)

As reported in Science Advances, alcohols including ethanol (the kind we drink) were detected in the comet Lovejoy (discovered, in its own remarkable story, by an amateur Australian astronomer in 2011) as it passed near the sun this January. As you might expect, an alcoholic comet represents organic chemistry at work in distant corners of the solar system, and could be evidence for an extraterrestrial origin of biomolecules. Simple sugars and amino acids found on comet Churyumov-Gerasimenko upon last fall’s Philae landing carried similar implications in a recent series of Science papers; the results from Lovejoy, among other advances, earned lead author Nicolas Biver the Farinella Prize at this year’s European Planetary Science Congress.

Comet Lovejoy from the ISS
From the ISS (Burbank, 2011)

Although all Earthly booze is produced by biological fermentation—and despite the controversial space bacteria that colonize headlines every few years—it’s unlikely that Lovejoy’s alcohol represents alien microbes at work. That conditions exist in our solar system to nucleate and preserve such a complex molecule may be even more remarkable, and informative to the origins of life.

Ethanol_methanol
Ethanol (L) and methanol (R)

This isn’t the first time alcohols have been detected on space’s breath: a cloud of methanol (one carbon smaller than ethanol) spanning 288 billion miles was identified back in 2006 in the W3(OH) region of our galaxy, 6,000 light years away. The Sagittarius B2 dust cloud, 25,000 light years from here, was shown in 2009 to contain both ethanol and ethyl formate, the aromatic element of raspberries (hopefully aliens like their vodka fruity). Alcohol content in distant galaxies has even been used to measure physical constants as precise as the mass of an electron—which, reassuringly, appears reasonably stable over at least the last 7 billion years (evidently Guinness wasn’t the first alcohol distributor in the business of setting standards).

ISS
ISS from Atlantis (NASA, 2010)

And in case you missed it this summer (I did), humans have been driving the alcohol content of space even higher. Since its first expedition in 2000, the International Space Station (ISS) has studied the effects of microgravity on slow physical processes (I remember marveling as a kid at my father’s photos of protein crystals grown in orbit). In 2011 Scotland’s Ardbeg distillery asked how gravity might affect the whiskey aging process, sending a small sample of scotch to the ISS for 2½ years; their results, posted last month in white paper and video formats, claim dramatic differences in flavor.

Japanese distiller Suntory sent six new whiskey samples to the ISS this August, so the story of space alcohol may have just begun; though according to Lovejoy, these molecules have long had a home in the stars.

Top photo credit: Mottar, 2013