Bold opinion pieces, RIP?

A few weeks ago, I lamented the passing of papers like Janzen’s Why mountain passes are higher in the tropics (1969) or Janzen’s Herbivore and richness hypothesis (1970) (the Janzen half of Janzen & Connell hypothesis) or the Hairston, Smith & Slobodkin (HSS 1960) paper best known as “why is the world green” even though that is not really the title. These papers were highly speculative, waved a little bit of data around, but mostly put out a hypothesis that attracted researchers for decades. But you don’t really see these kinds of papers any more. Hence my question of whether we should assume this category of paper has come to rest in peace (RIP) (i.e. are dead).

How pragmatism resolved the age old battle between rationalism and empiricism (or what is the scientific method?)

If you want to simplify philosophy of science down to the point of gross oversimplification, it has been a millenia long debate between rationalism and empiricism. Although both could be found among the classic Greeks, rationalism was dominate from the time of the Greeks to the Renaissance (almost 2000 years). Rationalism holds that knowledge comes from logical thought. Think Euclid who established the axioms/proofs style of geometry. Or Plato’s cave which emphasized that our senses are crude and misleading (observing mere shadows on the cave wall) in capturing the underlying true essence (the perfect objects outside the cave creating the shadows which we cannot see). Empiricism on the other hand believes that knowledge comes from our sensory experiences of the world outside our mind and mistrusts the mind. Empiricism and rationalism are endpoints of epistemology (the philosophy of how we know things). But they have also been major motivators for scientists framing how to do science.

ESA seeks input on gold OA, Plan S and the future of publishing

The President of the Ecological Society of America has written a nice blog post on the ESA website about the changing nature of publishing (and how this influences societies and their finances). The short answer is it has big impacts!

As I wrote a few weeks ago, a potentially new seismic shift is happening due to Plan S which seeks to go for pure Gold OA (100% OA journals) and eliminate hybrid OA, green (post a PDF on your website) OA, and other models like JSTOR and old fashioned subscription based models.

ESA is on top of this change and is seeking your input. Read the whole blog post for lots of good thoughts. But if you are tight for time, I have excerpted their request for input:

We are of course very interested in what our members think about this complex issue! Are you currently limited in your ability to access the literature – especially recent papers – and would you be in favor of a rapid shift to open access for ecological research publications? If you are active in submitting and publishing research papers – do you normally have the financial resources to cover the costs of article processing for fully open access journals? Do you have ideas about how to subsidize or afford the publication of papers in these OA journals from authors who cannot afford the processing charges?

ESA will assuredly be affected by continued evolution of the business model for scientific publishing. In order to understand the impact on our members’ professional lives, and not just on our revenues, it is important that we hear from you. I look forward to reading your thoughts. Email (esahq@esa.org), and use “publications” in the subject line. We will keep our members fully informed as Plan S and related developments move forward.

The trajectory of ecology – poll results

I recently surveyed our readers on what shape they thought the overall trajectory of ecology took. It was a fun post with a number of good comments. First I set up the question and polled the readers what shape they thought the overall trajectory of progress in ecology took. Then I argued in some detail that it was circular or spiral (and explored  what this implied). So its hard to know how many readers truly took the poll before reading my argument, and of course the subset of our readers who chose to answer a poll is clearly not random in a scientific sense.

But here are the results.

We had just over 200 respondents. Of these about 10% answered “other” and described their own trajectory.  These are interesting and I’ll mention some in a minute. But of those who went with one of the six choices I provided 37% went for circular or spiral, 35% went for some version of systematically increasing (linear, exponential or saturating) and 28% went for a random walk, so very roughly 1/3, 1/3, 1/3. Of course random walk is interesting because it contains elements of both circularity and a trendline (most random walks look like they contain a trend but also have noise and are likely to return to the beginning at some point). The spiral was far more popular than the circle, although some agreed with me that the vertical gain in the spiral was only methodological, but others felt the vertical gain of a spiral was an important feature.

I thought I would find a strong link between career stage and view of trajectory shape, but I didn’t. There might have been a weak signal of a U-shape (early career and late career being more likely to pick one of the upward trends and middle career  – postdoc, early permanent position – more likely to pick a circle or a random walk), but I didn’t see a strong enough effect size to want to pursue it further (read-only link to the data here: https://docs.google.com/spreadsheets/d/12AAXpbEwTbvW9_OmRxeJZwjGZM3eLl5ZlyudwhlnOwk/edit?usp=sharing).

