HistoryI decided to be a scientist when I was 7 years old after watching Carl Sagan on TV talk about neutron stars. By 16 I discovered the protein folding problem: a disarmingly simply stated problem whose solution lay at the heart of everything in biology. How hard could it be?So a degree in Biochemistry later, I did a PhD in the lab of a computational molecular modeller (Mike Sutcliffe) and got started on the problem of clustering protein structures from NMR. I wrote my first program in C and built my first web site with my characteristically stupid pun in the name - OLDERADO: On-Line Database of Ensemble Representatives and Domains [1] - to look at the results. Each morning I would go on the internet as it then was to check the dozen or so new sites that had sprung up the night before and which had been manually added to a list known as the ‘internet directory’ by someone ‘out there’ on the new web. Google appeared about a month later. Websites were going to be a big deal. Being an early adopter of web-based science seemed like a good bet.Then a move to London to be with Mike Sternberg, a world expert on protein structure prediction. I inherited an early protein fold recognition program (Foldfit [2]) written by Rob Russell, Mansoor Saqi, Paul Bates and Roger Sayle (of Rasmol fame) and had to improve it. The result was 3D-PSSM [3] and I made a ‘fancy’ website (read: 1990’s black background with gold, animated logo) for other people to use the program and for me to figure out where the bugs were. It worked great - we won the automated section of the international CASP competition in structure prediction, and hundreds of people started using the site. It was one of the first of its kind, which made it easier to stand out. Throughout I was mainly making the site to help me understand how my software worked in various situations. With so many different types of data to look at, I needed a way to sensibly display this info just to understand what was going on internally. This remains a critical focus.New techniques arose in the field and I sat on my laurels with 3D-PSSM. I neglected the site and realised only later how valuable a large internet audience is and how I had squandered it at its peak. So I vowed to try again and rebuild it from the ground up, this time properly. Using newfound skills in web development I created Phyre [4]. This did well in both scientific recognition and number of users so I was very pleased. But soon funding looked iffy and was about to run out. Funding I wondered if any users could help. So I asked on the Phyre page if anyone could write a letter of support for us that we could include with our application for funding. We received over 1,000 letters of support which was amazing and had a huge effect on our application. But I think it placed the funding bodies in a difficult position. Making web sites that help scientists use state-of-the-art tools is undoubtedly a good thing. These site are continuously working, 24 hrs/day reliably doing some work to help science. They seem like safe and sensible places to direct funding - IF they are widely used. IF they are widely used, the funding body would look deliberately negligent if they failed to fund it. But at the same time they are justified in thinking this is outside their remit. They decide on science funding, not tools. So new arms of the funding bodies started to form, dedicated to tools and resources. This is where we are today. But deciding how to handle funding for tools is a new challenge we are all still grappling with. The quest for funding is ever-present. It is critical that tools are maintained. How do you justify the maintenance cost? It is easy to fall through the funding cracks - it’s neither proper science, nor pure infrastructure. I get very paranoid about funding living in this limbo. But if user numbers and citations continue to increase, we are safe. These are the only ways to prove your value in this game. But this hopefully reflects real-world utility of the tools you create. So what’s the best way to maximise the utility of these tools to researchers?Build it, and they will comeGreat tools based on state-of-the-art algorithms often go unused and unnoticed - great science gets ‘hidden’ in the hands of a few people competing intensely over small absolute changes in accuracy using programs designed for no one but the developers. The gains to society and science by enabling more people to use these tools are far greater. But then they need to be far easier to use if more people are to use them. Hence my focus on user interfaces. The best way to learn what works for user interfaces is by using lots of them. And thinking about the types of question a user may have. Simply BE a user and every time you want to do something and CAN’T, write a program to do it. Accumulate these programs in a web site. This empowers me and anyone else who cares, with these new tools - a virtuous circle.‘BE the user’ sounds great. But it gets harder as you spend more time with computer development and less time working on a biological problem with real proteins. I don’t mean wet lab. Just computational analysis problems with specific proteins faced by real scientists. That’s the hardest part to remain connected to. For now I just imagine scenarios. I imagine all the combinations we can make by connecting our tools in different ways, and build some that seem most promising. I meet users at workshops to find out what they want. But this is where the next development needs to happen. How can I communicate effectively with 50,000 users about what they want and what I can deliver? This is the biggest challenge for me right now.Despite the funding complexities, we got funding for Phyre2 [5]. THIS time I can do it properly, I thought. Use the most up to date facilities in the browser to make it look nicer, easier to use, and add those new ideas I had or were suggested to me by users at workshops (PhyreAlarm, BackPhyre, One-2-one threading). I also tried to improve how a user could look both at sequence and structure at the same time in the browser to analyse a range of features. This led to the development of Phyre Investigator (one module in Phyre2) and honed my skills at javascript for the future. This most recent paper has again done well in the citation game which I hope reflects its usefulness to researchers ‘out there’ on the web.FoldingIt’s important to remember the reason I’ve done any of this, and that reason is the mystery of protein folding. The person that solves the protein folding problem (at least I hope it’s a person) won’t do it with pen and paper. It will be someone extremely adept at using a variety of tools that probably already exist individually, and who will put them together in the right way. That is generic problem solving. Make this easier for people, and problems in general get solved faster. With folding my main fear is this being one of the first major science problems where artificial intelligence gets there before us. Google DeepMind is after it, and we’ve seen what they’ve done to the game Go.Protein folding is the molecular biology equivalent of the Goldbach conjecture: The impossible task that no one would sensibly pay you to work on but you want to work on because of its elegant simplicity and deep importance. So you need to do something useful while you ponder the impossible. You find the most useful thing you can do for everyone else and for you. Keep it as close as you can to folding whilst maintaining an audience size that justifies your existence - i.e. homology modelling. Problems that no one has been able to solve for decades typically don’t fall over from expected directions of attack. To be a long-standing problem means most lines of attack that occur to people have been tried. So new lines must be found by looking further afield, in other areas of science where an analogous problem may have been thwarted. But to see the mapping between a problem in say physics or economics or mathematics, to the folding problem requires a decent understanding of both areas. So that means trying to learn physics, signal processing, quantum mechanics, maths, computer science, AI, etc. All in the hope of seeing a new angle from which to attack the problem. And it’s fun and fascinating. But you need to make yourself useful to the world and justify your salary. My most recent direct stab at folding involved eigen decomposition of protein contact maps. As you may surmise, I have not yet been contacted by Stockholm.Where to publish?Well it’s not really science is it? Its tools to do science. So it doesn’t sit easily with most journals. You can submit an ‘Application Note’ which is about a page describing your web server. This doesn’t really count as a proper scientific paper in many eyes. Or often authors will use their tool to do some rapidly thrown together analysis that makes what would otherwise be an application note pass for a normal scientific article. Neither of these scenarios is ideal. The way I see it, when I’ve made a tool I haven’t answered a biological question, but I’ve made it easier to answer many biological questions. In the end we went for Nature Protocols which is aimed at step by step instruction for how to use previously published tools. It fits, albeit somewhat uncomfortably.FutureSo Phyre2 has done very well in attracting users and now I’m on to Phyre3 which will be out shortly (end of 2017). Again it’s a full redesign, this time with two people on it, me on the front end and my colleague Stefans Mezulis on the back-end, using the browser to its best, new web tech, polished with a new engine (the PhyreEngine, naturally) and more hardware for faster processing of bigger genomes. Also an entirely new tool called PhyreRisk is being developed: a portal for analysing disease, mutations, structures and complexes. But the primary focus is still the same: utility. What do people want or need to do and what can be done computationally to help them. The better we can match what can be done computationally with what researchers want to do, the faster we will make progress in all of science. And maybe we’ll beat DeepMind to the answer to protein folding. ReferencesOLDERADO: On‐line database of ensemble representatives and domains. LA Kelley, MJ Sutcliffe, Protein science 6 (12), 2628-2630 (1997)Recognition of analogous and homologous protein folds - assessment of prediction success and associated alignment accuracy using empirical substitution matrices. Russell RB, Saqi MA, Bates PA, Sayle RA, Sternberg MJ. Protein Eng. Jan;11(1):1-9. (1998)Enhanced genome annotation using structural profiles in the program 3D-PSSM. LA Kelley, RM MacCallum, MJE Sternberg. Journal of molecular biology 299 (2), 501-522. (2000)Protein structure prediction on the Web: a case study using the Phyre server. LA Kelley, MJE Sternberg. Nature protocols 4 (3), 363-371. (2009)The Phyre2 web portal for protein modeling, prediction and analysis. LA Kelley, S Mezulis, CM Yates, MN Wass, MJE Sternberg. Nature protocols 10 (6), 845-858 (2015)

This article is the backstory behind: S. Van den Bosch, W. Schutyser, B.F. Sels, et al., Reductive lignocellulose fractionation into soluble lignin-derived phenolic monomers and dimers and processable carbohydrate pulps \cite{Bosch2015}. 

This is the backstory behind the scientific article entitled "Climate-related range shifts – a global multidimensional synthesis and new research directions" published in Ecography \citep*{Lenoir2015}.

The critical event that eventually led to the first of my meta-analysis papers on genetic rescue occurred in February 2007 at a book writing session on the second edition of “Introduction to Conservation Genetics” \citep{Frankham} at Jonathan Ballou’s house in the Washington, D.C. area. Upon reaching the topic of outbreeding depression (where the effects of crossing populations results in harmful fitness effects in the progeny), we both expressed serious disquiet that the risks of outbreeding depression were being overplayed, while the potential fitness benefits of crossing (genetic rescue) were largely being ignored. One of us said “we must be able to predict the risk of outbreeding depression”. A few days later inspiration struck and we had the key to doing this: harmful effects on fitness of crossing populations typically arise when the crossed populations have fixed chromosomal differences, and/or are adapted to different environments. We subsequently recruited Katherine, Ralls, Mark Eldridge, Michele Dudash, Charles Fenster and Robert Lacy and jointly transformed this insight into a paper that was published in Conservation Biology \cite{FRANKHAM_2011}. That work was critical to the ability to use genetic rescue (variously called outcrossing or augmentation of gene flow) as a tool to save small inbred population fragments from extinction, and thereby reduce population and species extinction risks. As genetic rescue had been attempted in very few cases, we decided to write a book on “Genetic Management of Fragmented Animals and Plant Populations” in an attempt to create a paradigm shift where the discovery of genetically differentiated populations was followed, not by the conclusion that separate management of fragments was required, but by asking if any of the populations were suffering genetic erosion (inbreeding, loss of genetic variation, reduced fitness, reduced ability to evolve and elevated extinction risk), and if so, was a genetic rescue attempt justified. I drafted Chapter 6 on Genetic rescue for the book, and then decided that it needed some examples which were put into a Table. At this point, I finally recognized that a fully-fledged meta-analysis was required, as there was no overview of the effects of outcrossing in a conservation context, i.e. when an inbred population fragment with low genetic diversity was crossed to another population and where the risk of outbreeding depression in the resulting progeny was low. The meta-analysis was done without external research funding as I have been officially retired since 2002 (but am still scientifically active) and do not have grant money for any of the work described here. I am great fan of meta-analyses: not only can they be done without research funds, but they are typically highly cited, similar to reviews, and are superior scientifically to them. By mining the literature, I found 156 relevant comparisons of inbred parents and their outcrossed progeny, and 145 had beneficial effects on fitness. Only one of the cases where crossing was harmful was a convincing case of outbreeding depression (in a selfing nematode), the others likely being chance observations due to low statistical power. The median fitness benefit from augmenting gene flow was 148% in wild/stressful conditions and 45% in benign/captive ones. Consequently, there are huge potential benefits from augmenting gene flow into population fragments suffering from genetic erosion, provided the risk of outbreeding depression in proposed crosses is low. Thus, the two main impediments to genetic rescue attempts have been removed. This paper was published in Molecular Ecology \cite{Frankham_2015} (currently 123 citations in Google Scholar), and was accompanied by a commentary from Donald Waller \cite{Waller_2015}. He praised the paper, but was not convinced about the persistence of the benefits over generations. Consequently, I did further analyses on my database to compare the effects of crossing on fitness in the F1, F2 and F3 generations and this confirmed that the benefits persisted to an extent that was, if anything, better than expected. This led to the publication of a second genetic rescue meta-analysis paper in Biological Conservations \cite{Frankham_2016}. Writing of our book continued (with Paul Sunnucks being added as another author) and it was submitted to Oxford University Press in December 2016. However, during the subsequent copy editing I realised that the second genetic rescue meta-analysis paper was incomplete, as the persistence of fitness benefits following crossing is expected to depend on the breeding system. Persistence of fitness benefits across generations is expected for outbreeders, but habitual selfing after crossing will lead to loss of benefits, while mixed mating species should experience only partial persistence of fitness benefits. I subsequently extended the analyses of my database from F3 to F13 and found no significant decline in fitness benefits for outbreeding species. Further, \citet{Bijlsma_2010} found no significant change in fitness between F10 and F15 generations in outbreeding Drosophila flies. The updated findings were included in the published version of our “Genetic Management of Fragmented Animal and Plant Populations” book \citep{Frankham_2017}. This was followed by a related paper calling for a paradigm shift in the genetic management of fragmented populations \citep{Ralls_2017}.

