I am very happy to share the news that our starting grant application to the Swedish Research Council has been granted 3.3 million SEK of funding for four years! This is fantastic news, as it allows us to further explore the interactions between bacteria in the human microbiome that are important for community stability and resilience to being colonized by pathogens. In the granted project, we will investigate environmental and genetic factors that are important for bacterial invasiveness and community stability in the human gastrointestinal tract.
Within the scope of the project, we will establish model bacterial communities and experimental systems for the human stomach and intestine. We will then investigate how disturbances, such as antibiotic exposure, change the interactions in these microbial communities and their long-term stability. Finally, we aim to identify genes that contribute to successful bacterial colonization or resilience to invasion of established communities in the human microbiome.
Aside from myself, Prof. Sara Lindén and Dr. Kaisa Thorell from the University of Gothenburg as well as Prof. Ed Moore at the university’s Culture Collection will be involved in this project in different ways. We will also collaborate with my former postdoc supervisor Prof. Jo Handelsman as well as Dr. Ophelia Venturelli at the University of Wisconsin-Madison. Finally, we will also collaborate with Dr. Åsa Sjöling at the Karolinska Institute. I look forward to work with you all over the coming four years! A big thanks to the Swedish Research Council for believing in this research and investing in making it happen!
I am very happy to announce today (on the European Antibiotic Awareness Day), that the EMBARK project that I am coordinator for got funded by JPIAMR with almost 1.4 million Euros over three years!
The primary goal of EMBARK is to establish a baseline for how common resistance is in the environment and what resistance types that can be expected where. That background data will then underpin efforts to standardize different methods for resistance surveillance and identify high-priority targets that should be used for efficient monitoring. In addition, EMBARK will develop and evaluate methods to detect new resistance factors and thereby provide an early-warning system for emerging resistance threats.
EMBARK is an international collaboration funded by JPIAMR. The consortium consists of myself, Thomas Berendonk (TU-Dresden, Germany), Luis Pedro Coelho (Fudan University, China), Sofia Forslund (ECRC Max-Delbrück-Centrum für Molekulare Medizin, Germany), Etienne Ruppé (INSERM, France) and Rabaab Zahra (Quaid-i-Azam University, Pakistan).
EMBARK has a website where the protocols and data generated during the project will be released. Follow our progress towards better monitoring of antimicrobial resistance in the environment here and on the EMBARK Twitter account: @EMBARK_JPIAMR!
The outcomes from a workshop arranged by JPIAMR, the Swedish Research Council (VR) and CARe were just published as a short review paper in Environment International. In the paper, which was mostly moved forward by Prof. Joakim Larsson at CARe, we describe four major areas of knowledge gaps in the realm of environmental antibiotic resistance (1). We then highlight several important sub-questions within these areas. The broad areas we define are:
- What are the relative contributions of different sources of antibiotics and antibiotic resistant bacteria into the environment?
- What is the role of the environment as affected by anthropogenic inputs (e.g. pollution and other activities) on the evolution (mobilization, selection, transfer, persistence etc.) of antibiotic resistance?
- How significant is the exposure of humans to antibiotic resistant bacteria via different environmental routes, and what is the impact on human health?
- What technological, social, economic and behavioral interventions are effective to mitigate the emergence and spread of antibiotic resistance via the environment?
Although much has been written on the topic before (e.g. 2-12), I think it is unique that we collect and explicitly point out areas in which we are lacking important knowledge to build accurate risk models and devise appropriate intervention strategies. The workshop was held in Gothenburg on the 27–28th of September 2017. The workshop leaders Joakim Larsson, Ana-Maria de Roda Husman and Ramanan Laxminarayan were each responsible for moderating a breakout group, and every breakout group was tasked to deal with knowledge gaps related to either evolution, transmission or interventions. The reports of the breakout groups were then discussed among all participants to clarify and structure the areas where more research is needed, which boiled down to the four overarching critical knowledge gaps described in the paper (1).
This is a short paper, and I think everyone with an interest in environmental antibiotic resistance should read it and reflect over its content (because, we may of course have overlooked some important aspect). You can find the paper here.