The suggestions under “Other” were also interesting and broadly included 4 categories:

• Variants on a systematic upward trend (e.g. logarithmic, power law with exponent of 3/4 of course, upwards staircase or very uneven steps that aren’t level, sigmoidal, step function, Kuhnian/punctuated equilibrium)
• Complexifications on random walks including multiple random walks, random walk with weak trend, chaotic, chaotic with multiple attractors (several people suggested multiple dimensions are needed)
• Several poetic versions (“More like a crystallisation process in which new nodes form and spread until they butt up against one another”)
• Pessimistic (systematic downwards) such as “downward slope” or “digging a deeper hole into a dark pit”

Probably the most comprehensive answer under “other” was “A combination of gentle progress superimposed with a lot of random noise and occasional bigger and more frequent smaller jumps (and “epicycles” within certain topics as they get rediscovered and renamed)”. It would be hard to disagree with that and that is probably a good place to end!

Open access and the reality of getting from here to there.

Open access (OA) publishing* has long been touted as an important reform needed in academic publishing. OA is when an academic journal article is published under an open license like CC-BY or CC-BY-SA** or public domain and is made available to readers without a paywall. The benefits of OA are obvious. Anybody anywhere can read a scientific paper without having to pay or have a subscription. It is hard to disagree that on some fundamental level science publishing should be out in the open like this.  And on a practical level researchers without university affiliations and in countries with libraries that cannot afford subscriptions will clearly benefit. And it might solve the problem of journal subscription prices increasing at a rate much faster than inflation and breaking the backs of libraries since subscriptions go away. Despite its benefits, OA is not the world we are in today – the traditional model has been focused on a reader pays (subscription) model. But I have come to think that the forces aligned behind OA have become strong enough to push us part way there. So how do we get from one model to another?

To be clear up front, this is not about whether OA is good or bad, I have my own (of course balanced and nuanced!) opinion*** . But here I just want to stipulate that OA is a viable worthy model. Instead, I want to talk about what the transition from today to full OA will or could look like. This is suddenly very timely given several recent events in ecological publishing:

What shape is the long trajectory of ecology? (updated)

It is fun to think about what shape is the trajectory of our field over the long haul, say the last century. Jeremy’s post on what topics ecologists should pursue got me thinking about this. Is the trajectory of ecology an asymptotic arc, a Michaelis-Menten or Ivlelv function. Always improving, getting  ever closer but never quite reaching the ideal? People have often suggested physics has this trajectory. Fundamental discoveries came quickly, but now more and more people spend more and more money to tease apart ever smaller order effects. Or is ecology a young field that shows a an upward straight line trend – major new advances coming in every year? Or even exponential growth once we got the groundwork laid? Or are we a random walk, wandering aimlessly around like the ants in anthill that got kicked over? Or may be we’re more systematic than those ants but we just keep going in circles? What do you think?

NB:  keep reading. If you submit your response to the Google survey it will collapse and create a large white space – keep scrolling down for the continuation.

I mentioned Jeremy’s poll got me thinking about this. One of the things that jumped out of the results to me was how often fields just got renamed. Metacommunities was rated very highly, while island biogeography was rated very low. But what is the overlap between island biogoegraphy and metacommunities? 90%? How productivity influences diversity was low, but BEF (Biodiversity Ecosytem Function) is trendy and is the exact same two variables with the direction of causality flipped. And diversity-stability was trendy – diversity stability is a question about how diversity affects the variance of an abundance time series while the unfashionable diversity-productivity is a question about how diversity affects the mean of an abundance time series – almost certainly topics that share processes (and data sets!).Clements-Gleason is about as out of fashion you can get. But it is not unrelated to the most trendy of all surveyed topics of range shifts in response to climate change. And it is strongly related to the trendy topic Jeremy didn’t survey of viewing community assembly as a set of three filters (abiotic, biotic and dispersal). In some of these cases we have almost literally just rebranded the ideas. In others we have shed a few ancillary pieces and added a few other ancillary pieces, partially remixing, but still leaving the inner cores recognizable.

I just finished editing the proofs on a paper defining macroecology (out in GEB in a few weeks). In it I point out that macroecology (1990s-2000s) was in part a backlash against the push for reductionist manipulative field experiments (1970s-1990s), and reductionist manipulative field experiments were in part a backlash against the MacArthurian push for simple models (1960s-1970s), and now macroecology is facing a push (2010s) to become less empirical and lean more on simple models! Have we moved anywhere?