This is the backstory of: From industrially weavable and knittable highly conductive yarns to large wearable energy storage textiles \cite{Huang_2015b}.

This is the Backstory behind Current developments in fluorescent PET (photoinduced electron transfer) sensors and switches \cite{Daly_2015}

Backstory of  Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephens \cite{Gantz2015}. Developing gene-drive technology:  In late 2014 Valentino Gantz, then a graduate student in my lab at the University of California, San Diego (UCSD), described to me an idea for a CRISPR-based strategy to uncover the effect of recessive mutations in a single generation by creating a self-propagating mutagenic genetic element.  In our discussion, it became clear that this element might also propagate itself through mating and be passed on to the next generation at frequencies much higher than predicted by  standard "Mendelian" inheritance, a phenomenon often referred to as gene-drive1.  Following a series of additional discussions within the lab and advisory faculty members at UCSD, including Marty Yanofsky (then chair of CDB), Bill McGinnis (Dean of Biological Sciences), Steve Wasserman, and Joseph Vinetz (member of UCSD Institutional Biosafety Committee), we planned, constructed, and safely tested (in Joe Vinetz's ACL2 insectary) this genetic system in the fruit fly Drosophila melanogaster.  We called this method the mutagenic chain reaction (MCR) in analogy to the polymerase chain reaction (PCR).  We now refer broadly to the use of self-propagating CRISPR-based genetic elements as "active genetics". We submitted a manuscript for publication in Science on December 31, 2014, describing a simple proof-of-principle experiment in which an MCR element inserted into the Drosophila yellow gene, which is required for body pigmentation, was transmitted to nearly all offspring.  This paper, which was published online on March 19, 2015 \cite{Gantz_2015}, attracted considerable media attention and is credited with being the first to experimentally demonstrate a CRISPR-based gene-drive in a multicellular organism with a dedicated germline.  The study was cited as one of the primary reasons for CRISPR being chosen as the breakthrough of the year in 2015 by Science magazine.  This discovery also was ranked #11 overall and #2 in biology in the 100 top discoveries of 2015 by Discover Magazine.Applying a gene-drive system to combat malaria:  One application of gene-drive technology under discussion since the mid-1960s \cite{CURTIS_1968} is to use one of many possible strategies  to generate an inheritance bias and spread a desired trait into a target population. For example, a gene-drive element could be used to either kill mosquitoes as a kind of genetic insecticide \cite{Burt_2003}, or to spread a trait throughout a mosquito population that rendered them incapable of transmitting malarial parasites \cite{2006}.   Anthony (Tony) James at the University of California at Irvine (UCI) is one researcher who has dedicated his career to combatting malaria.  Tony was the first person ever to clone and describe a protein-encoding gene from any mosquito \cite{James_1989} and in his lab he first developed reliable methods for producing transgenic mosquitoes \cite{Jasinskiene_1998}.  His group then engineered sophisticated genetic cassettes that produce single chain antibodies that were capable of fully blocking transmission of malarial parasites \cite{Isaacs_2012,Isaacs_2011}. These antibodies bind to and neutralize malarial parasites following a female mosquito feeding on blood (only female mosquitoes bite).  James proposed to use a gene-drive approach to spread the immunizing antibody cassettes into mosquito populations, which should render those mosquitoes incapable of transmitting malaria to humans.  The final prescient sentence of his most recent paper on that topic published in 2012 stated: "If coupled with a mechanism for gene spread, antibody-expressing, malaria-resistance transgenes could become a self-sustaining disease control tool" \cite{Isaacs2012}.  On January 9, 2015, shortly after submission of our paper to Science describing efficient transmission of the MCR element in Drosophila, Valentino and I contacted Tony to ask him if he might be interested in a collaboration in which we hooked up our gene-drive system to his "immunizing" gene cassette.  Tony enthusiastically agreed.  Based on subsequent discussions, Valentino designed and constructed an immunizing gene-drive element targeting insertion into a gene called kynurenine hydroxylase (kh), which is required for normal eye pigmentation.  Valentino sent the completed kh-MCR construct to the James group, who then injected this synthetic DNA into mosquitoes.  On July 29, 2015 the James team recovered 2 transgenic individuals carrying the kh-MCR construct (out of ~ 25,000 injected larvae screened).  The memorable email that Tony sent me reporting the first results indicating how the kh-MCR was transmitted to progeny was entitled: "Friar Mendel takes a break".  After analyzing the transmission of the kh-MCR element over four generations, we prepared a manuscript entitled "Highly efficient Cas9-mediated gene drive for population modification of the malaria vector mosquito Anopheles stephensi" \cite{Gantz08122015} , which is the subject of this Backstory.  This paper, published on November 23, 2015 in the Proceedings of the National Academies of Science (PNAS), described the highly efficient transmission of the kh-MCR element to >99% of offspring via male parents.  There was significant media coverage of this first demonstration of efficient CRISPR-based gene-drive in mosquitoes, which is still ongoing over two years later. Addressing safety, ethical, and societal aspects gene-drives:  Given the potential of gene-drive systems to alter wild populations, Valentino, Tony, and I have devoted significant effort to engage scientists, social scientists, governmental regulators, and the public to initiate discussion regarding the ethical use of gene-drive systems to benefit society.  These efforts have encompassed areas including ethics, political science, sociology, health policy, as well as government regulatory agencies to provide transparent and informative explanations of active genetics technology and it applications.  For example, we jointly co-authored an opinion piece in Science with 23 other colleagues suggesting precautionary measures for safe use of gene-drive systems in the laboratory \cite{Akbari_2016} and organized a UCSD/JCVI workshop on regulation of gene-drives \cite{Adelman_2017}.  We also provided briefs to the NAS and federal risk assessment agencies (e.g., an Obama administration risk assessment panel comprising members of the FBI, CIA and Department of Homeland Security as well as presentations to the JASON study group) and a series of presentations to university Biosafety (e.g., IBC) and bioethics groups.  We continue to participate in forums for scientific and community engagement and contribute actively to ongoing discussions on these important topics. A future vision for active genetics:  In January 2016, Valentino Gantz and I published our vision for the future of active genetics in a BioEssays review \cite{BIES:BIES201500102}.  In this review, we outlined applications of active genetics to gene-drive systems, auxiliary updating drive elements such as CHACRs, reversal drives such as ERACRs and eCHACRs, bi-partite trans-complementing drives, split-drive CopyCat site-directed transgenesis vectors, potential uses for human cell therapy applications, and a summary of the ethical and safety considerations associated with gene-drive technology.Acknowledgements The author thanks Anthony (Tony) James) and Valentino Gantz for helpful comments on this Backstory and for the joy of our shared adventure 1Early geneticists referred to this phenomenon as ‘meiotic drive’ 

This article is the backstory behind: S. Fritz, L. See, I. McCallum et al., Mapping global cropland and field size. Global Change Biology, 21(5), 1980-1992. doi: 10.1111/gcb.12838  