- Larsson DGJ, Andremont A, Bengtsson-Palme J, Brandt KK, de Roda Husman AM, Fagerstedt P, Fick J, Flach C-F, Gaze WH, Kuroda M, Kvint K, Laxminarayan R, Manaia CM, Nielsen KM, Ploy M-C, Segovia C, Simonet P, Smalla K, Snape J, Topp E, van Hengel A, Verner-Jeffreys DW, Virta MPJ, Wellington EM, Wernersson A-S: Critical knowledge gaps and research needs related to the environmental dimensions of antibiotic resistance. Environment International, 117, 132–138 (2018). doi: 10.1016/j.envint.2018.04.041
- Bengtsson-Palme J, Kristiansson E, Larsson DGJ: Environmental factors influencing the development and spread of antibiotic resistance. FEMS Microbiology Reviews, 42, 1, 68–80 (2018). doi: 10.1093/femsre/fux053
- Martinez JL, Coque TM, Baquero F: What is a resistance gene? Ranking risk in resistomes. Nature Reviews Microbiology 2015, 13:116–123. doi:10.1038/nrmicro3399
- Bengtsson-Palme J, Larsson DGJ: Antibiotic resistance genes in the environment: prioritizing risks. Nature Reviews Microbiology, 13, 369 (2015). doi: 10.1038/nrmicro3399-c1
- Ashbolt NJ, Amézquita A, Backhaus T, Borriello P, Brandt KK, Collignon P, et al.: Human Health Risk Assessment (HHRA) for Environmental Development and Transfer of Antibiotic Resistance. Environmental Health Perspectives, 121, 993–1001 (2013)
- Pruden A, Larsson DGJ, Amézquita A, Collignon P, Brandt KK, Graham DW, et al.: Management options for reducing the release of antibiotics and antibiotic resistance genes to the environment. Environmental Health Perspectives, 121, 878–85 (2013).
- Gillings MR: Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome. Frontiers in Microbiology, 4, 4 (2013).
- Baquero F, Alvarez-Ortega C, Martinez JL: Ecology and evolution of antibiotic resistance. Environmental Microbiology Reports, 1, 469–476 (2009).
- Baquero F, Tedim AP, Coque TM: Antibiotic resistance shaping multi-level population biology of bacteria. Frontiers in Microbiology, 4, 15 (2013).
- Berendonk TU, Manaia CM, Merlin C et al.: Tackling antibiotic resistance: the environmental framework. Nature Reviews Microbiology, 13, 310–317 (2015).
- Hiltunen T, Virta M, Laine A-L: Antibiotic resistance in the wild: an eco-evolutionary perspective. Philosophical Transactions of the Royal Society B: Biological Sciences, 372 (2017) doi: 10.1098/rstb.2016.0039.
- Martinez JL: Bottlenecks in the transferability of antibiotic resistance from natural ecosystems to human bacterial pathogens. Frontiers in Microbiology, 2, 265 (2011).
I read an interesting note today in Nature regarding the willingness to be review papers. The author of the note (Dan Graur) claims that scientists that publish many papers contribute less to peer review, and proposes a system in which “journals should ask senior authors to provide evidence of their contribution to peer review as a condition for considering their manuscripts.” I think that this is a very interesting thought, however I see other problems coming with it. Let us for example assume that a senior author is neglecting peer review not to be evil, but simply due to an already monumental workload. If we force peer review on such a person, what kind of reviews do we expect to get back? Will this person be able to fulfill a proper, high-quality, peer review assignment? I doubt it.
On the other hand, I don’t have a good alternative either. If no one wants to do the peer reviewing, that system will inevitably break down. However, I think that there would be better to encourage peer review with positive bonuses, rather than pressure – maybe faster handling times, and higher priority, of papers with authors who have done their share of peer reviewing the last two years? Maybe cheaper publishing costs? In any case, I welcome that the subject is brought up for debate, since it is immensely important for the way we perform science today. Thanks Dan!
I know that this is not supposed to be a political page, but writing this up, I realized that there is no way I can keep my political views entirely out of this post. So just a quick warning, the following text contains political opinions and is a reflection of my views and believes rather than well supported facts.
So, Swedish minister for education Jan Björklund has announced the government’s plan to spend 3 billion SEK (~350 million EUR, ~450 million USD) on “elite” researchers over the next ten years. One main reason to do so is to strengthen Swedish research in competition with American universities, and to be able to recruit top researchers from other countries to Sweden. While I welcome the prospect of more money to research, I have to say I am very skeptical about the nature of how this money is distributed. First of all, giving more money to the researchers that have already succeeded (I guess this is how you would define elite researchers – if someone has a better idea, please tell both me and Jan Björklund), is not going to generate more innovative research – just more of the same (or similar) things to what these researchers already do. If the government is serious about that Swedish research has a lower-than-expected output (which is a questionable statement in itself), the best way of increasing that output would be to give more researchers the opportunity to put their ideas into action. Second, a huge problem for research in Sweden is that a lot of the scientists’ time is spent on doing other stuff – writing grant applications, administering courses, filling in forms etc. Therefore, one way of improving research would be to put more money into funding at the university administration level, so that researchers actually have time to do what they are supposed to do. I will now provide my own four-point program for how I think that Sweden should move forward to improve the output of science.