This thread of thinking brought me back to one of my comprehensive written exam questions. At the University of Arizona, we got four written questions each of which was assigned a time frame of 3-5 days. These were fun questions and gave an opportunity to really think deeply about some topics (including some serious literature reading). One of my questions was in part “Briefly review the literature on interspecific plant-plant interactions”. I took a methodological approach to this question identifying the top 50 cited papers over the last 20 years in ISI Web of Science that used the phrase “plant competition”. I also reviewed several books and review papers on plant competition. Out of this I boiled out fourteen major research questions/themes in plant competition. They are listed in table 1 below. Then, just because I like to cause trouble and fervently believe in knowing the old literature, I dug out Clements’ et. al 1929 book “Plant Competition” (PC in the table) and Clements’ 1933 book on “Competition in Plant Societies” (PCS in the table). I skimmed these books for whether he addressed these same 14 themes and believed the same things as modern researchers.

Guess what! I concluded that Clements had already strongly and directly addressed (at least 50 years earlier) 12 of the 14 themes and reached the same conclusion as modern researchers on 11 of the 14 (again see table 1 below). One of the themes (non-equilbrial dynamics) was somewhat antithetical to Clements world-view (although he recognized disturbance) and another theme (diffuse competition) hadn’t really emerged. And on a third (allelopathy) Clements was active in the debate but believed it hadn’t yet been proven, where as modern researchers believe cases exist where it occurs.

So if you think I’m arguing for a circular shape to the long trajectory of ecology, you are right!  I think you could make a case that is actually a spiral. We come back to the same topic, but we do it in a better, more sophisticated way each time. Certainly in my Clements example, the methods were far more quantitative, the hypotheses more explicit, the mechanisms and language far less anthropomorphic (Clements loved to analogize to battles and warfare). So maybe a spiral? But the upward aspect of a spiral is primarily to be found in methods and language, not questions. And not answers. I think you could say the same thing about studying metacommunities instead of island biogoegraphy. So I’m not convinced the rising spiral aspect is central or the most important aspect (even if it is there).

Whether you believe there is a spiral or not, I think the circle is the central defining feature of the structure of the ecological trajectory. I only have 20 years of being an academic ecologist under my belt, and I already see circles everywhere. And when I read the literature further back in time I see them much more. You’re going to have a hard time convincing me I am wrong about circles (although of course that doesn’t mean you have to agree with me – maybe seeing circles is a bias of my mental processes – I am an intellectual lumper rather than splitter).

But I think the bigger question is whether the circular nature is a good thing, a bad thing, or a neutral thing? I can easily imagine most if not all people will say that a circle, if true, must be a bad thing. Nobody talks about the circular nature of progress in physics. It sounds insulting. But I am more sanguine. I think it is somewhere between neutral and positive. For one thing, I think the cycle time in ecology is about 25-30 years (there were two full cycles between Clements and the modern papers in my comps question). Not the least bit coincidentally the generation time of scientists is about the same. This means each time around it is a new group of scientists working on the topic. And that means the full circle of topics is covered in one scientists career. That makes it look like a rather more systematic and efficient exploration of what is ultimately a finite space, doesn’t it? And even if I don’t think the spiralling higher is a prominent feature, I do think reconceptualizing a topic every 25-30 years keeps it fresh, exciting and at the forefront of ecologists’ minds. And on a purely practical level, we do have to find new framings to get funding. The only way a circle looks bad is if we compare ourselves to physics and have physics envy. I do think a saturating function is a better description of physics. But physics is a very different science – it is not multicausal. In physics they discover the first order effect and find its formula, then they discover the second order effect and find its formula, and pretty soon the next generation is left explaining a few percent of the variability. Ecology doesn’t work that way. We have a list of the 5-20 things that matter, but we cannot rank order them. They are all equal. So we spend our time focusing for a while on competition, then moving on and focusing for a while on dispersal, and then moving on and focusing on exploitive interactions, and etc. Not better. Not worse. Just different. Circles are just fine for ecology!