This document was originally published at The Winnower and is the backstory behind Hart, V., P. Novakova, E. P. Malkemper, S. Begall, V. Hanzal, M. Jezek, T. Kusta, V. Nemcova, J. Adamkova, K. Benediktova, J. Cerveny, and H. Burda. 2013. "Dogs are sensitive to small variations of the Earth's magnetic field." Front Zool no. 10 (1):80. doi: 10.1186/1742-9994-10-80.Almost half a century ago, the first firm evidence for magnetoreception (i.e. the ability to sense the geomagnetic field) in the robin was provided, representing the first evidence for magnetoreception in a vertebrate (Wiltschko and Merkel 1966); a quarter century later Burda et al. (Burda et al. 1990) demonstrated magnetoreception for the first time in the laboratory in African mole-rats, the first demonstration in mammals. Over the last 25 years we have revisited the question of magnetoreception in mole-rats and made some spectacular discoveries (Marhold, Wiltschko, and Burda 1997, Nemec et al. 2001, Thalau et al. 2006, Wegner, Begall, and Burda 2006, Burger et al. 2010). Subsequently, magnetoreception has been described also in the blind mole rat Spalax ehrenbergi supersp. (Kimchi and Terkel 2001, Kimchi, Etienne, and Terkel 2004, Marhold et al. 2000), the laboratory mouse Mus domesticus (Muheim et al. 2006), the Siberian hamster Phodopus sungorus (Deutschlander et al. 2003), and in the bats Eptesicus fucus (Holland et al. 2006, Holland et al. 2008) and Nyctalus plancyi (Wang et al. 2007). However, the question if large mammals also sense the geomagnetic field was left unanswered.How to study magnetoreception in large mammals Some mammals, such as arctic caribous, North American bisons, African elephants and gnus, and Asian saiga antelopes, and, above all, diverse cetacean species are famous for their long range migrations, which require superb navigational capacities. Based on these capacities and on correlations between navigation failures and local disturbances of the geomagnetic field we may conclude that navigation capacities are based on magnetoreception (Klinowska 1985, Kirschvink, Dizon, and Westphal 1986). Apart from such indirect evidence there are also anecdotal reports on homing abilities of dogs, cats, horses etc. (just remember "Lassie Come Home"). Systematic research on navigational capabilities using homing paradigms is technically difficult. Besides that, there could be plenty of non-navigational reasons why displaced mammals do not return home. Conditioning (training) on magnetic stimuli in large animals is methodically difficult. The animals might switch on the magnetic compass sense only in certain contexts, e.g. when being outdoors, in unfamiliar surroundings, where they cannot rely on other senses, but not under laboratory conditions.However, looking for spontaneous expressions of magnetosensitivity, such as magnetic alignment is an easy and effective method to scan for magnetoreception in animals. Animals (and also humans) frequently adopt orientation in space which is not random (Begall et al. 2013): e.g. when sun basking they align perpendicular to solar rays (thermic alignment), trout in the brook aligns against the stream (rheo-alignment), a scenting dog aligns against the wind (anemo-alignment), the audience turns towards the speaker (alignment towards an attractor), grazing sheep on a slope wander along the contours (isocline-alignment). Apparently alignment has some advantages - it is comfortable, saves energy, or provides access to food, oxygen or information. And now imagine that there is no slope, no attractor, no wind and the sun is not visible. Will the orientation (body axis, heading) of a resting animal be random or might the animal prefer to adopt some particular compass direction? If we find that animals prefer a particular compass direction under these unconstrained conditions, we may hypothesize that such a non-random orientation represents a case of magnetic alignment, implying magnetoreception. Subsequently, we may test this hypothesis by changing the magnetic conditions and observing whether the orientation also changes. Scanning for cases of magnetic alignment is thus a suitable experimental paradigm for magnetobiological research and might provide new insights into meaning of magnetoreception in animals' everyday life. Why do animals do it? Which information do they get from the magnetic field? Can they save energy (get more comfort) when magnetically aligned? How do they sense the magnetic field?For over six years we have been following this research program and have reported magnetic alignment in grazing and resting cattle, roe deer and red deer (Begall et al. 2008) and disturbance of this alignment through extremely low frequency magnetic fields (ELF MF) produced by high voltage power lines (Burda et al. 2009). These papers raised high resonance all over the world. Skeptics did not like particularly the idea that ELF MF might influence the behavior (and welfare?) of animals (and human health?). They attacked our results (Hert et al. 2011), but we could show (Begall et al. 2011) that their study was heavily flawed and cleaned of errors it actually fully confirmed our original findings. Our results were subsequently confirmed in an independent study by Slabý et al. (Slaby, Tomanova, and Vacha 2013). In other studies we found magnetic alignment in hunting foxes (Cerveny et al. 2011), carps schooling in circular tubs (Hart et al. 2012), and mallard ducks landing on water (Hart et al. 2013). We concluded that magnetic alignment might help animals to synchronize and coordinate movement in a group, organize cognitive (mental) maps, measure the distance and the slope, and maybe enhance (focus) selective sensory attention. Our model mammals (cattle, deer, fox) were, however, rather "unhandy" and unmanageable for further research. We envisaged that dogs represent ideal model animals for further research, since they are widespread across the world and are highly receptive to learning.How to study magnetoreception in dogsOur established team of sensory ecologists from Essen, Germany, and wildlife zoologists from Prague, Czech Republic, asked dog owners (relatives, friends and students) to measure, in analogy with our previous research on cattle and deer, body orientation of feeding and sleeping dogs. We soon realized, however, that body orientation during these activities is influenced, consciously or unconsciously by the master, by house geometry etc. Besides that, the geomagnetic field inside buildings is mostly disturbed, and it would require many cooperators to get sufficient sample sizes. We noticed, however, that dogs defecating and urinating during a walk (actually they are marking their territories) are very selective about where to mark. We can prevent them to mark somewhere but we can hardly make them do the job when and where we wish. Well known, yet enigmatic and unexplained (though there are many ideas) is the circling (some) dogs sometimes perform before urinating or defecating. Every dog defecates on average once and urinates (marks) many times a day; keepers go with their dogs at least three times a day to a walk; if every walk (in the morning, afternoon, and evening) would follow another route, measurements of orientation of particular dogs cannot be considered pseudoreplications, as they would be done always at a different time, at different place, under somewhat different environmental conditions. We standardized the protocol, asked our volunteers to record compass direction of the body axis (heading) of defecating and urinating dogs, which would be unrestrained by walls and fences, i.e. in open field, off the leash, and outdoors (i.e. not at the home backyard or in the familiar garden). We recruited a team of almost 40 observers following 70 dogs of almost 40 breeds over two years, recording about 1,900 defecation and 5,600 urination events. After we closed sampling, we ran circular statistical analyses and were disappointed to see that there was no common preference for any particular compass direction. We analyzed the data with respect to sex, age, breed, and body mass of the dog, time of the day and month but no clear picture emerged. The subsamples, i.e. the numbers of records collected for particular dogs were not even. One dog, a male borzoi named Diadem, was recorded on a regular basis over a long time providing about 2,500 measurements of body orientation. Diadem's data showed to be a gold mine. We noticed that on some days and during some walks Diadem showed perfect compass preference (in his case for Northwest), while during some other walks and on some particular dates his orientation during marking was fully random. It was just by chance that, when analyzing the data, we heard a radio report about geomagnetic storms and the idea was born to check the "space weather" on those days when Diadem was apparently "disoriented". A comparison between "quiet" and "stormy" days confirmed that alignment could be correlated to "magnetic weather". In subsequent weeks and months we spent many hours of leisure time looking for different indices of magnetic weather at time and place of the particular walks and checking which of them correlate best with the "alignment achievement" of the dogs. We finally found that the best predictor of alignment was the speed (rate, slope) of changes in the magnetic declination at the time interval 30 minutes before the dog was urinating or defecating. This single factor had the power to extract a highly significant alignment from a random distribution.Most volunteers were aware of our previous findings and an unconscious bias in measurements could not be excluded. (Meanwhile we developed smart phone apps to measure the compass direction blindly, i.e., without showing the measured value.) None of us or of the volunteers who measured their dogs knew, however, the "magnetic weather" when taking or analyzing the measurements. Thus, the study was indeed fully blind.Why do the dogs do it?The dog has a mental map of its home range or creates such a map whenever being in an unfamiliar region. Our hypothesis is that when the dog marks or defecates, it uses these short stops to store the location ("coordinates") of marking cornerstones (as landmarks) in its memory. Doing so and/or calibrating its magnetic compass is probably easier for it when being aligned with the magnetic field. (When we read a map and use a compass outdoors we also align according to some directions and landmarks). Apparently, the dog needs calm "magnetic weather" to do so.The publication and its impactWe were quite excited about our findings as this was the first evidence for a) magnetoreception in dogs, b) sensitivity to such small changes of the geomagnetic field in a mammal, c) sensing small changes in polarity (rather than in intensity) of the magnetic field in an animal. Knowing that dogs can sense magnetic fields opens up new possibilities for investigation of principles and mechanisms of magnetoreception. Knowing that animals may sense small oscillations in the geomagnetic field and react with a behavioral change calls for considering this factor when studying and analyzing many aspects of animal behavior.Of course, we wanted to publish our results in a top multidisciplinary journal. Yet all the journals returned the manuscript immediately - as being of only minor interest for their general readerships. We assume that the editors were afraid to become embarrassed by publishing a study dealing with something as trivial as defecation. Maybe they have misunderstood its message. We are very grateful to Frontiers in Zoology, a top journal in zoology, for letting the manuscript to be peer reviewed. After passing the very quick but also very thorough review process, the paper was published during Christmas holidays in 2013. Still before our universities published a press release and before we made any advertisement for it, a report about it was published in the Journal of Improbable Research. Within one week after publication, the paper achieved an altmetric score of 1,715 and was accessed about 740,000 times. (The score rose to 2,854 and the number of accesses to almost 880,000 three months later.) We were contacted by many journals and newspapers, internet sites, radio and TV news, professionals and interested laymen. Many published reports were based on tertiary sources and most of the "reporters" have never read the original article, although it is freely accessible in the internet. The message of our article was reduced to the statement that dogs prefer to face northwards when defecating. (Something we never claimed.) Many applauded while others berated. We were often rebuked for wasting tax money for nonsense research. People claiming this have perhaps never deliberated on possible costs of such studies. This research on dogs was done in our leisure time - we walked with our dogs in the same way as millions of people do all over the world - but we took also compass, paper and pencil, and in the evening when others were watching TV, surfing in the web or going in for their hobbies, we analyzed our results. So - it was our hobby and we had fun doing it. We have experienced immense reactions upon our research already before, when we described magnetic alignment in cattle. Our studies dealing with other animals aroused much less interest. Based on our experience we were not surprised that our article on dogs made quite a splash. Many dog owners assume they "know" everything about dogs and are qualified to comment. Very few people have pet deer, foxes, mole-rats or shrews, so our work on these animals did not challenge them personally.A study that makes people laugh and then they start to think The Journal of Improbable Research which started this hype is dedicated to research that makes people laugh and then think. We believe that this will be also the fate of our paper. Indeed, finding that dogs can sense and recognize small fluctuations of the geomagnetic field provides us with lots of stuff to think seriously about.ReferencesBegall, S., H. Burda, J. Cerveny, O. Gerter, J. Neef-Weisse, and P. Nemec. 2011. "Further support for the alignment of cattle along magnetic field lines: reply to Hert et al." J Comp Physiol A no. 197 (12):1127-1133. doi: 10.1007/s00359-011-0674-1.Begall, S., J. Cerveny, J. Neef, O. Vojtech, and H. Burda. 2008. "Magnetic alignment in grazing and resting cattle and deer." Proc Natl Acad Sci U S A no. 105 (36):13451-5. doi: 10.1073/pnas.0803650105.Begall, S., E. P. Malkemper, J. Cerveny, P. Nemec, and H. Burda. 2013. "Magnetic alignment in mammals and other animals." Mammalian Biology no. 78 (1):10-20. doi: 10.1016/j.mambio.2012.05.005.Burda, H., S. Begall, J. Cerveny, J. Neef, and P. Nemec. 2009. "Extremely low-frequency electromagnetic fields disrupt magnetic alignment of ruminants." Proc Natl Acad Sci U S A no. 106 (14):5708-13. doi: 10.1073/pnas.0811194106.Burda, H., S. Marhold, T. Westenberger, W. Wiltschko, and R. Wiltschko. 1990. "Magnetic compass orientation in the subterranean rodent Cryptomys hottentotus (Bathyergidae, Rodentia)." Experientia (46):528-530.Burger, T., M. Lucova, R. Moritz, H. OelschlŠger, R. Druga, H. Burda, W. Wiltschko, R. Wiltschko, and P. Nemec. 2010. "Changing and shielded magnetic fields suppress c-Fos expression in the navigation circuit: input from the magnetosensory system contributes to the internal representation of space in a subterranean rodent." Journal of The Royal Society Interface no. 7 (50):1275-1292. doi: 10.1098/rsif.2009.0551.Cerveny, J., S. Begall, P. Koubek, P. Novakova, and H. Burda. 2011. "Directional preference may enhance hunting accuracy in foraging foxes." Biology Letters no. 7 (3):355-357. doi: 10.1098/rsbl.2010.1145.Deutschlander, M., M. Freake, C. Borland, J.B. Phillips, R.C. Madden, L. Anderson, and B. Wilson. 2003. "Learned magnetic compass orientation by the Siberian hamster, Phodopus sungorus." Animal Behaviour no. 65 (4):779-786. doi: 10.1006/anbe.2003.2111.Hart, V., T. Kusta, P. Nemec, V. Blahova, M. Jezek, P. Novakova, S. Begall, J. Cerveny, V. Hanzal, E. P. Malkemper, K. Stipek, C. Vole, and H. Burda. 2012. "Magnetic alignment in carps: evidence from the Czech christmas fish market." PLoS One no. 7 (12):e51100. doi: 10.1371/journal.pone.0051100.Hart, V., E. P. Malkemper, T. Kusta, S. Begall, P. Novakova, V. Hanzal, L. Pleskac, M. Jezek, R. Policht, V. Husinec, J. Cerveny, and H. Burda. 2013. "Directional compass preference for landing in water birds." Front Zool no. 10 (1):38. doi: 10.1186/1742-9994-10-38.Hert, J., L. Jelinek, L. Pekarek, and A. Pavlicek. 2011. "No alignment of cattle along geomagnetic field lines found." Journal of Comparative Physiology A no. 197 (6):677-682. doi: 10.1007/s00359-011-0628-7.Holland, R.A., J.L. Kirschvink, T.G. Doak, and M. Wikelski. 2008. "Bats use magnetite to detect the Earth's magnetic field." PLoS ONE no. 3 (2):e1676. doi: 10.1371/journal.pone.0001676.Holland, R.A., K. Thorup, J.M. Vonhof, W.W Cochran, and M Wikelski. 2006. "Navigation: Bat orientation using Earth's magnetic field." Nature no. 444 (7120):702-702. doi: 10.1038/444702a.Kimchi, T., A. S. Etienne, and J. Terkel. 2004. "A subterranean mammal uses the magnetic compass for path integration." Proc Natl Acad Sci U S A no. 101 (4):1105-9. doi: 10.1073/pnas.0307560100.Kimchi, T., and J. Terkel. 2001. "Magnetic compass orientation in the blind mole rat Spalax ehrenbergi." J. Exp. Biol. (204):751-758.Kirschvink, J.L., A.E. Dizon, and J.A. Westphal. 1986. "Evidence from strandings for geomagnetic sensitivity in cetaceans." J. Exp. Biol. (120):1-24.Klinowska, M. 1985. "Cetacean stranding sites relate to geomagnetic topography." Aquatic Mammals (1):27-32.Marhold, S., A. Beiles, H. Burda, and E. Nevo. 2000. "Spontaneous directional preference in a subterranean rodent, the blind mole-rat, Spalax ehrenbergi." Folia Zool. (49):7-18.Marhold, S., W. Wiltschko, and H. Burda. 1997. "A magnetic polarity compass for direction finding in a subterranean mammal." Naturwissenschaften (84):421-423. doi: 10.1007/s001140050422.Muheim, R., N. M. Edgar, K. A. Sloan, and J. B. Phillips. 2006. "Magnetic compass orientation in C57BL/6J mice." Learn Behav no. 34 (4):366-73.Nemec, P., J. Altmann, S. Marhold, H. Burda, and H. Oelschlaeger. 2001. "Neuroanatomy of magnetoreception: The superior colliculus involved in magnetic orientation in a mammal." Science no. 294 (5541):366-368. doi: 10.1126/science.1063351.Slaby, P., K. Tomanova, and M. Vacha. 2013. "Cattle on pastures do align along the North-South axis, but the alignment depends on herd density." Journal of Comparative Physiology A no. 199 (8):695-701. doi: 10.1007/s00359-013-0827-5.Thalau, P., T. Ritz, H. Burda, R. E. Wegner, and R. Wiltschko. 2006. "The magnetic compass mechanisms of birds and rodents are based on different physical principles." J R Soc Interface no. 3 (9):583-7. doi: 10.1098/rsif.2006.0130.Wang, Y., Y. Pan, S. Parsons, M. Walker, and S. Zhang. 2007. "Bats respond to polarity of a magnetic field." Proc Biol Sci no. 274 (1627):2901-5. doi: 10.1098/rspb.2007.0904.Wegner, R. E., S. Begall, and H. Burda. 2006. "Magnetic compass in the cornea: local anaesthesia impairs orientation in a mammal." J Exp Biol no. 209 (Pt 23):4747-50. doi: 10.1242/jeb.02573.Wiltschko, W., and F.W. Merkel. 1966. "Orientierung zugunruhiger Rotkehlchen im statischen Magnetfeld." Verh. Dtsch. Zool. Ges. (59):362-367.

