How do we fix the publishing system. Three (doable?) solutions.

I’ve been playing for a while with some ideas that are at the same time potential solutions, and to some extent doable. But I am aware some are highly unlikely to happen due to social dynamics. They play around with ideas related to reducing the number of papers we publish and changing the evaluation and discovery systems in place.

  1. The Synthesis Journal: This would be a non-for-profit ideal journal that only publishes anonymous papers. There are two types of papers a) Wikipedia consensus-type method papers with the aim to create standard methods. The beauty is that the metadata of newly collected data would indicate clearly which method was used e.g. ISO-345, which has an associated data format and hence combining those is easy programmatically. Bots can even crawl the web if metadata is in EML format looking for studies using standard methods. Methods have no public authors and are achieved by consensus. b) The second type of paper are synthesis papers. Those are dynamic papers that collate data collected with standard methods to answer general ecological questions using modern programmatic workflows. As new data is created following a), the model outputs are updated, as well as the main results. Versioning can do its magic, here. To avoid having field workers that create data and synthesizers that get credit, anonymous teams donate their time to this synthesis endeavor. Hence the anonymity. This will limit also the number of synthesis papers published.
  2. The Cooperative of Ecologists: This is something I really like. Cooperatives have a long tradition of allowing the development of common interests in a non-capitalistic way. Entering in the cooperative would be voluntary (some references or formal approval may be necessary). Duties can involve adhering to a decalog of good practices, publishing in a non-selective style repository, giving feedback to twice the number of manuscripts you sign as the first author, and evaluating a random peer per year with a short statement (no numerical values). The benefits are getting feedback on papers (you can use it to update your results as you see) and having yearly public evaluations you can use for funding/promotion. With one evaluation per year, you can quickly see how your peers judge your contributions to the field. One of the core problems of the publishing system is the need to be evaluated. This moves the focus of evaluation outside where you publish your papers, and these evaluations can highlight better aspects such as creativity of ideas, service, etc…
  3. Crowd-sourced paper evaluation plug-in: As stated in the previous posts, one of the main problems is that we use where papers are published not only serve to discover what we should read, but also to evaluate our performance. I know that a single index will never make the evaluation job, this is why we need to diversify the options for evaluators (grant agencies, hiring committees, … ). Right now, in addition to the number of papers and the journal prestige / IF, metrics like citations received, F1000-type evaluations, or alt-metrics are already available. DORA-style narrative CVs are also great, but hard to evaluate when the candidate lists grow dramatically. So, what if a plug-in exists for internet browsers where you can log in with your ORCID? Each time you visit a webpage of a scientific paper (including archives), a simple three axes evaluation emerges. You can rate with three simple clicks it’s 1) robustness (sample size, methods, reproducibility) 2) novelty (confirmatory, new hypothesis, controversial) 3) overall quality. I am sure these axes can be better though, and reproducibility may be an automatic tag (yes/no) depending on data/code statements. You can also view the evaluations received so far. With enough users, this can be a democratic powerful tool to create one more option to be evaluated. Plus, recommendation services may be built upon it. I would love to read a robust controversial paper liked by many of my peers. I believe this is not complex technologically, and if done in a user-friendly way, can help the transition to publish in non-selective free journals or archives. This also selects for quality and not quantity. I know cheating is possible, but with verified ORCID accounts and some internal checks to identify serial heaters/unconditional fans and the power of big numbers, this may work.

This is it. If it was not clear, the aim of the post is to think outside of the box, and lay out a few ideas, not a detailed bulletproof plan.

Where the hell I publish now?

The scientific publishing system is hindering scientific progress. This is known and I won’t repeat myself or other more detailed analysis dissecting the problem of publishers making massive profits on our behalf without (almost) any value added (e.g. Edwards and Roy 2017, Racimo et al. 2022).