1. Researchers need more time
My first point is that researchers need more time to do what they are supposed to do – science. This means that they cannot be expected to apply for money from six different research foundations every year, just to receive a very small amount of money that will keep them from getting thrown out for another 8 months. The short-term contracts that are currently the norm in Sweden create a system where way too much time is spent on writing grant applications – the majority of which will not succeed. In addition, researchers are often expected to be their own secretary, as well as organizing courses (not only lecturing). To solve this we need:
- Longer contracts for scientists. A grant should be large enough to secure five years of salary, plus equipment costs. This allows for some time to actually get the science done, not just the time to write the next application.
- Grants that come with a guaranteed five-year extension of grants to projects that have fulfilled their goals in the first five years. This further secures longevity of researchers and their projects. Also, this allows for universities to actually employ scientists instead of the current system which is all about trying to work around the employment rules.
- More money to university administration. It is simple more cost efficient to have a secretary handling non-science related stuff in the department or group, as well as economic people handling the economy. The current system expects every researcher to be a jack of all trades – which efficiently reduces one to a master of none. More money to administration means more time spent on research.
2. Broad funding creates a foundation for success
Another problem is that if only a few projects are funded repeatedly, the success of Swedish research is very much bound to the success of these projects. While large-scale and high-cost projects are definitely needed, there is also a need to invest in a variety of projects. Many applied ideas have originated from very non-applied research, and the applied research need fundamental research to be done to be able to move forward. However, in the shortsighted governmental view of science, the output has to be almost immediate, which means that applied projects are much more likely to be funded. Thus, projects that could do fundamental discoveries, but are more complicated and take longer time will be down-prioritized by both researchers and universities. To further make situation worse, Björklund et al. have promised more money to universities that cut out non-productive research, with almost guarantees that any projects with a ten-year timeframe will not even be started.
If we are serious about making Swedish research successful, we need to do exactly the opposite. Fund a lot of different projects, both applied and fundamental, regardless of their short-term value. Because the ideas that are most likely to produce short-term results are probably also the ones that are the least innovative in the long-term. Consequently, we need to:
- Spend research funding on a variety of projects, both of fundamental and applied nature.
- Secure funding for “crazy” projects that span long periods of time, at least five to ten years.
3. If we don’t dare to fail, we will not have a chance to win
Finally, research funding must become better at taking risks. If we only bet our money on the most successful researchers, there is absolutely no chance for young scientists to get funded, unless of course they have been picked up by one of the right supervisors. This means that the same ideas get disseminated through the system over and over again, at the expense of more innovative ideas that could pop up in groups with less money to realize them. If these untested ideas in smaller groups get funded, some of them might undoubtedly fail to produce research of high societal value. But some of them will likely develop entirely new ideas, which in the long term might be much more fruitful than throwing money on the same groups over and over again. Suggestions:
- Spend research funding broadly and with an active risk-gain management strategy.
- Allow for fundamental research to investigate completely new concepts – even if they are previously untested, and regardless (or less dependent on) previous research output.
- Invest in infrastructure for innovative research – and do so fast. For example, the money spent on the sequencing facilities at Sci Life Lab in Stockholm is an excellent example of an infrastructure investment that gains a lot of researchers at different universities access to high-throughput sequencing, without each university having to invest in expensive sequencing platforms themselves. More such centers would both spur collaboration and allow for faster adoption of new technologies.
4. Competing with what we are best at
A mistake that is often done when trying to compete with those that are best in the class is to try to compete by doing the same things as the best players do. This makes it extremely hard to win a game against exactly those players, as they are likely more experienced, have more resources, and already has the attention to get the resources we compete for. Instead, one could try to play the Wayne Gretzky trick: to try to skate where the puck is heading, instead of where it is today. Another approach would be to invent a new arena for the puck to land in, where you have better control over the settings than your competitors (slightly similar to what Apple did when the iPod was released, and Microsoft couldn’t use Windows to leverage their mp3-player Zune).