This article was originally published at The Winnower and is the backstory behind Peters, D.P., and S.J. Ceci. 1982. "Peer-review practices of psychological journals: The fate of published articles, submitted again." Behavioral and Brain Sciences no. 5 (02):187-195. doi:10.1017/S0140525X00011183.How the project was initiated. In 1978, one of us (SJC) was a newly hired assistant professor of psychology at the University of North Dakota, and the other one us (DPP) was in his fourth year as an assistant professor, one year away from the all-important tenure decision. One day at lunch with several colleagues, a discussion took place about bias in publishing. A senior colleague opined that a recent publication in a prestigious psychology journal would never have been published if the author had not been an eminent researcher from Harvard. He argued that if he had submitted the same manuscript for publication, it would have been rejected in a New York minute. We were not so sure. This individual's own difficulties getting his work published colored his view of science and prompted his conspiracy feelings.

This is the backstory of:  A randomized, double-blind phase 2 clinical trial of blosozumab, a sclerostin antibody, in postmenopausal women with low bone mineral density \cite{Recker_2015}Lilly conducted a clinical trial of Blosozumab, and before it was approved by the FDA, they abandoned it completely.

This article was originally published at The Winnower and is the backstory behind Cook, J., D. Nuccitelli, S.A. Green, M. Richardson, B. Winkler, R. Painting, R. Way, P. Jacobs, and A. Skuce. 2013. "Quantifying the consensus on anthropogenic global warming in the scientific literature." Environmental Research Letters no. 8(2) (024024). doi: 10.1088/1748-9326/8/2/024024.In 2004, Naomi Oreskes published a paper in Science investigating the level of agreement in the peer-reviewed literature on climate change (Oreskes 2004). Among the 928 'global climate change' papers published between 1993 to 2003, not a single paper rejected the scientific consensus that humans were causing global warming. This result was featured by Al Gore in his Oscar winning film, An Inconvenient Truth.This was the first of several papers investigating scientific consensus among climate scientists. A survey of over 3000 Earth scientists found that the higher the expertise in climate science, the greater the level of agreement on humanity's role in climate change (Doran and Zimmerman 2009). Among climate scientists actively publishing climate research, 97% agreed that humans were significantly changing global temperature.A similar result was obtained two years later in a study collating public declarations on climate change (Anderegg et al. 2010). Among scientists who had published peer-reviewed research on global warming, around 97% endorsed the consensus.When you consider that not a single national scientific organization in the world disputes the consensus, the conclusion is inescapable. The scientific agreement that humans are causing global warming is overwhelming and robust.However, this conclusion has yet to seep into public consciousness. A 2012 survey of Americans found that 57% of the public disagree or are unaware of the scientific consensus (Pew 2012). There is a gaping chasm between public perception of consensus and the 97% reality.In light of this, we decided to update Oreskes' examination of the peer-reviewed literature by adding another decade of peer-reviewed research to the analysis. The period examined was 1991 to 2011. We also broadened the search by adding 'global warming' papers (Oreskes originally searched only 'global climate change' papers). The larger sample of over 12,000 papers allowed us to examine the evolution of consensus over the 21-year period.Research was done by a team of volunteer researchers, all of them members of the Skeptical Science team. Skeptical Science is a website whose purpose is to refute climate misinformation with peer-reviewed science. This was a citizen science effort with a mix of team members, including a diversity of academics from all over the world. This included a climate scientist from Canada, chemistry and environmental scientists from the USA, a meteorologist from England and yours truly, a social scientist from Australia.The initial challenge was maintaining motivation among the volunteers over several months, as we read and rated over 12,000 abstracts (not just once but twice in order to double check each others' ratings). The work was tedious but not without its rewards - one rater reported feeling giddy when he encountered an abstract rejecting the consensus! I later learnt that there had been two similar efforts to measure the level of consensus in published climate papers. In both cases, the sample size was around 1000 papers. Both efforts were never completed. Had I known this, perhaps I wouldn't have been so ambitious with our sample size.Another hiccup during the process was our website getting hacked (Lacatena 2014). Rather than cope with multiple email threads, we collaborate and discuss our research in a private web-based forum. Midway through the rating process, the forum was hacked and published online. This led to a number of bloggers poring over years' worth of private conversations, including discussions about our consensus research. The research was suspended for a short period while we relocated our forum and the online abstract rating system.Our paper was rejected by the first two journals we submitted to. The reason? Establishing scientific consensus is stating the obvious. To paraphrase the reviews: tell us something we don't know! We worked hard to overcome this potential difficulty, including novel methods and results in our analysis. We invited authors of the climate papers in our analysis to categorize their own research, providing an independent measure of consensus. In our resubmission, we were careful to more strongly emphasize the novel aspects of our research.Our paper was accepted by Environmental Research Letters, a journal launched in 2006 that already has an impact factor rivaling such prestigious journals as Geophysical Research Letters and Climatic Change. One of our priorities was making our paper open-access. Hiding it behind a pay wall would have been hideously unproductive, given our aim of increasing public awareness of consensus. The fee to make the paper open-access was USD$1,600. We put the call out for PayPal donations in a Skeptical Science blog post (Cook 2013a). It took 9 hours to raise the funds.Once our paper (Cook et al. 2013) was published, our results generated a great deal of interest. Distributing press releases from the universities of myself and my coauthors led to media coverage in over 28 countries, including a number of non-English speaking countries (thank goodness for Google Translate). Interest peaked when President Obama's Twitter account tweeted about our research to 31 million followers (Obama 2013b). Several weeks later, President Obama mentioned the 97% consensus in a landmark speech on climate change (Obama 2013a).Altmetrics is a website that measures chatter about scholar articles by monitoring mainstream media and social media outlets such as blogs and Twitter. Our paper was ranked as the 11th most talked about scholarly paper in 2013 (Altmetric 2014). Sadly, we were pipped out of the top ten by a paper about Sudoku. Our research was also listed in the top 5% of all scholarly papers. This last statistic, ranking the level of social media chatter on all academic papers ever published, does need to be taken with a grain of salt. There was no one in 1859 tweeting "OMG! Tyndall just discovered GHGs!"Not all of the chatter was glowing. In less than a year, over 200 attacks on our research have been published. There have been blog posts, cartoons, reports, a YouTube video, a paper, TV interviews, and testimonies in government hearings. The one thing these attacks have in common is almost all were conducted by individuals or groups who reject the scientific consensus on human-caused global warming.Why did our research provoke such strong reaction? Ours is the latest episode in over two decades of attacks on scientific consensus. In 1991, a fossil fuel group spent $510,000 on a PR campaign to reposition global warming as theory, not fact (Oreskes 2010). In recent years, the most common climate myth promoted by conservative columnists was "there is no consensus" (Elsasser and Dunlap 2013). Attacking the consensus is a central strategy by opponents of climate action.Our research has also withstood some criticism from several academics that don't dispute the consensus. In these cases, I've been diligent in promptly and publicly responding to comments on our research by respected academics.Law and psychology professor Dan Kahan questioned whether communicating the scientific consensus was an optimal approach, given that it may provoke a negative reaction from those dismissive of climate change (Kahan 2013). In response, I outlined the evidence for both the efficacy and importance of consensus messaging (Cook 2013b). Consensus information increases both acceptance of human-caused global warming (Lewandowsky, Gignac, and Vaughan 2013) and support for climate policy (Bolsen, Leeper, and Shapiro 2013). But crucially, consensus messaging was shown in an Australian experiment to partially neutralize the biasing influence of ideology with conservatives showing a greater increase in belief in human-caused global warming than liberals (Lewandowsky, Gignac, and Vaughan 2013). A study with U.S. participants found that the increase in perceived consensus in response to consensus information was greatest among conservatives (Kotcher et al. 2014).Climate scientists at the Climate Change National Forum also questioned the value of the research, arguing that scientists should be discussing more nuanced questions than human-caused global warming (Forum 2014). In response, I pointed out that while the fundamental fact that humans are causing global warming was considered settled by scientists decades ago, the general public continue to be confused over even these fundamental elements of climate science (Pew 2012).Climate scientist Mike Hulme argued that instead of discussing consensus, we should be talking about policy options (Hulme 2014). In a co-authored response, Stephan Lewandowsky and I argued that this was a counterproductive argument, given that those wishing to delay climate policy have focused on casting doubt on the consensus (Lewandowsky and Cook 2014). The entire point of reinforcing that the science on human-caused warming was settled was to move us to beyond the science to where the debate should be happening - what should we do about it?Attacks on our research continue unabated. Those wishing to delay climate action will continue to cast doubt on the scientific consensus. At the same time, climate scientists and science communicators will continue to debate the most effective ways to communicate the realities of climate change. And social scientists continue to research the role of consensus messaging. I am part of this research strand, exploring the psychology of consensus and the impact of misinformation on public perceptions.ReferencesAltmetric. 2014. Altmetric 2014 [cited Mar 1 2014].Anderegg, W. R., J. W. Prall, J. Harold, and S. H. Schneider. 2010. "Expert credibility in climate change." Proc Natl Acad Sci U S A no. 107 (27):12107-9. doi: 10.1073/pnas.1003187107.Bolsen, T., T.J. Leeper, and M.A. Shapiro. 2013. "Doing What Others Do: Norms, Science, and Collective Action on Global Warming." American Politics Research. doi: 10.1177/1532673X13484173Cook, J. 2014. Be part of a landmark citizen science paper on consensus. Skeptical Science 2013a [cited Mar 1 2014]. Available from http://www.skepticalscience.com/Be-part-of-landmark-citizen-science-paper-on-consensus.html.Cook, J. 2014. Communicating Scientific Consensus: John Cook responds. The Cultural Cognition Project at Yale Law School 2013b [cited Mar 1 2014]. Available from http://www.culturalcognition.net/john-cook-on-communicating-con/Cook, J., D. Nuccitelli, S.A. Green, M. Richardson, B. Winkler, R. Painting, R. Way, P. Jacobs, and A. Skuce. 2013. "Quantifying the consensus on anthropogenic global warming in the scientific literature." Environmental Research Letters no. 8 (2) (024024). doi: 10.1088/1748-9326/8/2/024024.Doran, Peter T., and Maggie Kendall Zimmerman. 2009. "Examining the Scientific Consensus on Climate Change." Eos, Transactions American Geophysical Union no. 90 (3):22-23. doi: 10.1029/2009EO030002.Elsasser, Shaun W., and Riley E. Dunlap. 2013. "Leading Voices in the Denier Choir: Conservative Columnists' Dismissal of Global Warming and Denigration of Climate Science." American Behavioral Scientist no. 57 (6):754-776. doi: 10.1177/0002764212469800.Forum, Climate Change National. 2014. Quantifying the consensus on anthropogenic global warming in the scientific literature" by John Cook et al: 97% of climate scientists agree that humans are causing global warming. Climate Change National Forum 2014 [cited Mar 1 2014]. Available from http://climatechangenationalforum.org/quantifying-the-consensus-on-anthropogenic-global-warming-in-the-scientific-literature-by-dr-john-cook-et-al-97-1-agree-that-humans-are-causing-global-warming/Hulme, M. 2014. Science can't settle what should be done about climate change. The Conversation 2014 [cited Mar 1 2014]. Available from http://theconversation.com/science-cant-settle-what-should-be-done-about-climate-change-22727Kahan, D. 2014. Annual "new study" finds 97% of climate scientists believe in man-made climate change; public consensus sure to follow once news gets out. The Cultural Cognition Project at Yale Law School 2013 [cited Mar 1 2014]. Available from http://www.culturalcognition.net/blog/2013/5/17/annual-new-study-finds-97-of-climate-scientists-believe-in-m.htmlKotcher, J., T. Meyers, E. Maibach, and A. Leiserowitz. 2014. Correcting misperceptions about the scientific consensus on climate change: Exploring the role of providing an explanation for the erroneous belief. In The International Communication Association.Lacatena, B. 2014. A Hack By Any Other Name - Part 1. 2014 [cited Feb 27 2014]. Available from http://www.skepticalscience.com/hack-2012-1.htmlLewandowsky, S., and J. Cook. 2014. Establishing consensus is vital for climate action. The Conversation 2014 [cited Mar 1 2014]. Available from https://theconversation.com/establishing-consensus-is-vital-for-climate-action-22861Lewandowsky, Stephan, Gilles E. Gignac, and Samuel Vaughan. 2013. "The pivotal role of perceived scientific consensus in acceptance of science." Nature Clim. Change no. 3 (4):399-404. doi: http://www.nature.com/nclimate/journal/v3/n4/abs/nclimate1720.html - supplementary-information.Obama, B. 2013. Remarks by the President on Climate Change. The White House 2013a2013]. Available from http://www.whitehouse.gov/the-press-office/2013/06/25/remarks-president-climate-changeObama, B. Twitter Post 2013b. Available from https://twitter.com/BarackObama/status/335089477296988160.Oreskes, N. 2004. "Beyond the ivory tower. The scientific consensus on climate change." Science no. 306 (5702):1686. doi: 10.1126/science.1103618.Oreskes, N. 2010. My facts are better than your facts,: spreading good news about global warming. Edited by M.S. Morgan and P. Howlett, How do facts travel? Cambridge: Cambridge Univesity Press.Pew. 2012. More Say There Is Solid Evidence of Global Warming. Pew Research Center for the People & the Press.