I find it more useful to think about the implications of being circular than bemoaning being circular. In particular, it means ecology needs to be a field that teaches (at least to its graduate students) the history of its ideas. Its one thing to go around the circle with self-awareness. Its quite another to fool ourselves into thinking we are going in a line upwards. Physicists almost never bother with citations of old ideas (e.g. Newton’s 3 laws or Maxwell’s 4 equations). But I think ecologists always will and always should know and be able to trace the roots of their ideas at least one cycle back, and ideally 2 or 3 cycles back. It keeps us humble. And you know what, even if we have a fresh take, our ancestors were not idiots – reading their work can only improve our own.

What do you think? Do you buy my circle argument? Do you think a spiral is crucially different from a circle? If we are a circle is that good, bad, or neutral? What does a circle imply for how we do ecology?

 

Table 1 – The 14 major questions in plant competition in the 1980s-1990s and what Clements thought about them circa 1950

Fact	Clements
Plant competition exists and is common	This is no news to Clements. The fact that both of the references have the phrase “plant competition” in the title and describe numerous experiments on this subject is enough.
Plant competition is often highly asymmetric	Clements regularly uses terms like dominant and subdominant. He understood the relation to size as well. “In general, the taller grasses enjoyed a decisive advantage over the shorter, but this was often counterbalanced by an earlier start or greater resistance to drouth [sic] or cold on the part of the latter. Not infrequently one species would acquire and hold the commanding position in the community and the other would perforce content itself with a subordinate role” PCS p 26. In his review of research prior to the writing of his book, he cites many authors who recognize the importance of light (PC).
Plant competition occurs both above- and below-ground	Clements regularly talks about differences in root structure or shoots as a form of competition and relates this to their roles in the community (e.g. “bisects were employed to exhibit the root and shoot relations” PC p. 39). He did not have the sophisticated experiments today that allow us to say “root competition is more important in such and such condition”
Competition is density dependent and non-linear	Clements certainly understood this, although the terms were not in use in his day. His experimental growth of crops at varying densities and the record of yield clearly showed the same non-linear pattern we observe today. However, he made no attempt to tie his results to any mathematical equations or models.
Competition varies over space and time	Clements was well aware of this. One section in PCS is entitled “Struggle between forest and prairie” and he explores the differentiating factors. It is also clear from his writing that he was keenly aware of variations in soil, probably much more than most plant ecologists today. In a number of his field experiments he captured drought years and he talks about how this changes things (e.g. PC chapter 6) and he designed his experiments specifically to “disclose the effect of different seasons and climates on the intensity and outcome of competition” PCS p. 24
Other trophic levels affect competition	Clements has a nice discussion on how grazing (either by cows or bison) affect the competition between buffalo grass and tall grass PCS pp. 28-29. He also talks abut how he designed his experiments “to evaluate the influence of animals, especially cattle and rodents, in the process [of competition]” PCS p.24. I could not find a mention of mycorrhizae in a brief review of Clements, but they were certainly known in his time (Allen and Allen 1990 cites a couple of papers published in the 1920’s)
Allelopathy occurs	Clements knew about allelopathy and was part of the debate weighing in against it. He talks about “the whole problem of toxic secretions and soil toxins, and their possible role in competition. In spite of the excellent work done by Bedford and Pickering (1914) in this field, the existence, nature and role of supposed toxic substances are still subject to grave doubt (Clements, 1921) and much more extensive ecological research in various climates and soils will be necessary to a solution” PC p.35
Productivity and disturbance affect competition	Clements was well aware of the role of disturbance and productivity although he did not seem to have a clear-cut idea of increasing or unimodal curves over gradients of increasing productivity or disturbance. For example he stated “Where annual mowing is the rule, Poa pratensis invades in force and assumes the role of a dominant” PC p. 37
Plants compete for resources and R* is predictive	Although he was certainly aware of the role of nutrients, he tended to downplay their role compared to today: “As to the things for which plants compete, the results show that, in general, water is the most important. Light usually comes next, with minerals a close third, though the former permits a proportionally greater reduction before becoming critical.” PCS p. 35
Plants can have differentiated niches to coexist	Although the niche language was not yet in vogue, it was certainly no news to Clements. “Competition is closer between species of like form than between those of dissimilar form” PC p. 11 His description of the competition between Sporobolus asper and Andropogon furcatus gives a very detailed mechanistic description of their different niches (based mostly on drought resistance vs. growth ability) PC pp.48-49.
Non-equilibrium conditions can prevent competitive exclusion	Although familiar to the with the role of disturbance (see above), I believe this idea would have been foreign to Clements.
Competition can be diffuse, non-specific, and contingent	If the terms were explained, I suspect Clements would agree that this was true, but I also think it was not central to his way of thinking. Most of his experiments were pairwise.
Competition can be hierarchical	Clements had no doubts of this. See the quotes under the asymmetry section. Again, he did not have the neatly defined theory of inclusive niches and centrifugal organization as we describe it today, but he knew the mechanics of systems that fit this description.
Competition influences succession	Clements has a five page review of the relation between succession and competition (PC p. 21-26). This may be one area in which he went further than people accept today. For example, “the outcome of each period of competition is the dominance of the best-equipped community, until the incoming of prairie or forest puts an end to the waves of invasion and conquest” PCS p. 36