For Sweden, this would mean that we should not throw some bucks at the best players at our universities and hope that they will be happy with this (comparably small) amount of money. Instead, we should give them circumstances to work under that are much better or appealing from other standpoints. This could be better job security, longer contracts, less administrative work, securer grants, more freedom to decide over ones time, and larger possibilities to combine work and family. Simply creating a better, securer and nicer environment to work in. However, Björklund’s suggestions go the very opposite way: researchers should compete to be part of the elite community, and if your not in that group, you’d get thrown out. Therefore, I suggest (with the risk of repeating myself) that we should compete by:
- Offering longer contracts and grants for scientists.
- Giving scientists opportunities to combine work and family life.
- Embracing all kinds of science, both fundamental and applied, both short-term and long-term.
- Allowing researchers to take risks, even if they fail.
- Giving universities enough funding to let scientists do the science and administrative personal do the administration.
- Funding large-scale collaborative infrastructure investments.
- Thinking of how to create an environment that is appealing for scientists, not only from an economic perspective.
A note on other important aspects of funding
Finally, I have now been focusing a lot on width as opposed to directed funding to an elite research squad. It is, however, apparent that we also need to allocate funding to bring in more women to the top positions in the academy. Likely, a system which favors elite groups will also favor male researchers, judging from how the Swedish Foundation for Strategic Research picks their bets for the future. Also, it is important that young researchers without strong track records gets funded, otherwise a lot of new and interesting ideas risk to be lost.
In the fourth point of my proposal, I suggest that Sweden should compete at what Sweden is good at, that is to view researchers as human beings, which are most likely to succeed in an environment where they can develop their ideas in a free and secure way. For me, it is surprising that a minister of education representing a liberal party wants to excess such control over what is good and bad research. Putting up a working social security system around science seems much more logical than throwing money at those who already have. Apparently I have forgotten that our current government is not interested in having a working social security system – their interest seem to lie in deconstructing the very same structures.
In December, Alex Bateman, whose opinions on open science I support and have touched upon earlier, wrote a short correspondence letter to Nature  in which he again repeated the points of his talk at FEBS last summer. He concludes by the paragraph:
Many in the scientific community will admit to using Wikipedia occasionally, yet few have contributed content. For society’s sake, scientists must overcome their reluctance to embrace this resource.
I agree with this statement. However, as I also touched upon earlier, but like to repeat again – bold statements doesn’t make dreams come true – action does. Rfam, and the collaboration with RNA Biology and Wikipedia is a great example of such actions. So what other actions may be necessary to get researchers to contribute to the Wikipedian wisdom?
First of all, I do not think that the main obstacle to get researchers to edit Wikipedia articles is reluctance to doing so because Wikipedia is “inconsistent with traditional academic scholarship”, though that might be a partial explanation. What I think is the major problem is the time-reward tradeoff. Given the focus on publishing peer-reviewed articles, the race for higher impact factor, and the general tendency of measuring science by statistical measures, it should be no surprise that Wikipedia editing is far down on most scientists to-do lists, so also on mine. The reward of editing a Wikipedia article is a good feeling in your stomach that you have benefitted society. Good stomach feelings will, however, feed my children just as little as freedom of speech. Still, both Wikipedia editing and freedom of speech are extremely important, especially as a scientist.
Thus, there is a great need of a system that:
- Provides a reward or acknowledgement for Wikipedia editing.
- Makes Wikipedia editing economically sustainable.
- Encourages publishing of Wikipedia articles, or contributions to existing ones as part of the scientific publishing process.
Such a system could include a “contribution factor” similar to the impact factor, in which contribution of Wikipedia and other open access forums was weighted, with or without a usefulness measure. Such a usefulness measure could easily be determined by links from other Wikipedia articles, or similar. I realise that there would be severe drawbacks of such a system, similar to those of the impact factor system. I am not a huge fan of impact factors (read e.g. Per Seglen’s 1997 BMJ article  for some reasons why), but I do not see that system changing any time soon, and thus some kind of contribution factor could provide an additional statistical measure for evaluators to consider when examining scientists’ work.
While a contribution factor would be an incitement for researchers to contribute to the common knowledge, it will still not provide an economic value to do so. This could easily be changed by allowing, and maybe even requiring, scientists to contribute to Wikipedia and other public fora of scientific information as part of their science outreach duties. In fact, this public outreach duty (“tredje uppgiften” in Swedish) is governed in Swedish law. In 2009, the universities in Sweden have been assigned to “collaborate with the society and inform about their operations, and act such that scientific results produced at the university benefits society” (my translation). It seems rational that Wikipedia editing would be part of that duty, as that is the place were many (most?) people find information online today. Consequently, it is only up to the universities to demand 30 minutes of Wikipedia editing per week/month from their employees. Note here that I am referring to paid editing.