In the last years, cost-effective alternatives to publish our results have emerged and I don’t think technical aspects are an issue anymore. I think the problem is that when I publish something, I want to be read. I know that if I publish in certain journals, the day before the paper is published almost all researchers interested in that topic will see my paper. I also want to be evaluated. Most funding agencies still use where you publish as a quality indicator of your contribution (consciously or unconsciously), not to mention that the same paper published in a given journal will receive much more citations than if published elsewhere, if citations are what funding agencies will look at, bypassing the infamous IF. 

My approach so far has been trying to publish in Society Based Journals. Despite most of these journals still partnering with big publishers, I heard that most have a decent deal with publishers (but I also heard some got terrible deals). The advantages are obvious. Those are well read and evaluated, have no APC, and the money they make reverts to the societies. The drawback is that not all my papers are top papers that can find a home there, and that the papers are not open access (you pay to read). This is secondary for me in a world with SciHub, but still important. In addition, this model is getting slowly outdated, and some of those journals are already changing to pay to publish model. Paying high APC (anything > 200 EUR for the EU standard) is a bad replacement for the current system in my opinion.

I made a quick tally and in the last 5 years (2017-2021) I published:

  • 32 papers in Society Based Journals with no APC. Wow! These include BES, ESA, Nordic SE, AAAS, Am Nat, and other conservation and Behavioural societies.
  • 6 in Selective Journals that require APC (but about half of the time my co-authors paid for the APC), such as PNAS, Nature Communications, or Scientific advances, but also other less fancy. I try to minimize those because, despite their visibility, I prefer to invest money in salaries, then in publishers, but if I (or my lab group) can publish in e.g. PNAS, this is money well invested regarding career advance. Let’s be honest.
  • 5 in Non-Selective Journals with APC such as Plos, Open Science B, Sci Reports, PeerJ… Not always my decision, and while I support non-selective journals, especially if non-for-profit or with sustainable policies, their APCs are increasing in an unsustainable way.
  • 3 in For Profit Selective Journals without APC. Despite trying to convince my co-authors to avoid those, I do not always succeed. Yes, I had 1 paper published in Elsevier last year (sorry). The other two are high-impact journals whose visibility might compensate for the balance (TREE and Nature E&E). Everybody has a price.
  • 2 Free to publish – Free to read Journals. This is the way to go! One is in a Journal I did not know until recently. The other is the newly created Peer Community Journal, which I support. Other Journals in this list are Web Ecology, Journal of Pollination Biology, Ecologia Austral, and to be honest, not much more that I know (and Ecosistemas, despite it publishes mostly in Spanish). I am also looking forward to the new EU-Horizon Journal, but it’s closed to EU-Horizon projects, and I think it still costs quite a lot to the EU per article, so indirectly, we are still paying for it.

While I am happy with the last 5 years’ record regarding where I published, I think this is not enough. I want to publish more in free-to-publish – free-to-read journals, especially if I am the first author (I got tenure already). But I also want those to be read. Our Peer Community Journal paper has almost no citations despite being quite good (IMHO). I am sure that if it was published in Ecology Letters it will have now several more citations.

So how do we fix this? I have some ideas, but nothing clear. The next posts will explore those ideas.

Resources about Ecology Journals:

Conserving biodiversity will need true sacrifices.

[this is a half-baked reflection after a lab meeting discussion on the EU biodiversity policies. Thanks to the lab and especially to Elena Velado for the discussion]

We are embedded in a culture where the only valid success is complete success. Making compromises, or renouncing something to focus on other priorities is often seen as a weakness if not a failure. There is no better example than what we see every day in the movies. Even when the main character has to make a sacrifice, in the end, he or she ends up gaining everything, including what they sacrificed. For example, you need to let go of your true love, but then you discover that was the way to secure it. You renounce your dream job for your family, and this allows you to find an even better job and be successful also in that dimension. You need to betray your friends to save the galaxy, and your friends still love you for that. You get the point. We are in a culture where we are expected to do small sacrifices to gain it all anyway, so in the end, you really don’t sacrifice anything.

