Monday, 28 December 2020

On how open access improves accessibility to ecological science: does it?


Recently, I attended (if virtually) the Annual Meeting of the British Ecological Society (BES), termed this year,“Festival of Ecology”. A really nice meeting, amazingly well organized and with an attractive program. Among a variety of activities which I was interested in, there was the obvious one: a visit to the BES stand where societal publications are traditionally exhibited.


Because of my interest in applied ecology, I was rapidly attracted to a new journal aimed at improving the linkage between science and solution of the increasing environmental issues related to anthropogenic activities. This is the 7th BES journal which states that the way in that scientific data and information may reach practitioners is, among several changes,  by including new article types (such as “Data Articles”) in a flexible format1. An additional aspect in this sense, is avoiding the paywall by making the journal fully open access.

This latter issue got me thinking. In fact I have  been ruminating on Open Access for some time now. One idea that comes to my mind, as an ecologist working and living in the developing world, is that many serious environmental issues related to an increasing human population (e.g., deforestation, desertification, waste accumulation) occur in the developing world. Paradoxically, open access is far from a solution to accessibility to science in these countries and regions. For starters, publication costs for open access are formidable for any one doing science on a shoe-string as many of us do. Let me illustrate: page charges for an article in say PLOS One is equivalent to 3 monthly salaries of junior, full-time researcher in Argentina today. And this is not the most expensive example.

Of course, the catch here is that, on the one hand, publications are not paid from your salary but from grants. But it takes no saying: research grants in the poorer parts of the world are also minimal and are ‘scaled” to GDP,etc. Then, there are waivers and discounts for papers submitted by authors (all authors?) from impoverished countries. The criteria here is based usually on a list that is provided by the publisher, which often has a grey zone in which several countries fall (say again as an example, Argentina). For these countries, that are not listed for automatic waivers, these do not exist straightforwardly. In any case, the waiver is applied if, a letter requesting it accompanies the submission of the manuscript (and usually not once it has been accepted). To me, this is not only not “automatic”, but in an even more unfriendly manner, it seems like begging. Pretty awful. 

Now, having a paywall is often described as strong limitation for those working in the less favored parts of the planet, to access science. This may be true to some extent although it again feels patronizing and to some degree ignores how much of world outside Europe and North America, exerts research. Some journals even boast of “opening” access of those issues published several years back (never mind the fact that scientists are keen mostly on the latest developments). With over 20 years’ experience in research in a developing country (yes, for ever “developing” Argentina!) I have some doubts which I wish to share here. 

Firstly, many publishers have special deals and arrangements with national or regional governments or even with given academic institutions where full access to their journals is provided for a global fee, which is clearly much less than an individual subscription or paper download.  I’m not sure how many publishers and countries reach these kinds of arrangements, by I’m personally aware of a few and this clearly allows for access to the latest science, if partially. Then, there is a variety of routes to access recent papers hidden behind the paywall.  Some, such as the website run by Alexandra Elbakyan are so popular that it is very unlikely that you will encounter any trouble in finding “that” paper you so badly wanted to read. I’m pretty sure that no one working in the developing world has not heard about this website or even used it more than once. If against the established rules, we can all agree on the fact that such model exists. Finally, you can e-mail the corresponding authors who, if they have not already uploaded a pre-print version of their work on personal websites, will more often than not, e-mail you their work almost immediately.

So, my take here is that open access is oversold. As an author I will always go for publication in journals with no page charges whenever possible.  As a reader, I do not feel the paywall is the most important threat to my science.  I’m fully aware of the costs of publishing and that these should not be underestimated. And that these need to be paid somehow. This is not the issue. The issue is that open access is not the "free access" alleged. If we are to forward our research on pressing environmental issues, there are much bigger issues that need our attention. We also need to think new ideas to guarantee full and unlimited access to our science. Maybe the Covid-19 pandemic- all papers dealing with it are free to access worldwide- may inspire new working models. 



1. Cadotte, M., Jones, H. &  Newton, E. (2020). Making the applied research that practitioners need and want accessible. Ecological Solution and Evidence, Vol 1:1.