Another way of increasing the economic appeal of writing Wikipedia articles would be to encourage funding agencies and foundations to demand Wikipedia articles or similar as part of project reports. This would require researchers to make their findings public in order to get further funding, a move that would greatly increase the importance of increasing the common wisdom treasure. However, I suspect that many funding agencies, as well as researchers would be reluctant to such a solution.
Lastly, as shown by the Rfam/RNA Biology/Wikipedia relationship, scientific publishing itself could be tied to Wikipedia editing. This process could be started by e.g. open access journals such as PLoS ONE, either by demanding short Wikipedia notes to get an article published, or by simply provide prioritised publishing of articles which also have an accompanying Wiki-article. As mentioned previously, these short Wikipedia notes would also go through a peer-review process along with the full article. By tying this to the contribution factor, further incitements could be provided to get scientific progress in the hands of the general public.
Now, all these ideas put a huge burden on already hard-working scientists. I realise that they cannot all be introduced simultaneously. Opening up publishing requires time and thought, and should be done in small steps. But doing so is in the interest of scientists, the general public and the funders, as well as politicians. Because in the long run it will be hard to argue that society should pay for science when scientists are reluctant to even provide the public with an understandable version of the results. Instead of digging such a hole for ourselves, we should adapt the reward, evaluation, funding and publishing systems in a way that they benefit both researchers and the society we often say we serve.
- Bateman and Logan. Time to underpin Wikipedia wisdom. Nature (2010) vol. 468 (7325) pp. 765
- Seglen. Why the impact factor of journals should not be used for evaluating research. BMJ (1997) vol. 314 (7079) pp. 498-502
The Swedish Foundation for Strategic Research (SSF) has made public their grants to the research leaders of the future (link in Swedish), aiming to help and promote young researchers with a lot of potential and ambition to build their own research groups within their fields. 18 persons got 10 million SEK each (roughly 1.5 million USD), and also a leadership education. However, SSF obviously believes that men are superior in building and leading research groups, as 14 of the researchers were men (that’s 78%).
It is often argued that the reason that men get more and larger grants than women  is that they are more abundant in academia and that the over-representation of men will solve itself given sufficient time. This makes the SSF decisions particularly saddening. These 18 researchers represent the future of Swedish research, and SSF thinks that the research of the future is better of being led by… men. Alarmingly, the foundation’s statements on gender equality (in Swedish) says that (my translation):
The foundation for strategic research views gender equality as something self-evident, that should permeate not only the operations of the foundation, but also all activities that the foundation supports. Thus, the foundation strives towards that all treatment should be gender neutral, and that the under-represented gender should be given priority when other merits are similar. In an equal nation, research resources of men and women should always be taken advantage of, within all areas.
Still, only 20% of the chosen researchers are women. You may think this is a one-time-only event, but no, no, no, it’s much worse than this. In 2005, six of 18 researchers chosen were women (33%), in 2002 six out of 23 (26%), and 2008 six of 20 (30%). It seems that the SSF regards equality to mean 70% men, 30% women. That’s pretty bad for a foundation says it “views gender equality as something self-evident, that should permeate not only the operations of the foundation, but only all activities that the foundation supports.” Obviously, the words on equality are just words, and women still have a long way to go before treated equally by foundations supporting research.
In the long run, this inequality only cements the established norm with men on the top of the research departments. Wennerås and Wold wrote in 2000 that “junior scientists’ frustration at the pace of their scientific productivity is normal at the beginning of their careers, when they do most of the benchwork by themselves. But female scientists tend to remain at this level their entire working lives” . Maybe it would be a good idea for the directors of the SSF to read this, and think about what their actions actually mean for the future of strategic research, and contemplate why women are leaving academia to a much larger extent than men . Because research funders has a huge responsibility for the future of the scientific community.
- Wennerås and Wold. Nepotism and sexism in peer-review. Nature (1997) vol. 387 (6631) pp. 341-3
- Wennerås and Wold. A chair of one’s own. Nature (2000) vol. 408 (6813) pp. 647
- Handelsman et al. Careers in science. More women in science. Science (2005) vol. 309 (5738) pp. 1190-1