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A Long Journey to Reproducible Results

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A Long Journey to Reproducible Results COMMENT EVOLUTION The astonishing CONSERVATION How power SPACE Documentary ETHOLOGY Patrick Bateson, range of Charles Darwin’s politics hijack US parks celebrates 40 years of NASA’s pioneer in animal-behaviour domestic discoveries p.389 for private gain p.390 Voyager probes p.392 science, remembered p.394 compound found in red wine — could extend lifespan in lab animals. The possibility of drugs that stall age- ing launched companies and a scientific subfield, but work in the field brought the realization that robust longevity outcomes SINCLAIR STAMMERS/SPL could be challenging to replicate. Ageing research has long battled to distance itself from pseudo scientific claims. Irreproduc- ible results from respected labs raised the spectre of yet more false promises. This had a chilling effect: some researchers (includ- ing G.J.L.) paused work on pharmacological compounds for years. Nonetheless, scores of publications continued to appear with claims about com- pounds that slow ageing. There was little effort at replication. In 2013, the three of us were charged with that unglamorous task. We have certainly not resolved discrepan- cies in the literature. But, by tracking the indi- vidual lifespans of more than 100,000 worms, we have found how crucial it is to understand sources of variability between labs and exper- iments. We even see hints of new biology that may explain discrepancies. The free-living roundworm Caenorhabditis elegans is about 1 millimetre long. BROADER PROBLEM Improved reproducibility often comes from pinning down methods. Scientists study- ing autophagy — the process by which cells A long journey to remove degraded components — have co ordinated efforts to craft and update extensive guidelines on, for instance, how to quantify that a component has been engulfed or how to verify that a gene is involved in the reproducible results 5 process . In another, now-famous example, Replicating our work took four years and 100,000 worms two cancer labs spent more than a year try- ing to understand inconsistencies6. It took but brought surprising discoveries, explain Gordon scientists working side by side on the same J. Lithgow, Monica Driscoll and Patrick Phillips. tumour biopsy to reveal that small differ- ences in how they isolated cells — vigorous stirring versus prolonged gentle rocking — bout 15 years ago, one of us (G.J.L.) as much as 67%. Numerous phone calls and produced different results. got an uncomfortable phone call e-mails failed to identify why this apparently Subtle tinkering has long been important in from a colleague and collaborator. simple experiment produced different results getting biology experiments to work. Before AAfter nearly a year of frustrating experiments, between the labs. Then another lab failed to researchers purchased kits of reagents for this colleague was about to publish a paper1 replicate our study. Despite more experiments common experiments, it wasn’t unheard of chronicling his team’s inability to reproduce and additional publications, we couldn’t work for a team to cart distilled water from one the results of our high-profile paper2 in a out why the labs were getting different lifes- institution when it moved to another. Lab mainstream journal. Our study was the first pan results. To this day, we still don’t know. members would spend months tweaking to show clearly that a drug-like molecule A few years later, the same scenario played conditions until experiments with the new could extend an animal’s lifespan. We had out with different compounds in other institution’s water worked as well as before. found over and over again that the treat- labs3,4. Around the same time, there was a Sources of variation include the qual- ment lengthened the life of a roundworm by roiling debate about whether resveratrol — a ity and purity of reagents, daily ©2017 Mac millan Publishers Li mited, part of Spri nger Nature. All ri g24hts rAUGUSTeserved. 2017 | VOL 548 | NATURE | 387 COMMENT fluctuations in microenvironment and range of Caenorhabditis strains and species. the idiosyncratic techniques of investiga- WORM WONDERS C. elegans and C. briggsae may look alike 7 tors . With so many ways of getting it wrong, Years of work greatly reduced lab-to-lab under the microscope, but genetically the two variability (A). Labs reproducibly found that 10 perhaps we should be surprised at how often species are as different as a whale and a bat . 