The EU Green Deal is also embedded in this narrative, where we are promised that with a “small” economic sacrifice, we can conserve biodiversity, and in doing so, we will enhance our well-being and our economy. No real sacrifices and a vision that changing gears to support biodiversity will allow us to keep growing economically. I love this story, and it would be great to switch to a more sustainable future with no real costs. In fact, I used the fallacy that conserving pollinators is cost-effective because they will increase your crop yield. But this is not completely true. When going deeper, we also showed that pollinators worth conserving are not usually the ones who deliver crop pollination (Kleinj et al 2016) and that the costs of sustaining pollinators do not always compensate economically via an increase in yield (Scheper et al in prep). This does not mean we shouldn’t safeguard pollinators, but that doing it only for economical reasons is not going to work. At some point, we need to sacrifice something, and it’s our choice.

The danger of a narrative that ignores real situations of compromise where you need to sacrifice things that make your life easier, and not acknowledge that there are trade-offs that force us to choose is that we create false expectations. Expectations that we will always win in all axes. But narratives are important because they prepare society to make decisions. And we need honest narratives now to prepare us to take those decisions tomorrow. Only by being clear on the fact that we will need to make decisions and renounce something in order to gain another thing will set us in the right framework.

We should start the conversation on what are we willing to sacrifice or compromise and what not to conserve biodiversity. Indeed, we may discover some sacrifices are not as hard as they look, especially for the average citizen. Maybe we prefer to have one more species of butterfly in the EU than having a few rich people traveling to space for pleasure. Maybe we prefer to eat strawberries only in spring, but have birds migrating through our wetlands. It’s all about educating ourselves and being aware we decide our future, but not selling fairy tales.

Our behavior is heavily influenced by the context we live in. The first step to change behaviors is to create the adequate context, and for me, this context needs an honest narrative that acknowledges trade-offs and prepares us to take informed decisions.

Your PhD data is a treasure

You will never have as much time as during your PhD to collect high-quality data. I didn’t realize it at that time, but detailed data you really know and understand is a lifetime companion. I used mine for its main purpose during my PhD, but also to test new methods when I needed to test those with data. In addition, it contributed to several synthesis papers, including an ongoing one led by someone at my lab right now. This makes at least five papers I used this data so far. As the data is openly available for a long time it was also used by several other synthesis papers. All this preamble is to encourage you to love your data!

When I collected the data I did most of the bees id’s myself (I had lots of help from experts such as Jordi Bosch, but in the end, it was me who ran through all the samples). This implies I identified several individuals to moprhospecies level, and I couldn’t put a name in all my pollinators. I would say this is typical for many ecological studies, and we always cross fingers this is good enough at the ecological community level. More than 10 years later I decided to properly identify by taxonomonists the full collection (which I managed to keep all this time while traveling through three countries!)

Almost 30% of individuals changed from morphospecies to being properly identified at the species level. Among those, most morphospecies belonged to a single species, but not all. In general, I underestimated the number of species present from 81 to 114. Several similar species were lumped together by my ignorance. However, to my relief, this did not change drastically the relative differences between the 12 sites, as seen in the figure. Connectance and the number of links per species decreased for all sites at similar rates, but some metrics are less consistent, such as nestedness, but nestedness is also a metric known to be quite volatile.

Quick comparison between the new (corrected) and old (morphospecies) dataset for some common metrics such as connectance, species richness, links per species, nestedness or H2.

As I said, the data was released in different places. Web Interaction Database has a copy of the data in matrix format, which makes it hard to split the data e.g. by dates. Web of Life has even a more drastic pooling, which I am not sure how they did it, as I was not contacted by them, but I noticed all sites are pooled, including invaded and non invaded sites. FigShare had the best data so far, and it is associated with a paper and its analysis, so it’s better to keep this version at the morphospecies level for historical reasons. Hence, the new release of the data, with all new identifications is at Mangal. The webpage is very nice, and you can access programmatically all the networks in R.

mgs <- search_datasets("bartomeus")
mgn <- get_collection(mgs)
mgn; names(mgn)
tg <- as_tbl_graph(mgn[[1]])

I am a bit embarrassed by the lower quality of the original data, but better fixing it now than never. Long life to data!