Friday, 23 October 2020

Global warming. So much progress, huh? (a message for the younger scientists)





Last weekend, while tiding an old trunk full of notes and papers and other stuff that sits in our lounge under a zillion plant pots, I came across this Newsweek cover I show above.  The leading title: “No more hot air. Its’ time to talk sense about the Environment” caught my eye immediately. The issue is dated June 1992, that is 28 years ago and referred to a United Nations Earth Summit (actually the first one) that was held in Rio de Janeiro that year. Among a list of issues that were on the table then, I noted and agenda (named Agenda 21) through which industrial nations would help poor countries develop their economies without damaging their environments.

The IPCC was created in 1988 (and was awarded a Nobel Prize in 2007) and the Kyoto protocol was signed by many countries in 1997. Yet, I often wonder how much has been achieved since then or if we have done enough. We see glaciers melting, droughts and floods more often than expected or in new areas, and several biological groups thoroughly dropping in numbers (pollinators, for example). At the same time, we are, to some degree, going “electrical” when it comes to mobility and also, we see that industrial emissions- give or take- have at least not increased worldwide as could have.  But these are simple observations. Hard core data on the change inflicted upon climate by us, is available and uncontestable.

We can agree on the fact that not all world leaders are up to the challenge. In fact only recently, some have ushered dominant countries to sign-off international protocols and treaties. Still, if some a little more than others, most societies have become more attentive to what global warming implies. In turn, an array of world class ecologists and climate scientists (to state a few examples) have tackled the issues from many angles and published many papers, often in high impact journals.  Many have delivered conferences, talked to policy makers and participated in international panels on global change. But, how has this translated into bettering the lively hoods of those living in poorer countries without damaging the environment? How much has been done, not just in reducing emissions but in keeping the world’s diversity, including crucially important forests healthy, as a part of our struggle against global change?

Producing food for all of us in a sustainable manner remains (to me at least) and utopia. Let us consider one example: Argentina. A large country with 45 million citizens whose GDP relies strongly on agricultural produce and that is not usually listed as a poor country. Once considered, the “The Barn of the World” because of its high productivity for growing cereals and exporting such produce, Argentina also bears a variety of climates, landscapes and ecosystems: from snowy peaks, to sweltering swamps: from glaciers to rain forests. Also, the country has been listed 9th in terms of biodiversity richness. Considering forests for instance, while not a “forest country”, 10% (26 million ha) of its land surface area is currently covered with natural forests and there are an estimated 1.3 million ha. of forest plantations (I’ll talk about this issue another day).

But these forests in Argentina suffer greatly. It has been estimated that in the period 1930-2005, 66% of the natural forests were lost, mostly to agriculture1. According to FAO, deforestation rates in Argentina are among the highest of South America2, reaching up to 1 million hectares per annum. Moreover, by increasing land for agriculture in this way, it does not seem we have achieved much in terms of economy development. GDP per capita for Argentina in 2018, was under 12 US dollars, compared to industrialized economies such as the USA, with nearly 63 US dollars or 47 USD reported for the same year in Germany. 

Of course, we are all aware of the role played by forests in mitigating global warming, among other-not less important- sustainability related issues. So what part of “developing the economies of poorer nations without damaging their environments” stated 28 years ago, have we missed? Just imagine this pattern I describe for Argentina in many (too many!) countries-even poorer- around the World.   As scientists we have done a great deal, but it seems we still fail in converting the much looked for impact factors of our publications into policies. The next generation of ecologists may need to pay more attention to this. Or, at least, this is something we need to ruminate on further.


PS: The trunk made it to Argentina with clothes and -I imagine- a great deal of expectations, brought by my spouse’s grandmother when she came escaping poverty and lack of opportunities found in post WWII Europe. It is ironic that as of today-75 years later-, Argentina has more than 40% of its population in sheer poverty, inflation rates exceed 45% yearly and unemployment rarely has fallen below 10%.

1. Dirección de Bosques (2005). Primer Inventario Nacional de Bosques Nativos. Informe nacional. Proyecto Bosques Nativos y Áreas protegidas BIRF 4085-AR, 1998-2005.Argentina.gob.ar. 
2. Zak, M. & Cabido.M.2010. El avance de la agricultura es la mayor causa de deforestación. Argentina Investiga.

Wednesday, 12 August 2020

To cite or not to cite, that is the (authors) question!


 

“Como te gustan las citas”, pregunta el caballero, acodado en la barra, a una señorita a su lado. Ella contesta sin dudarlo, “Apellido, Título y Año,…y vos?”