9 SOURCE: REF. some worm strains can switch between experimental findings are reproducible. long-lived and short-lived populations (B). Our results are both encouraging and sobering. We anticipate that compounds that TO THE WORMS extend lifespan across such genetic diversity A Comparison across labs LESS VARIABILITY, BIG DISTINCTIONS One organization focusing on inconsist- Chart shows an average of 728 experiments in may be good candidates for further study. encies in ageing studies was the National 3 species and 22 isolates from 3 dierent labs. (Microscopic wormsYears might of work thus greatly eventually reduced lab-to-lab variability (left). This revealed that certain worm strains (example, right) seem to adopt long-lived or short-lived states. Institute on Aging (NIA) at the US National be used to find life-extending compounds in Institutes of Health. After all, the NIA was 100 humans.) We have found one compound that Labs Comparison across labs Same strain, different lifespans paying for the work and realized that the Rutgers lengthens lifespanShowing across allaverage strains of 728and experiments spe- from Each line represents an experimental run of 35 results needed to be iron-clad. The NIA also Buck cies. Most do so in3 only species two and or 22 three isolates strains, from 3 dierent labs. worms. Here, C. briggsae JU1264 from the Buck lab. had a success story; its Intervention Testing Oregon and often show detrimental effects in others. 100 Program had discovered that the drug rapa- 50 This raises a series of intriguing mechanis- 100 Labs Short lived mycin extended the lifespans of mice at three tic questions, and might help to explain the Rutgers Long lived independent labs applying a common pro- living (%) Worms genetic influences in an individual’s response Buck 8 Oregon tocol . The NIA initiated the Caenorhabditis to an ageing intervention. xx day range Intervention Testing Program with similar 0 Other discrepancies50 are probably based on 50 between the goals, and tasked us — three researchers 0 25 50 small methodological differences in survival shortest and longest Days with different areas of expertise who had not assays. For example, small fluctuations in surviving Worm survival rate (%) rate survival Worm worms. worked together before — to systematically temperature in incubators and lab benches (%) rate survival Worm test ageing interventions in the nematode B Same strain, different lifespans are likely to be significant, as are differences 0 0 Caenorhabditis elegans. Each line represents an experimental run in food quality. of 35 worms — in this case, Caenorhabditis 0 25 50 0 25 50 In the lab, these worms live on agar plates briggsae strain ED3092. It is a rare project that specifies methodsDays Days and are fed a diet of live bacteria. Test com- with such precision. In fact, several mouse pounds are mixed into the agar or feedstock, 100 researchers have argued that standardiza- and longevity is assessed by mobility — if tion is counterproductive — better to focus a worm moves when prodded with a metal on results that persist across a wide range of wire, it’s alive! This technique has been used conditions than to chase fragile findings that by worm researchers for more than 25 years. 50 occur only within narrow parameters. Our first task, to develop a protocol, seemed We argue that another way forward is to What prompts straightforward. living (%) Worms distinct states is chase down the variability and try to under- But subtle disparities were endless. In one still unknown. stand it within a common environment. particularly painful teleconference, we spent 0 We are now working together to search for an hour debating the proper procedure for 0 25 50 molecular differences that distinguish short- picking up worms and placing them on new Days lived and long-lived batches of worms within agar plates. Some batches of worms lived a full the same strain, a phenomenon we never day longer with gentler technicians. Because could have uncovered had we not eliminated a worm’s lifespan is only about 20 days, this are not the same). This simple technology nearly all other sources of variability. is a big deal. Hundreds of e-mails and many removed small recording errors that could We have learnt that to understand how teleconferences later, we converged on a disproportionately affect statistical analyses. life works, describing how the research was technique but still had a stupendous three- Once this system was in place, variability done is as important as describing what was day difference in lifespan between labs. The between labs decreased. After more than a observed. ■ problem, it turned out, was notation — one year of pilot experiments and discussion of lab determined age on the basis of when an methods in excruciating detail, we almost Gordon J. Lithgow is a geneticist at the egg hatched, others on when it was laid. completely eliminated systematic differences Buck Institute for Research on Aging in Short lived 9 We decided to buy shared batches of reagents in worm survivalLong across lived our labs (see ‘Worm Novato, California, USA. Monica Driscoll from the start. Coordination was a nightmare; wonders’). is a developmental biologist at Rutgers we arranged with suppliers to give us the same Our data revealed another, startling source University in Piscataway, New Jersey, USA. lot numbers and elected to change lots at the of variation. Even in a single lab perform- Patrick Phillips is an evolutionary geneticist same time.
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