On getting tenure…

There are important points in life that are prone to self-reflection. Getting tenure in the Spanish research system is one of them. Last week I won a highly competitive permanent position as a researcher at CSIC and I am incredibly happy to get the opportunity to work full time to advance science with the stability required. Since then, three contrasting thoughts have emerged in my mind.

First, I have an immense feeling of gratitude. I am completely conscious that the way I do science is only possible because I am not alone in this journey. A huge number of people has supported my ideas, gave me opportunities to try things, shared their knowledge with me. Thank you all! It was pretty flattering to get so many congratulations over the past week. Plus, I have to admit it the journey has been pretty fun so far.

Second, I still feel uneasy with the full selection process. All 20 candidates competing for the position deserved a stable research position. CSIC keeps evaluating quantity over quality and most positions get filled by researchers over 40, and often older. Being considered a “young researcher” at 39 and with two kids it’s not funny anymore. The hyper-competitiveness we are immersed is damaging careers, but also science itself. Sometimes I feel we are not longer doing science, but running on a hamster-wheel.

Third, I got this position by privilege. My parents supported me while doing my degree and always encouraged me to take risks and explore new paths. It’s easier to do when you have a safety net. Neither me nor my family had remarkable health of economic problems. I am a white man and as such I never experienced harassment of any type. Even with the wind at my back, it was bloody hard to survive in academia in Spain. This implies we are missing a lot of brilliant researchers that didn’t had it that easy.

Now is time to reconsider things. Inertia is very powerful, but now I have the freedom to decide (to certain degree) what science I want to do and how. Let’s use this power wisely. And let’s fight to change the system from the inside.

Book reviews and stories behind the papers

I quite enjoy writing about what I read, as well as the stories behind the papers I wrote, because there is always much more than what its finally printed. I post here two pieces recently published in other blogs / journals and a new story behind a paper with a looong history.

1- A book review of one of the books about bees I enjoyed the most: The Solitary Bees: Biology, Evolution, Conservation. by Danforth, Bryan N., Minckley, Robert L., and  Neff, John L.:

2- The story behind an R package we wrote to better understand species coexistence: htttps://

3- A story behind a recently published paper or “Why some bees have big brains?”

Today we publish a paper I am quite proud of, as we break new ground after a very long journey. In a nutshell, we investigate bee brain evolution and show that some surprising results.

Microtomography scan of a bee brain.

Back in 2009 I read “pollinators cognitive ecology” book and I started working with Daniel Sol on cognitive ecology of birds. The seed was planted. Fast forward a couple of years, I assaulted Marc Seid in an Entomological Society of America conference to ask about extracting brains of hymenopterans. He kindly invited me to his lab and I learnt the technique, but that was nothing we can do as a side project without proper funding. In 2015 we finally got funding and Ferran Sayol (the lead author) spent some time with Marc dissecting bee brains. That was a lot of work, complemented with more brains from Europe in the subsequent years. Overall, we weighted brains for > 100 bee species. Probably, we multiplied by 10 the amount of data existing on bee brain size. This is already a huge step forward! The next hurdle was getting a proper phylogeny of those 100 species, which required further collaborations. At the end, all the pieces fell finally together!

First, we show that sociality do not require larger brains. This is not surprising, as it was suggested before for other insect groups, and even for vertebrates it’s controversial. Surprisingly, being specialist do requieres having bigger brains. This was unexpected at first based on what we know for vertebrates, but it may be more intuitive than we think. For bees, navigation skills for locating and remembering resources is essential, specially if you are specialised in a few resources. However, handling different types of flowers is not as challenging as eating very different resources such as insects, grain, etc… Moreover, parasitic species tend to have also larger brains (but our sample size is tiny for those), which reinforce the idea big brains are needed for navigation and location of nests. Have a look at the paper, It’s very cool!