 

In scientific writing, recognizing others work when it is due, is very important for a variety of reasons. For starters, it is the right thing to do, but also, it relates to the idea that scientific knowledge builds upon earlier acquired information, very much like each brick of a wall is set upon a previously laid brick. When we write a paper, we acknowledge previous work by citing it.

 

Now, having said this, why is it that more often than not, students or junior scientists struggle when it comes to appropriately citing in their texts and in using the “right” reference list? One common issue-the use of too many references- could be assigned to some degree of lack of confidence in some statements. When one is writing your own first papers, you may often feel the need to refer to all that literature you have been struggling to read. But another emerging situation, is the ease with which we can cite work nowadays. Most researcher currently handle literature databases that are citation-ready, and with a simple click, can add a full citation to your reference list. Of course, this does not solve the issue of actually reading these papers and of how to use them in a text correctly.

 

Here are some thoughts on this that may prove helpful. First, my strategy to begin writing, is to do so without citing. I try to establish some coherent flow in each paragraph and maybe, when I know a reference is needed, I open brackets and write some reminder like “citation needed, or “XXXX, 2010 or so”. Later, when re-reading the text (which will happen a lot!), I will complete the full citation. I find this method prevents me from getting distracted from what I want to say in a given sentence or paragraph. After all, it is me trying to communicate an idea through writing. As the saying goes, “Drive it as if you stole it”.

 

Another thing I encourage my students to do, is to minimize the reference list. Sometimes you write a given statement that has become standard knowledge in the field your work on, and so there is no need to cite there. For example, if your work reports a study on behavioral ecology in which there is an obvious implication to evolution by natural selection, and you are writing a paper for a specialized journal, you may find that refering to Darwin’s “Origin of Species”1 does not add much. This may be especially true for the methods and analysis sections. You would exceptionally, if ever, cite Fisher’s2 work when analyzing data using ANOVA in an ecological study. Needless to say, is that these citations will naturally be referred to when writing and essay on evolution or a handbook of stats.

 

Also, I feel there is little added value to the reader, when a string of citations breaks a sentence right in the middle. It surely will read better if citations are located at the end of it, even if you struggle with the issue that some of the references, relate to a part of the sentence and not the whole idea there developed. For example, when listing the presence of a given insect or plant in different countries, we could be tempted to place each reference after each country mentioned. This could be reasonable, unless your list includes, say, 12 countries and this results in a choppy, very long sentence. Why no instead, list all references at the end of the sentence and let the reader-if she/he wants to delve into each country, figure it out later? You sacrifice a little precision for the sake of a better, more fluent reading. We must remember that scientific writing has its rules and practice, but as we have to deal with an increasing load of literature to read and understand, we appreciate good writing more than ever.

 

In sum, using citations appropriately has less to do with the best reference managing software you may have downloaded on your laptop and more with developing good writing skills. Hand checking the reference list and giving it a format (an asset promoted by every available software) can be cumbersome but to gain a proper perspective, think about how much effort and time it takes to plan your paper, collect that data and write it up. Also, do note that many journals are going towards format-free submissions.

 

Now, this is not intended to undermine the help these literature handling programs definitely do (in fact some are very practical and have reduced the use of paper and storage space immensely), but do remember that adding a PDF to your database, does not imply that you have read it! Of course, editors and reviewers get annoyed when the reference list is wrong, incomplete or a given, very relevant citation is missing in the text. But trust me, you are more likely to see rejection, or a bad review if your study is faulted or if your paper poorly drafted, than because of a missing reference. And, I think we all would agree, that having to read a paper several times, to understand where the author is going, can be even more frustrating.

 

 

1.     Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray.

2.     Fisher,R.A. 1925. Statistical Methods for Research Workers. Edinburgh: Oliver & Boyd.

Tuesday, 21 July 2020

On what is a “good” question.




On what is “good” question.

“Nothing shocks me, I am a scientist” (Indiana Jones, in “Indiana Jones and the Temple of Doom”)

Early on, as students of the natural sciences we learn the scientific method. The principle behind it is hypothesis testing, a process through which a conjecture or hypothesis is put to test with some experiment that allows us to manipulate factors.  In ecology, the application of this approach took a little longer than in other fields, probably because the discipline has a strong background of natural history: describing species, where they lived and what they did. We can easily picture the first ecologists as thoughtful observers of nature.  Also, manipulating factors, carrying our controls and assuring repeatability are high, often difficult to achieve, goals.