This article was originally published on The Winnower and is the backstory behind Nittono, H., Fukushima, M., Yano, A., & Moriya, H. (2012). The power of kawaii: Viewing cute images promotes a careful behavior and narrows attentional focus, PLoS ONE, 7(9), e46362. doi:10.1371/journal.pone.0046362In this paper, I reported three experiments to demonstrate that people who viewed pictures of kittens and puppies, as compared to those who viewed pictures of adult animals, perform better on subsequent tasks that require dexterity and carefulness and tend to focus on the finer details of an object [1]. To be honest, I am not a pet lover. In more than forty years of life, my family and I have never had any kittens and puppies of our own. I have been a researcher in psychophysiology for twenty years, measuring activities in the brain and the autonomic nervous system in connection with various psychological phenomena. I had never dreamt of doing this kind of "pop" research up until a few years ago when a third-year student of mine asked me if she could study human reactions to kawaii items as the theme of her diploma thesis.Kawaii is one of the most popular words in contemporary Japan. Roughly speaking, it means "cute," "lovely," "pretty," "adorable," etc. This word is frequently uttered to express the speaker's favorable evaluation toward an object or person. Because it is used too often, sociologists and journalists have discussed for decades that kawaii is a key concept to understand the characteristics of modern Japanese people and culture. Nevertheless, many believed that it was out of the scope of science. "It is difficult," I said, "but if you really want to do so, try it." While she recorded psychophysiological responses to human and animal baby pictures [2], I carefully read through many articles regarding kawaii, from "The Pillow Book," an essay written by a Japanese court lady around the year 1000, to the most recent fashion magazines. As a psychologist, I was curious why people love kawaii so much and thought that there should be a psychological factor that reinforces the behavior of admiring and possessing kawaii items. At that point I was confident that, when done well, this line of research would attract much public attention, at least inside Japan.Shortly after we started this investigation, an interesting psychology paper was published in the US. The authors argued that viewing pictures of baby animals promotes behavioral carefulness [3]. Because the results initially sounded odd but intriguing, I tried to replicate and extend the findings in a Japanese sample with support of three other students of mine. This is how and why I started the experiments reported in the paper in question.As many other projects were going on in parallel, it took about two years to complete three experiments. The paper was first submitted to Psychological Science, which is one of the most highly reputed journals that publish many exciting psychology papers. However, it was rejected immediately without being sent out to reviewers, because the paper made "a useful but incremental contribution to the literature" rather than reporting "groundbreaking findings." Needless to say, I had been aware that the study lacked true originality and was, in essence, a replication. On the other hand, I was pretty sure that this topic would attract public attention, so we decided to submit it to an open access journal, PLoS ONE. Before resubmission, however, I added a twist. Originally, the paper was titled "The power of cuteness," which was more comprehensible for an international audience. However, I deliberately changed it to "The power of kawaii," with the Japanese public in mind. I also inserted a short paragraph at the beginning of the paper to introduce what kawaii is and what it means in Japanese culture.After the second revision, it was published in September 2012. Fortunately, the editor and reviewers never asked me to change the title to a "plainer" one. Therefore, it became the first peer-reviewed scientific paper with the word kawaii in the title among more than 23 million citations in PubMed. Before publication, for the first time in my life I asked a public information officer from my university to put out a media release.The research was positively received. On the day of publication and the following several days, I was interviewed by a dozen of Japanese newspapers, radio hosts, and TV personalities. Furthermore, over seventy international news and blogs featured our findings, which surpassed my predictions. There were remarkable differences in the focus of interest between Japanese and international news media. While Japanese media mainly focused on the idea of scientific research on kawaii, other media passed over this aspect and just focused on the finding that viewing pictures of kittens and puppies may benefit work performance.What enabled this research study to generate so much attention? It was partly due to luck, of course. With hindsight, however, there seem to be several factors that increased the likelihood of an article gaining wider attention in society. First, the study originated from a layperson's question. Second, the topic was well-framed in a local cultural background. Third, the finding itself was relevant to a wider, international audience for different reasons than those that pertained to the original culture. Fourth, it was published in a popular open access journal that is easily accessible by everyone via the Internet. Last but not least, what I learned from this experience is that, in order to publish a paper that is influential amongst the general public, it is important to conduct not only a groundbreaking study but also a study that replicates previous findings and extends them in a proper direction that many people are interested in learning more about.REFERENCES1. Nittono, H., Fukushima, M., Yano, A., & Moriya, H. (2012). The power of kawaii: Viewing cute images promotes a careful behavior and narrows attentional focus, PLoS ONE, 7 (9), e46362. doi:10.1371/journal.pone.00463622. Nittono, H., & Tanaka, K. (2010). Psychophysiological responses to kawaii (cute) visual images [abstract]. International Journal of Psychophysiology, 77, 268-269. doi:10.1016/j.ijpsycho.2010.06.1073. Sherman, G. D., Haidt, J., & Coan, J. A. (2009). Viewing cute images increases behavioral carefulness. Emotion, 9, 282-286. doi: 10.1037/a0014904