Sayol, F., Collado, M.A., Garcia-Porta, J., Seid, M.A., Gibbs, J., Agorreta, A., San Mauro,
D., Raemakers, I., Sol, D., Bartomeus, I. (2020) Feeding specialisation and longer generation
time are associated with relatively larger brains in bees. Proc. R. Soc. B 20200762

A simple observation of single plant flower production

Violeta and Ignasi Bartomeus

As a simple game with the kids, we started counting daily flower production on a single plant of Cistus albidus that we transplanted last year (so it’s 3-4 year old, and 1.5 meters tall). It turned out quite surprising! I was expecting a clear peak of flowering around a normal distribution, but the flowering went on for > 100 days (very rainy season), with two distinctive flowering peaks. When C. crispus started flowering we did the same with another single individual (1 m tall). In this case, the peak is more clear.

Flower production per day of two individuals of two Cistus species. Days start counting from 1 January (day 55 = 23 February). The date of nest completion by three Osmia bicornis species is marked (O.b1, 2 and 3).

We also recorded nest completion by three Osmia bicornis female bees that regularly visited C. albidus. Bee “O.b1” completed two nests, but the other two only one. Note it took a long time for O.b1 to build the second nest!

Conclusions: Now I have way more questions than when I started. I wonder about individual lifetime flower production over years, variability across individuals, relationship with fitness, how this compare to community level phenology patterns, …

Bees of my garden

This is basically a quick note for me to remember which bees visited us these last years. As I am keen on promoting pollinator-friendly gardens, this may be interesting for someone else. Maybe.

Context: We moved to this house two springs ago. It has a ~4*8 m garden and is located in a residential area with allotments (great for bees) nearby.

2018: The garden was a perfect lawn without a single flower + a patch of bamboo and a patch of bird-of-paradise flowers (useless for native bees). I don’t remember seeing any bee that year. I stopped watering the lawn (makes no sense in Seville to have a water-consuming lawn).

2019: We dig out the bamboo and the bird-of-paradise flowers (harder than I would ever though!) and planted Rosemary, Lavanda, Rockroses, and Teucrium. I also removed a 1*4m patch of lawn to plant some vegetables. I added vertical bamboo reeds (I had plenty!) in the soil and add a few old logs in a corner.


  1. Eucera sp. Early season in lavanda.
  2. Chalicodoma sicula in Teucrium.
  3. Megachile sp nesting in the ground (in a pot!) Entering leaves, Honeybee size.
  4. Ceratina curcubitina (?) nesting in the vertical bamboo reeds.
  5. Holpitis sp. hovering around the logs.
  6. Xylocopa violacea Loves teucrium. Males using some horizontal bamboo reeds to sleep.
  7. Apis mellifera Rare, in teucrium.

2020: I installed a couple of bee hotels for megachilids, let the lawn go wild. The grama is still languishing, now intermixed with clover (Trifolium repens), melilotus (Melilotus sp.), and other annuals well-adapted to our climatic conditions.

Bees: (Eucera, Chalicodoma and the big Megachile not seen again)