It was in the late 1950’s, and through the strong influence of researchers such as Robert Mc Arthur, that hypothesis testing has become more of rule in the ecological sciences1. The idea that papers begin with a conceptual framework which is confronted to data obtained in the field, in the lab or through theoretical modeling, is nowadays common in the scientific literature.

To a significant degree, teachers of ecology courses at all levels, and student supervisors, invest much effort in conveying how the scientific method should and can be used in ecological research. Often, we repeatedly bring back to focus during talks, classes and meetings on specific issues such as discussion on which specific method is best for a given case or on the best approach analysis our data, by formulating this query: “What is your question, again?”

While I strongly endorse this approach both in my own work and during my lectures and student meetings, I often wonder about the natural history. John Lawton, in his somewhat controversial writing titled “(Modest) Advice for graduate students” published in Oikos 65, in 1992 raised this issue2. While auto ecological studies are interesting, he says, there are millions of species out there, making it impossible to study each in detail and to conclude in this way, nature’s workings. While it is clear that a poor grasp of ecological theory leads to the “wrong” kind of questions, so will a limited knowledge of the species or system we choose as our study model.

As we all know, not all questions that come to mind, are “good” questions. Sometimes we observe fascinating aspects of nature and imagine experiments. Often, though we de not fully handle the basic biology which allows us to set these questions in a proper evolutionary and ecological setting.  Here it is when supervisors and teacher play a key role. Let me note here that “good” or “bad” are not the best adjectives to classify anyone’s work, I only use them here to make a point. I could rephrase this by saying which kind of studies (if well executed) will see easier publication in high impact journals. As Lawton (1992) stated in his paper intended for students “avoid picking species because they are cute, ‘interesting’ and cuddly or because nothing is known about it”.

Interestingly, Mac Arthur was often wrong in his interpretation of natural process and systems. Not on purpose but because he dared explore innovative ideas, often with weak data1. He managed to get them published then, but maybe not in today’s publishing world. He started from ideas and then looked for the data, often with limited use of the standing literature.  It seems nothing shocked him! But it also generated controversy.

I admire and get excited when I attend talks and seminars that show both, passion and a deep knowledge of biology of the plant, animal, fungus or bacteria they have focused their work on, and a sound theoretical framework.  I bow to presenters who, while offering results at geographical scale, study species interactions or tackle the effects of global change on species distributions, or else use several slides to explain their modellng approach, can then take questions as far from their work as for example of the molecular context or on the foraging behavior of the species involved in their work.  

So, let us-without doubts- embrace the scientific method heartily in ecological research. But in doing so, I hope we can also keep alive, that curious biologist that is fascinated by nature’s wonders. Also, let us not repress innovation or creativity in thinking our questions. We will often be wrong and will have to deal with (manuscript) rejection, but I’m sure at the end, we will come to “better” questions and a better understanding of how nature works.



1.     Fretwell, S.D. 1975. The impact of Robert MacArthur on ecology. Ann. Rev.Ecol.Syst.
2.     Lawton, J.H. 1992. (Modest) Advice for graduate students” Oikos 65:

Tuesday, 14 July 2020

In the beggining




The combination of a generalized lockdown with a snowy winter got me in the mood of starting this blog in July 2020. I wish to share some of my thoughts on ecological science from Southern Argentina, via this blog.

I have also led the International Journal of Pest Management since 2012 and as from 2021 will be Editor-in-Chief of Ecological Applications, one of five journals managed by the Ecological Society of America (ESA).  I will  write on random things, all ecology. I expect to write some comment on those papers published in EA that have, for some reason caught my eye. Of course all thoughts and opinions will be solely mine.

Finally, because I teach Population Ecology and Behavioural Ecology at the Universidad del Comahue in Bariloche, I will write about the experience of teaching ecology to graduate students.  I enjoy teaching no end...but Zoom clases...well this is another story, soon to begin for me. Our second term, when I will be teaching starts on August 24, but with no physical presence. Let's see how it works.



I hope you enjoy it!

On how open access improves accessibility to ecological science: does it?

Recently, I attended (if virtually) the Annual Meeting of the British Ecological Society (BES), termed this year,“Festival of Ecology”. A re...