This article was originally published at The Winnower and is the back story behind Cole, T.J., M.C. Bellizzi, K.M. Flegal, and W.H. Dietz. 2000. "Establishing a standard definition for child overweight and obesity worldwide: international survey." BMJ no. 320 (7244):1240. doi: 10.1136/bmj.320.7244.1240.Obesity in humans came to be recognised as a serious public health concern during the 1960's, when several national and international obesity societies were founded. But the focus was initially on adults, and it took a further 30 years for the concern to extend to children. This was because obesity is to some extent an inter-generational condition, with fat parents begetting fat children, so it took time - more than a generation - for the levels of obesity in children to rise sufficiently to cause alarm. Once the danger was recognised, researchers from all over the world rushed to carry out prevalence studies to quantify the scale of the problem, and many such studies were published during this time.However there was a serious problem - nobody could agree on how to define child obesity. As a result each study used its own definition, with the unfortunate consequence that the methods were incompatible and the prevalence rates could not be compared across studies. This highlighted the need for a unified international definition that all could use, which would allow the effort being put into measuring child obesity prevalence to be properly harnessed.The International Obesity Task Force (IOTF) was another reflection of the rising concern about obesity. It was set up in 1994 by Philip James as a policy and advocacy think tank, and its initial action was to prepare what became the first scientific report on the global epidemic of obesity, published as a WHO expert technical report in 2000. This work highlighted the lack of a proper definition for child obesity, and a second IOTF initiative was to convene a workshop on child obesity in Dublin in June 1997 to address the deficiency. The purpose and summary of the workshop were later published (Dietz and Bellizzi 1999, Bellizzi and Dietz 1999). The primary outcome of the workshop was a definition of childhood obesity that appeared in the BMJ (Cole et al. 2000), a paper which has since been cited 5,391 times by Web of Science (an average of 350 citations per year) and 10,125 times by Google Scholar (as of 8 May 2014).Obesity is more complicated to diagnose in children than in adults, because children increase in height, weight and body fat naturally as they grow. The difficulty is to decide when the pattern of growth is excessive. So to define child obesity requires three components: a measure to define the amount of body fat; a reference population to define the distribution of the body fat measure by age and sex, and a centile cut-off to define the point in the body fat measure distribution corresponding to obesity. For historical reasons there were in fact two cut-offs, one for obesity and a less extreme one for overweight. The workshop agreed to use body mass index (BMI or weight/height 2) as the measure of body fat, an uncontroversial choice as it matched the usage in adults. However the other two components of the definition were novel: large nationally representative samples of children from Brazil, Great Britain, Hong Kong, the Netherlands, Singapore and USA (n = 192,727) that were used to establish the distribution of BMI internationally; and (my idea) centile cut-offs of BMI chosen to match the universally accepted adult cut-offs of BMI 25 (overweight) and BMI 30 (obesity) at age 18 years. This ensured that the child and adult definitions were consistent with each other, a notable advance on previous definitions.Centile charts are widely used to assess growth in paediatric practice, and previous obesity definitions had used the 85th and 95th centiles of BMI as overweight and obesity cut-offs. The shapes of the centile curves on the chart can be estimated with a statistical technique called the LMS (λ-μ-σ) method which I developed with Peter Green (Cole and Green 1992). LMS allows one to construct any required centiles, in particular those that pass through BMI 25 and 30 at age 18. The calculations were done for each of the six samples separately, and the cut-offs were then averaged.One indicator to justify the approach taken was to see how close to each other the centiles based on the separate samples were. It turned out that the Singapore cut-offs were a different shape from all the others, the Singaporean children being relatively fatter in early puberty (Cole et al. 2000), and the first version of the paper excluded the Singapore cut-offs on that basis. However the BMJ reviewers said they should be retained, and in retrospect this was a wise decision - the anomalous pattern of BMI change with age seen in the Singapore sample has since been seen in other datasets too.Another early intention of the authors was to develop cut-offs to identify underweight as well as overweight, based on the same BMI reference data. Child malnutrition is as big a public health problem as obesity in many parts of the world, and cut-offs based on BMI would have advantages over the weight-for-height cut-offs then in use. However it proved to be too ambitious at the time, and only in 2007 was the follow-up paper published (Cole et al. 2007). It has been cited 580 times to date. More recently the underlying methodology has been overhauled, and it is now possible to present the information in the form of a BMI growth chart (Cole and Lobstein 2012).It is interesting to speculate as to why the 2000 paper was such a runaway success. The first ingredient was its authors: Bill Dietz and Katherine Flegal were both well-known and respected obesity researchers from the US Centers for Disease Control and Prevention, which encouraged the paper's take-up in the USA. Mary Bellizzi was Secretary of the IOTF, and this emphasised the international nature of the definition. I provided the statistical framework on which the work was based. The second ingredient was the wide variety of countries providing data, giving reassurance to researchers that the cut-offs were indeed international and could be applied with confidence to children from their own country. By contrast the World Health Organization (WHO) international growth reference was at that time based on US data, and this was politically uncomfortable in parts of the world where the pattern of child growth was clearly different from that in the USA.A third ingredient was the way the cut-offs were constructed, linked to the widely used adult definition. This provided reassurance that the cut-offs were not just a statistical artefact but were based on existing practice. And finally the paper's publication in the BMJ, a general medical journal with very broad reach, ensured that it received widespread publicity from day one. The BMJ itself was impressed by the high citation rate of the paper, and used it as the example in a discussion piece about how the internet was altering the nature of literature citations (Delamothe 2002).Overall the paper's timeliness was the key - it addressed a problem that researchers worldwide were struggling with, while at the same time providing them with psychological and political reassurance that it was valid to use. This was confirmed by an exhaustive IOTF review of child obesity published in 2004 which quoted many studies with prevalence rates based on the definition (Lobstein, Baur, and Uauy 2004). As the Abstract Conclusion of the 2000 paper concisely summarised it,"The proposed cut off points, which are less arbitrary and more internationally based than current alternatives, should help to provide internationally comparable prevalence rates of overweight and obesity in children."ReferencesBellizzi, M. C., and W. H. Dietz. 1999. "Workshop on childhood obesity: summary of the discussion." American Journal of Clinical Nutrition no. 70 (1):173S-175S.Cole, T J, M C Bellizzi, K M Flegal, and W H Dietz. 2000. "Establishing a standard definition for child overweight and obesity: international survey." British Medical Journal no. 320 (7244):1240-3.Cole, T J, K M Flegal, D Nicholls, and A A Jackson. 2007. "Body mass index cut-offs to define thinness in children and adolescents: international survey." British Medical Journal no. 335:194-7.Cole, T. J., and P. J. Green. 1992. "Smoothing reference centile curves: the LMS method and penalized likelihood." Statistics in Medicine no. 11 (10):1305-19.Cole, T. J., and T. Lobstein. 2012. "Extended international (IOTF) body mass index cut-offs for thinness, overweight and obesity." Pediatr Obes no. 7 (4):284-94. doi: 10.1111/j.2047-6310.2012.00064.x.Delamothe, T. 2002. "Is that it? How online articles have changed over the past five years." BMJ no. 325:1475. doi: doi: 10.1136/bmj.325.7378.1475.Dietz, W. H., and M. C. Bellizzi. 1999. "Introduction: The use of body mass index to assess obesity in children." American Journal of Clinical Nutrition no. 70 (1):123S-125S.Lobstein, T, L Baur, and R Uauy. 2004. "Obesity in children and young people: a crisis in public health." Obesity Reviews no. 5 (Suppl 1):4-85.

This article was originally published at The Winnower and is the backstory behind Edgar, R. C. 2004. "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res no. 32 (5):1792-7. doi: 10.1093/nar/gkh340.First off I should say that my career path was not planned or plannable, so you can't follow in my footsteps except to go where there is no path.From a young age (7 years old), my vocation was to be a scientist, and I quickly settled on theoretical physics because physics is everything - any explanation of the natural world eventually bottoms out in the laws of physics (yeah, I'm a hard-core reductionist and proud of it). At high school and college, I was pretty good at math and physics, but once I started my PhD I got a shock because I discovered that many people were much smarter than me. A few months after starting my postdoc I concluded that I would always be a mediocre physicist and would never make much of a contribution, so I quit. That was very difficult because physics had been my life's dream, but in retrospect physics was the wrong field for me; I'm more of a natural programmer than a natural mathematician. Like many failed physicists in the mid-80s, I got into the software business and ended up starting my own company in San Francisco. I sold the business to Intel in 1999, and in 2001 I was burned out and quit with no idea what to do next.I didn't want to start another business, which is what most entrepreneurs do, and I didn't want to retire and play golf (or more likely tennis). I knew about the human genome project and the importance of software algorithms - it was very appealing to me as a software guy that you could do important things just with strings of letters without knowing all that tedious biochemistry. Biology=strcmp (). So while it didn't occur to me that I might actively work on that stuff, I thought it would be fun to learn something about it, and crashed a seminar at UC Berkeley and met a newly-hired professor named Kimmen Sjolander. She was looking for students to help her code up some algorithms for summer research experience, and I volunteered. The result was a multiple alignment program called SATCHMO (Edgar and Sjolander 2003), which worked pretty well but was no better than CLUSTALW according to BALIBASE, which was the only available benchmark at that time.Being a competitive guy, I was dissatisfied with that, and started a systematic project to figure out what did and didn't work in multiple alignment algorithms, because it seemed to me that the programs had many ideas in them, but it wasn't clear which of the ideas helped or hurt the results. At that time, Gotoh's PRRx had the best accuracy (except maybe for T-Coffee; I don't remember) but the code was unfriendly and slow and hardly anybody used it. So I started from the PRRx algorithm and systematically varied the elements of the algorithm with all the alternatives I could find in the literature or dream up myself. That was the line of work that led to MUSCLE (Edgar 2004). (As an aside, the MAFFT people followed a similar strategy independently, and it's remarkable how much the original MAFFT and MUSCLE v1 resembled each other. MAFFT got published first and was better than my first attempt; I had to "borrow' a couple of their ideas in order to do better than MAFFT (Katoh et al. 2002). For example, we both had k-mer counting to build the first tree, but I was using 3-mers in the usual alphabet and they used 6-mers in a compressed alphabet, which gave slightly better results.So MUSCLE was a result of some financial independence I had after selling my business. I've supported myself and my research from my savings for the past decade. You can think of me as unemployed, independent and/or a gentleman scholar of modest means (like, say, my fellow-countryman Charles Darwin). It's hard to know how people have perceived my unconventional status. Everyone feels misunderstood and dismissed by peers sometimes (reviewers, editors, conference organizers), so it's impossible to say whether I would have been better accepted if I had a conventional affiliation. MUSCLE has been helpful because many people have heard of it. That gave me some street cred early on, and surely helped open other doors.I don't see any lessons here to help young scientists, so in an attempt to avoid becoming a bad influence I will defer to a more accomplished scientist, Richard Hamming, who has much better advice in his lecture, "You and Your Research" (Hamming 1986)ReferencesEdgar, R. C. 2004. "MUSCLE: multiple sequence alignment with high accuracy and high throughput." Nucleic Acids Res no. 32 (5):1792-7. doi: 10.1093/nar/gkh340.Edgar, R. C., and K. Sjolander. 2003. "SATCHMO: sequence alignment and tree construction using hidden Markov models." Bioinformatics no. 19 (11):1404-11. doi: 10.1093/bioinformatics/btg158.Hamming, R. You and Your Research 1986. Available from http://cmp.felk.cvut.cz/cmp/teaching/YouAndYourResearch.pdf.Katoh, K., K. Misawa, K. Kuma, and T. Miyata. 2002. "MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform." Nucleic Acids Res no. 30 (14):3059-66. doi: 10.1093/nar/gkf436.

This article was originally published at The Winnower and is the backstory behind Rozas, J., J.C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. "DnaSP, DNA polymorphism analyses by the coalescent and other methods." Bioinformatics no. 19 (18):2496-2497. doi: 10.1093/bioinformatics/btg359.The paper describes the version 4 of the DnaSP (DNA Sequence Polymorphism) software, a bioinformatics tool used to analyze and interpret DNA sequence polymorphism data (Rozas et al. 2003). The software implements a number of analytical methods, some of them developed by our own research group. Formally, the project began in 1994, but it has a history going back a few years ago, during my PhD studies (University of Barcelona, under the supervision of Professor M. Aguade) and, later during my Postdoc (Harvard University; at the laboratory of Professor R. C. Lewontin). At this time, I was performing some DNA variation analysis and, importantly, there was not any convenient software for the data analyses of such early studies. Thus, I started the development of DnaSP mainly because at that time there was no software to conduct such analyses.The analysis of DNA sequence polymorphisms and SNPs (single nucleotide polymorphisms) provides valuable insights into our understanding of the evolutionary meaning of DNA polymorphisms. For instance, both demographic (such as population expansions) or selective events, left distinctive molecular hallmarks on the patterns and levels of within-species DNA sequence data. Therefore, the analyses and interpretation of DNA polymorphism data can inform about, for example, past population growth or decline events, gene flow among populations, or the impact of natural selection (Begun et al. 2007, Nielsen 2005, Rosenberg and Nordborg 2002).Determining the impact of natural selection in molecular evolution and in adaptation is a fundamental question in evolutionary biology and evolutionary genomics. In this context, the detection of both positive (adaptive or Darwinian) and negative (purifying) selection is of great interest. Besides the deep conceptual implications, it might provide insights into our understanding of the biological function of genes and genomic regions. Indeed, positive selection promotes advantageous DNA sequence changes, which are ultimately responsible for evolutionary adaptations and novelties. The characterization of genomic regions shaped by this kind of selection has profound implications not only in evolutionary biology but also in our understanding of gene function. Negative selection, on the other hand, purges deleterious mutations favoring, therefore, the conservation of DNA sequences. Hence, these evolutionary conserved regions are, likely, to be functionally important and might uncover novel unknown biological functions. Moreover, DNA polymorphism data are very valuable powerful tools (as molecular markers) in a wide range of disciplines such as biomedicine, animal and plant breeding, conservation genetics, epidemiology genetics, or forensics.DnaSP is industry-standard software to compute population genetics analyses including coalescent-based methods, the state-of-the-art framework to analyze DNA sequence polymorphism data (Rozas et al. 2003, Rosenberg and Nordborg 2002, Librado and Rozas 2009, Wakeley 2009). DnaSP is a multi-purpose software package that allows conducting exhaustive analysis using a very friendly graphical user interface (GUI). The main features of the software are as follows: (i) accommodates large data sets; (ii) computes many population genetic statistics describing the level and patterns of DNA polymorphism within and between populations; (iii) conducts computer simulation coalescent-based tests; (iv) generates graphical outputs rendering the information readily understandable sequence polymorphism and SNP data.Although DnaSP version 4 was published in 2003, the first article (describing the first version of the software) was sent to publish to the scientific journal CABIOS (Computer Applications in Biosciences; currently named as Bioinformatics) in 1995, and it was quickly accepted (Rozas and Rozas 1995). Indeed, the other publications were also quickly accepted and published, including the most recent one (Librado and Rozas 2009). We think that this was because a combination of factors. First, it describes software for DNA polymorphism data analysis, and when the first version was released, there was no software of its kind. Second, it allows the computation of powerful and comprehensive state-of-the-art statistics and methods. Third, it provides a very easy to use GUI and with a learning curve that was extremely short. Fourth, the software can read a number of format data files, so it was very easy to input the data to the software to proceed with the analyses. Finally, the software provides an exhaustive help both to explain how to perform the analyses but also their scientific basis.ReferencesBegun, D.J., A.K. Holloway, K. Stevens, L.W Hillier, Y. Poh, M.W. Hahn, P.M. Nista, C.D Jones, A.D. Kern, C.N. Dewey, L. Pachter, E. Myers, and C.H. Langley. 2007. "Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans." PLoS Biol no. 5 (11):e310. doi: 10.1371/journal.pbio.0050310.Librado, P., and J. Rozas. 2009. "DnaSP v5: a software for comprehensive analysis of DNA polymorphism data." Bioinformatics no. 25 (11):1451-1452. doi: 10.1093/bioinformatics/btp187.Nielsen, R. 2005. "Molecular Signatures of Natural Selection." Annual Review of Genetics no. 39 (1):197-218. doi: 10.1146/annurev.genet.39.073003.112420.Rosenberg, N.A., and M. Nordborg. 2002. "Genealogical trees, coalescent theory and the analysis of genetic polymorphisms." Nat Rev Genet no. 3 (5):380-390. doi: 10.1038/nrg795.Rozas, J., and R. Rozas. 1995. "DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data." Computer applications in the biosciences : CABIOS no. 11 (6):621-625. doi: 10.1093/bioinformatics/11.6.621.Rozas, J., J.C. Sanchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. "DnaSP, DNA polymorphism analyses by the coalescent and other methods." Bioinformatics no. 19 (18):2496-2497. doi: 10.1093/bioinformatics/btg359.Wakeley, J. 2009. Coalescent Theory. An Introduction. Greenwood Village: Roberts and Company Publishers.