  1. Xylocopa violacea lots in teucrium (March-April), and females using the new bee hotels and expanding the canes.
  2. Anthophora sp. Rare in teucrium.
  3. Osmia bicornis mainly in Cistus albidus. 3 females, 4 nests and 2 not finished.
  4. Hylaeus sp. visiting broccoli. I think they nest in the vertical reeds also.
  5. Ceratina curcubitina (?). A real explosion this year. All vertical canes full. Cistus crispus, teucrium, broccoli, strawberries, Melilotus, clover.
  6. Anthidium manicatum (?) in Teucrium. Males patroling and females gathering leave hairs. Earl morning to late evening (May).
  7. Anthidiellum breviusculum (?) in clover.
  8. Hoplitis sp1. Again in the logs. Also in Lavanda from time to time. No idea where are they nesting.
  9. Andrena sp. Very rare (seen three times maybe?). In C. crispus and once I saw it digging in the vegetable plot, but never again.
  10. Apis mellifera in Teucrium and clover. More common this year, to my disgrace.
  11. Lasioglossum sp (the golden one, similar to gemmeus) in Brocoli.
  12. Megachile sp. in Melilotus A very small one close to M. apicalis. It nests in the vertical reeds and uses petals to close them.
  13. Hoplitis sp2. Late season. Looks like adunca, but I have no echium nearby. Active at dusk, but no nests completed yet (still active, but is already 30ºC). UPDATE: two nests colsed + two not finished by 7 June

Maybe I am missing some super tiny bees, as the ceratinas + hylaeus + lasioglossums sometimes fly fast and who knows what else is mixed there. All ID’s are mine, so maybe some are incorrect.

13 species in 2019, 16 overall! Looks like megachilids are over-represented. I miss more Andrenas, and I did not see a single parasite yet. No bumblebees, but this is expected as they are rare in Seville. Next year, more!

Managing people: Radical candor in academia.

As researchers, we are supposed to be good at a plethora of things. Managing people is one of those things that nobody teaches us, but that ends up being pivotal for the lab functioning. In fact, I would say that researchers, in general, don’t feel comfortable being a boss and see the time invested in managing people as a burden that prevents them to do more important things such as actual research. I’ve been there, and I think that it is pivotal that (we like it or not, we are good at it or not) we assume part of our job as IP is to be a boss, and we try to be a good one.

With this in mind, I have read several pieces on scrum and agile culture and tried to understand how to create an efficient and happy team. The last book I read was Radical Candor, by Kim Scott. It is focused on managing people at big companies, but I think a lot of stuff can be applied to academics.  The main message of the book is that you need to create a culture of caring for people (and for the science you are doing) and of giving clear and honest feedback.


I think that in academia (in general) we are good at caring personally (small labs, with people passionate for science and mind alike, makes it easier), but we don’t always challenge directly. In my own experience, when things go well, it’s super easy for me to give honest feedback and improve the project even more, but when someone is under-performing I have a hard time making that clear, and this is bad for you, for him/her and for the team.

The following are basically notes for me and the lab, with no ambition to be comprehensive or detailed:

The book makes crystal clear that spending a morning listening to your team complain about personal stuff, or about an internal fight or celebrating their success is an integral part of your job. Not a distraction. Your job. This makes it easier to allocate time to that in your daily schedule.

It also encourages focusing not only on people writing the important papers, but on hard workers that make this possible. Having a “stable” lab technician who solves the day to day field and lab work is the best decision I toke as PI so far. Invest in core people. This is really hard in academia where positions depend on short term projects.

Do not personalize. People are not sloppy, they may have done a particular job in a sloppy way. Then, Its easier to fix specific actions. The “Situation-behaviour-impact” chain is the best to describe a problem. The best feedback is given often and in impromptu situations, is specific about the problem and offers solutions.

If you want feedback (or criticism as stated in the book) to be part of your team, cultivate it at all levels. Encourage criticism also towards yourself (or your ideas) and among your peers.  I like the following process to encourage criticisms, starting by listening (not by replying to criticism or cutting it or offering excuses). When you got criticism, ask to give details and strive to understand it. Do not react. (I’ll apply this also to my normal life).


I was reinforced on running retrospectives after papers are published in the lab. The book also recommends blocking time for thinking and for working on personal projects, something I am also doing (albeit I should do more) so I don’t spend the day in meetings.

Finally, It made me think about the lab culture. It’s hard to judge internally, but I would like to think the lab culture is to be open and replicable (even if we often do not achieve it!), to put people first and to be risky in our ideas and approaches (even if this means we often go for the big picture, and miss some of the important details). We also are committed to outreach.