This is the Backstory of  Nanopatterned Textile-Based Wearable Triboelectric Nanogenerator \cite{Seung_2015}.

This article was originally published at The Winnower and is the backstory behind: Robert Nemiroff, Teresa Wilson, Searching the Internet for evidence of time travelers, The Winnower 4:e140984.46096 (2014). DOI: 10.15200/winn.140984.46096How is it that a paper that could not get published had the fourth highest reported Altmetric score for all scientific contributions in 2013 (Liu 2014)? This contribution to the Grain has the interesting backstory, written at the request of a Winnower editor. Hang on -- this (long) story includes enthusiastic graduate students, numerous rejection emails, a wife with an encyclopedic knowledge of Doctor Who, a parody by a popular late night talk show host, and an unsolicited offer to buy the movie rights. I could not make this up.First of all, the topic itself is a controversial one, as made clear immediately by the work's title "Searching the Internet for Evidence of Time Travelers" (Nemiroff & Wilson 2014). It is perhaps accepted common knowledge that people who believe in time travelers are crackpots and their ramblings are not to be believed. For the record, I do not believe that traveling back in time is possible, nor do I believe that time travelers are among us. I never did. However, I was not so absolutely sure that I did not check, with the help of students, in as scientifically a manner as possible.Next, a little background about me. I am a (full) professor of physics at a state school in the USA, Michigan Technological University to be precise. I would not have gone on this unusual journey -- a journey that ended up probing the limits of science publishing -- if I did not have tenure. Some people might say that trying to publish an article on such an outrageous topic is an abuse of tenure and an indication that tenure is outdated and should be abolished. Others might say that situations like this are exactly the reason why tenure was invented.THE RESEARCHIt is hard to say when the project really started. Even when I was in grade school I was interested in physics, would read a lot of science fiction, and would sometimes think about the possibility of time travel. I overheard occasional speculation where people would say that if they could travel back in time they would bring back winning lottery numbers, and therefore wondered if some lottery winners were also time travelers. After reading a few accounts, I concluded: generally not. Still, in the back of my mind, I continually wondered if there was any good way to find a real time traveler.In 2009 I read a brief Facebook exchange on the page of a friend highlighting this same topic -- if people from the future were here, how could we tell? Apparently, other people speculated about this as well. I wondered "what if a future-person did an Internet search on something they could not have known about at the time?" I had access only to the log files of an astronomy web site that I help write and administer and so I did a quick search through some log files for queries involving comets that were not known about at the time. I found nothing of note. Past that, I mentioned the idea to a graduate student of mine but nothing much more was done. We had plenty or "real" research projects to work on.During the summers of recent years, I am fortunate enough to have a group of students working with me, including both graduate and undergraduates students. In the summer of 2013, there were five students in all, and at summer's start I tried to come up with projects for each of them. As a group, my students and I would meet twice a week, once at the school and once at my home where we would play poker. The poker was for chips, not money, as pride seems to be a sufficient motivator for students and academics. Part of the idea of meeting over poker-playing was to create a setting where we could all talk about science in an informal setting. At one of these meetings, toward the beginning of the summer, I brought up the question of time travel and challenged my students to come up with ways of searching for time travelers in as scientific and verifiable method as possible.The students LOVED this topic. Every meeting we would talk in increasing depth about how real scientific searches for time travelers might proceed. It was not so easy as it might seem. As expected, investigating lottery winners came up -- but we quickly agreed that it would be pretty difficult to check on them. Idea after idea was suggested and discarded. Disqualifying attributes included taking too much time to investigate, creating too much expensive travel, requiring private or inaccessible information, or not being easily falsifiable. It was easy to come up with bad ways -- was there any good ways that we could actually try?Drawing on my past experience, I suggested the Internet. This quickly became far and away the most popular method to discuss. One reason is that the modern Internet is a mark of the student's generation, and they knew attributes, sites and search methods that I did not. A good tool, we soon decided, was "prescient information" -- information that could not have been known at the time. For example, say in the year 2010 your neighbor keeps asking you if Pope Francis has been elected yet. Repeatedly. "No", you might say, repeatedly, followed sometimes by "who is Pope Francis?" After a while you might ask your friends if they know anything about a "Pope Francis." Were this to persist, one might tweet a query on Twitter. No one would know. The whole name "Pope Francis" did not exist in the public lexicon before March 2013. This "unknowable at the time knowledge" became the basis for the most scientific set of searches for time travelers that we could afford the time and money to do. And the name "Pope Francis" was indeed a factor.So we searched. Graduate student Teresa Wilson soon took the lead. It was a lot of fun! We searched with Google and Bing, we searched Facebook, Google Plus, and Twitter -- everywhere we could for "unknowable at the time knowledge". Eventually we narrowed the focus to two well-thought out search terms to keep things manageable: "Pope Francis" and "Comet ISON". I included my old search strategy of looking for prescient searches in the log files of the Astronomy Picture of the Day web site (Nemiroff & Bonnell 1995). We also posted a request for active communication over the Internet -- for time travelers to contact us before the request was given.We found nothing. We uncovered no "unknowable at the time knowledge" during our limited search of the Internet. Time travel may be discoverable, but we didn't discover it. Still, given the pervasiveness of the Internet and the vastness of the online databases that major web sites like Twitter hold -- ours, it appeared, was the most comprehensive search for time travelers ever. I therefore began writing it up.Now this paper was fun to write. I had been reading about the science and fiction of time travel for 40 years, and here was a chance to use some of this arcane knowledge. I wasn't sure if the result would be publishable. The manuscript, written mostly in 2013 July and August, turned into a strange fusion of two completely different paradigms -- that of classic knowledge about time from people like Einstein and Godel -- and that of modern knowledge about the fast-changing Internet including sites like Google and Facebook. I would send versions of the paper to Wilson to add on to and edit. In my opinion, the resulting manuscript was quite well written.THE SPECTACULAR FAILURE OF EARLY PUBLICATION ATTEMPTSOur first attempt to publish "Searching the Internet for evidence of time travelers", in late September of 2013, was at a classic physics journal that deals with foundational questions at the heart of physics. I have decided not to mention any journal or editor names involved in the rejection of the manuscript. I uploaded the paper to the journal and waited. A few days later, I received an email saying that the journal would not send the manuscript out for review. There was no specific reason given, but the email included a list of attributes that they require in a paper, with the implication was that our manuscript lacked one or more of these attributes. The email was signed by a very famous physicist. I don't really know if this famous physicist ever really read the manuscript -- this email could have been a form-letter email sent out by someone in the front office. I decided to reply -- an effort to reject their apparent rejection -- by asking the famous editor how (s)he really knew, experimentally, that time travel was not possible. I waited. One week. Two weeks. One month. Nothing. No reply.Don't worry, I told Teresa, this work can still be published -- there are other opportunities. I have a friend in the physics department who is on the editorial board of a reputable physics journal and he has asked me, on occasion, if I would consider submitting a paper to that journal. Previously, I had not. Now, I considered it. I gave him the manuscript to read. He knew this would be a "hot potato" but did encourage me to submit it. So I did. About a week later, I received a polite email saying that the manuscript was on a topic inappropriate for this journal. They would not send it out for review and would not consider it further. True to form, I again responded with an impassioned email asking them to reconsider. A few weeks later -- a reply -- but no change. My friend speculated that, quite possibly, there was disagreement among the journal editors about how to handle the manuscript, but that in the end they went with the more conservative course of action. A third physics journal geared more toward the philosophy of physics soon responded similarly.Soon it was December and I had lost hope that the manuscript would be accepted by a journal before Wilson and I presented the main concepts in a poster at the January meeting of the American Astronomical Society (AAS). Possibly because I had attended almost every Winter AAS meeting for the past 20 years and knew so many AAS people, the meeting organizers had accepted the abstract even though it was more physics than astronomy. For this I was grateful. Even though I checked the box indicating that the research was, in my opinion, worthy of press attention, the AAS did not select the paper as a press highlight.Although I anticipated some interesting discussions at the AAS, I was now worried that by presenting only a sketchy poster, others might research, write, and publish on this idea themselves before we ourselves could get it into a journal. I therefore decided to upload the manuscript to a standard web site that posts manuscripts and papers both before and after publication, the arXiv at http://arXig.org/. That way, at the AAS poster, I could at least refer to a finished but unpublished manuscript. Now over the course of my career, I routinely submitted manuscripts and papers that I wrote to the arXiv and received only an occasional email in response. I was grateful, again, that my upload of the manuscript to the arXiv was successful (although they reclassified it), since arXiv does reject manuscript that its editors consider unworthy. The manuscript was uploaded to arXiv.org on 2013 December 26 (Nemiroff & Wilson 2013). My wife and I left on a long car trip the very next day from our home in Michigan to the US east cost to visit relatives, honor a standing speaking engagement I had in New York City the next week, and attend the AAS meeting near Washington, DC the week after.VIRAL EXPLOSIONOn the road, I received an unexpected call from a major US news outlet: NBC. I called them back from a rest stop off Interstate 80. They wanted to know about the time travel paper. "What time travel paper?" I asked. The editor had seen our manuscript on arXiv and wanted to interview me. I was surprised that they even knew about the manuscript on arXiv. Hundreds of manuscripts appear on arXiv daily and it is understood that many of them are not finished works.I replied that I was presenting a poster on the topic at the AAS meeting in two weeks and asked if I could postpone this interview until then. I was surprised at his reply. He said he couldn't wait until the AAS meeting -- the manuscript is already "all over the Internet." Wow. So I gave the interview (Boyle 2014). And soon after, another. The emails poured in. Now almost every time we stopped, I returned someone's email or phone request. I have never had a published paper become so popular, not even papers accompanied by a press release -- and this manuscript was neither published nor promoted by a press release.I decided to ride the publicity wave, trying to see this as an unexpected ride on the amusement park of life, and guessing that I would never have this chance again. I set aside about an hour a day during the next few weeks to do phone interviews and answer email about the time travel manuscript. I referred several interviews to Wilson as well. Apparently, much of the public was seeing this in a different light than journal editors. Most of the coverage was quite positive, but possibly the highest profile report -- on the Colbert Report -- appeared to focus on the seeming silliness of expecting a time traveler to tweet about the future (Colbert 2014). Oh well. Several of the write-ups were excellent, with one high point was the front web page of Der Spiegel where the manuscript was a focal point in a discussion about data sharing being limited by web behemoths like Facebook and Google.At the AAS meeting it turned out that many people who approached our poster already knew about the work. Again, most comments were positive, but then again people with negative comments would be less likely come up and volunteer them. At least three journal editors approached, each separately, and each said that they admired the work but they could never publish something like this in their journal(s). Conversely, one journal editor asked me to submit the manuscript to his journal, but eventually even that journal's editorial board decided the topic was too far afield to send out for review.The most unexpected email I received was from a movie producer who wanted to buy the movie rights. Neither the producer nor I had ever heard, previously, of a scientific manuscript being optioned for movie rights. I discussed the situation with my wife and we debated whether the request was actually some sort of joke. I called back with some questions and so far as we could tell, the offer seemed legitimate. In fact, a Google search showed that the movie producer had a history of making several low-budget independent films. About a month later, after some haggling, he mailed both Wilson and me each a check for $100. Although few actual options are made into movies, I have been in contact with the producer who relates that he is working on a script.LAST TRY FOR AN ESTABLISHED JOURNALGiven encouragement from colleagues, the press, and a movie producer, I decided to try to publish the manuscript in an established journal one last time. Based on some savvy advice from a friend, I agreed to approach a really famous journal that actually had published papers involving the possibility of time travel before. I felt encouraged as I uploaded the manuscript, thinking how cool it would be for this prestigious journal to publish a manuscript that other less prestigious journals had so quickly rejected.So the prestigious journal also rejected the manuscript without review. In their borderline-mocking rejection email, the corresponding editor reported that another editor for this journal had said that the idea behind the manuscript was not even new -- a Doctor Who episode had explored this very concept previously. The precise episode was even mentioned.I was taken aback. Could I have gotten this idea from Doctor Who and not realized it? I could not remember so, and I did not recall even seeing the episode the rejection email referenced. I mentioned this to my wife who surprised me by saying that she herself has seen -- or knew about -- every Dr. Who episode since the modern reboot in 2005, and could say definitively that the main idea of this manuscript was not involved. Still, to be extra sure, we rented the episode in question and watched it in its entirety. My wife was right -- the idea of searching for "unknowable at the time knowledge" over the Internet just was not in this episode. After more thought, my wife gave me the title of the one other Doctor Who episode that might have something relevant to our search in it. So we also rented that episode as well and nothing in it, from start to finish, was relevant to the time travel manuscript.I then responded to the prestigious journal's editor relating my Doctor Who investigation and implying that, given my wife's encyclopedic knowledge of Doctor Who, no episodes at all were directly relevant to the search methods of our manuscript. I then asked them, in light of the manuscript's now verified novelty, to reconsider and send the manuscript out for peer review. In a bid for more respect, I also related that not only had I published in this journal before, but I had been a referee for this journal previously as well. In the response, the editor said that (s)he has now sent the article out to another editor, one who is quite famous in this area, but who also agreed that this paper should be rejected without being sent out for peer review. In this reply, the famous editor said:"I should point out that most stock markets around the planet devote considerable resources to looking for temporally anomalous market behavior --- unusual trading patterns before significant news events. When found, such signals are not typically attributed to time travelers, but more prosaically to insider trading."I agree! This is one reason why we did not look for evidence of time travel in stock market trading. Early on, our group had discussed (briefly) this idea. On one hand, I was glad that finally we had a real criticism to address, but on the other hand, this famous editor's comment indicated to me, once again, that the journal editors did not fully appreciate the novelty, power, simplicity, and falsifiability of our approach. Instead, they gave straw-man criticisms that really meant, in my view, that they did not want to consider a manuscript so unconventional. In my reply, I argued in detail against this criticism and again asked that the manuscript at least be sent out for formal peer review. Alternatively, I asked for a clear reason that the paper was being rejected. Ultimately, however, these arguments went nowhere. The journal editors would do neither, and eventually asked me to stop emailing them on this topic. So I stopped.ON TO THE WINNOWERSoon after the manuscript on arXiv went viral, I received an email from Joshua Nicholson of the Winnower asking if I would write a piece about the manuscript for the web publication's "Grain" section. Apparently, the arXiv manuscript's Altmetric score of over 2,000 had alerted him. I initially replied then that I would but I was still trying to figure out what to do with the manuscript itself. Josh replied that the manuscript could eventually be uploaded to the paper section of the Winnower and opened for public review. I had not heard about the Winnower before, but soon read up on it. Even so, at the time, I tried first for a more established journal. Now that publication in an established journal seemed unlikely, and given that I would not publish this in a "scam" journal even given numerous email advertisements, I took a closer look at the Winnower.The public review inherent in the Winnower's paper section seemed to me to be an excellent idea. I was somewhat skeptical, though, that many authors would submit their papers to this section. A key reason, in my opinion, was the "prisoner's dilemma". Although it would likely benefit the entire community to adopt a public review, it would tax individual authors primarily because of the lack of current reputation of the Winnower. Papers published on the Winnower would not, at least at first, carry the same weight during promotion and tenure deliberations as papers published in a journal with an established reputation.My opinion on this draws on a similar situation that I found myself in several years ago. In 1999, along with a colleague, I started the Astrophysics Source Code Libary (ASCL: Nemiroff & Wallin 1999) based on the idea that opening up the source codes behind peer-reviewed papers would increase falsifiability and benefit the astrophysics community. Since a more healthy astrophysics community is in everyone's interest, I hoped that the ASCL would become quickly popular. I was wrong. In reality, few people contributed their codes, at least at first. I did not appreciate that the extra work and the possibility of revealing poorly written code led to a "prisoner's dilemma" for code authors. Only after a new ASCL editor solicited codes, a new editorial board created policy, and new submission perks were added including having each code appear as a separate citation -- effectively a separate paper that could be cited and included in a publication list -- did the ASCL become popular (Allen et al. 2013). Even now, however, many scientists who would agree that it is a good idea to release paper-enabling source codes still do not submit their own codes to the ASCL.Nevertheless, Wilson and I were out of options, and so if we wanted our manuscript published anywhere besides the arXiv, it would be on the Winnower -- or nothing. Therefore Wilson took the last version of our paper that we submitted to the above-unmentioned prestigious journal and reformatted it for the Winnower. I uploaded the paper in early May of 2014. I might add that we have always welcomed peer review -- now including open peer review -- as evidenced by our pleading with journal editor after journal editor to send our paper out for review. That our manuscript might help advance a more open and healthy system of peer review as deployed on the Winnower was an unexpected perk. If the reader would like to read and even review the paper, please feel free to do so -- this opportunity can be found at the reference at the end of this contribution: Nemiroff & Wilson (2014).WHY DID THE MANUSCRIPT GO VIRAL?We did not know, before hand, that the original manuscript would become so popular. There are several reasons, in retrospect, that likely contributed to its popularity. First, the manuscript incorporates two attractive topics -- time travel and the Internet. Interesting papers on each topic are typically popular in their own right -- but a good paper combining the two -- possibly even more so. By coincidence, however, the manuscript actually touched on a third popular topic -- religion -- by using the search term "Pope Francis". Reporting on a paper that convolved time travel, the Internet, and religion, it turned out, created an irresistible opportunity for many editors and bloggers.On the negative side, the manuscript appears to some, at first sight, like watching a train wreck. It portrays that scientists -- who claim to be worthy of respect -- think that a ludicrous concept like time travel is real. It therefore draws in a reader possibly wondering things like "are the authors crazy?" or "do they also believe in the Easter Bunny and leprechauns?" or "are scientists (again) wasting taxpayer money?" Such readers might be disappointed that no evidence of time travelers was reported, as reading about the self-destruction of haughty scientists might have been more gratifying. On the money-wasted angle, when doing a Reddit interview about the manuscript, I respond to a question about how this research was funded with the fake answer that we used money left over from our study "Does Tax Payer Money Burn Any Better Than Regular Money?" (Nemiroff & Wilson 2014). In reality, this was an unfunded project.I'd like to think, however, that the most important factor in the manuscript's popularity was that it portrayed a really cool idea that was fun to think about. To quote Will Oremus on Slate "[authors] had me at the first line of the abstract: 'Time travel has captured the public imagination for much of the past century, but little has been done to actually search for time travelers. Say, that's a good point!" (Oremus 2014).Although surprised by the degree, I did think the paper would garner some public attention. That is because the paper was motivated by aspects of science that interest the public rather than funding agencies. After the paper's initial submission, I engaged in a short email exchange with Fraser Cain, the publisher of the Universe Today web site. We considered the idea that perhaps there is room in the world of publishing for science motivated primarily BY public interest, instead of IN THE public interest. Such a journal would involve serious peer-reviewed papers about what science really has to say about time-travel, warp drives, and creating black holes in the lab, to mention three ideas that deal with astrophysics. Conversely, the journal could also include some hard science fiction that draws from very modern science discoveries into short fiction pieces as realistically as possible. Other areas of science and engineering should also be included. Possibly publication could be coupled with a small amount of Kickstarter-like funding. Cain and I have not discussed the idea further -- we are both too busy -- but if anyone out there on the Internet wants to explore this idea further, consider me a supporter.REFERENCESAllen, Alice. et al. 2013. The Astrophysics Source Code Library: Where do we go from here? arXiv:1312.5334.Boyle, Alan.2014. Internet Search for Time Travelers Turns Up Nothing ... This Time.http://www.nbcnews.com/science/weird-science/internet-search-time-trave....Colbert, Steven. 2014. Time Travel Research in Cyberspace.http://thecolbertreport.cc.com/videos/b9gbou/time-travel-research-in-cy....Lischka, Konrad. 2014. Spuren aus der Zukunft: US-Forscher suchen Zeitreisende im Netz.http://www.spiegel.de/netzwelt/web/us-forscher-suchen-zeitreisende-im-n....Liu, Jean. 2014. Interactions: January High-Five (2014). Altmetric Blog.http://www.altmetric.com/blog/interactions-january-high-five-2014/.Nemiroff, Robert & Wilson, Teresa. 2014. We searched for time travelers who inadvertently posted unknowable-at-the-time knowledge to the Internet. Ask us anything!http://www.reddit.com/r/IAmA/comments/1va4vq/we_searched_for_time_trave....Nemiroff, Robert J. & Bonnell, Jerry T. 1995. Bulletin of the American Astronomical Society. 27:1291. Astronomy Picture of the Day: http://antwrp.gsfc.nasa.gov/apod/astropix.html.Nemiroff, R. J. & Wallin, J. F. 1999. Bulletin of the American Astronomical Society. 31:885. The Astrophysics Source Code Library: http://www.ascl.net/.Nemiroff, Robert J., & Wilson, Teresa. 2013. Searching the Internet for evidence of time travelers. arxiv.org/abs/1312.7128.Nemiroff, Robert, & Wilson, Teresa. Searching the Internet for evidence of time travelers, The Winnower, https://thewinnower.com/papers/searching-the-internet-for-evidence-of-t....Oremus, Will. 2014. Physics Professors Search Internet for Time Travelers, Don't Find Any. Slate.http://www.slate.com/blogs/future_tense/2014/01/03/professors_search_in....