What academics can learn from business III: good meeting culture

This is the third in a series of things I think academia would do well to look to and learn from business (also see how many business hats an academic wears and business advice books). When I left the business world and went back to graduate school in 1997, there were many things I liked better about the academic culture. But there was one thing that jumped out at me as immediately badly flawed in academic culture: meetings. Everything about them – when held, why held, how held. To be sure a good meeting is a combination of artful guidance by its leaders and participants and a bit of luck. But there are some clear rules of thumb that help.

What academics can learn from business II: the best business books

In the first post in this series I argued that whether you know it or not if you are training to be a PI in an academic (or government or NGO) environment, you basically have to wear a bunch of different hats corresponding to all the different functions a business has from human resources to sales and marketing to management. What you may not know is that the business world is absolutely aflood in advice/self-help books on every topic under the sun. It’s a bit of a joke really. Every year hundreds of books come out claiming to show you how to be the best in the world. But people buy them. And read them. Even if they don’t want to they have to read some of them because they become the lingo du jour. It won’t impress the boss if you have a vacant look when she uses the latest buzz word. From my business days, I recall having to read a book called “Crossing the Chasm” before an executive retreat because the boss expected it and we were all going to talk about it. It was, to say the least, fluffy. It took a couple of hundred pages to say what could have been said in 20. And it was entirely anecdotal. It short it was a typical self-help book. One concept and a bunch of inspiration. And it was totally off target – it was all about moving from selling to early technology adopters to the mass market. Only our products were never going to move to the mass market. Ironically if you’ve ever flipped through an inflight magazine you will see an add promising to save busy executives time by provided digested versions of all the important business books for the year.

For those of you who identified some gaps in skills relative to the list I laid out and want some advice on where to go to develop some of those skills, I want to provide you my own version of the digest. Here I will summarize (but definitely encourage you to read) key points from four books to help develop some of the business skills most academics don’t get trained in. I’m not going to offer anything in human resources, accounting or general counsel (although see this post on intellectual property law). They are boring and country specific and most academics matter them with the patience and kindness of the people doing these functions in their university. And of course I am not going to refer you to a book to learn how to do your core function of science. But I’ve got suggestions for management, marketing, sales, and time management. And I’m not going to say this repeatedly. But every one of these books is short and fluffy and a very quick read. And easily available second hand (business books sell at much higher volume than academic books for some reason …). So if a book on my list interests you, I strongly encourage you to go read it. It will cost you $5-$10 and two hours.

What academics can learn from business I: the hats a PI (or grad student) wears

I spent 9 years working as a computer consultant for a private company, consulting with many very large companies that are household names. At the age of 30 I left business for academia and for the most part am much happier and feel like academia is a much healthier place to work for me. But there are days and times I find myself remembering my days in business and wishing academia would be more like business. I’ve mentioned in the past that I think business has at least the potential for doing a better job of dealing with bullies and harassment.  In general, I’ve found academics have a lot of curiosity about life “on the other side” and what areas businesses do things better. So I’ve planned a series of blog posts on the topic*.

This post is focused on using business language to be more clear about the roles a PI needs to fulfill (and for that matter most graduate students and postdocs need to at least begin learning how to do and in other cases outright take responsibility for on their own). I frequently make the following analogy with my graduate students.  I tell students that they are president of their own company (which starts with only themselves as an employee but often grows to have a dozen or more workers) and they need to know and wear all of the hats a company president wears including human resources, marketing, etc. Even if we’re in academia and not profit-motivated, humans are humans, and human enterprises all have the same basic needs.

Science, advocacy, and honesty

About a year ago, shortly after the March for Science, I wrote a three part series on living as a scienitst in a post-fact world (how we got there, why humans rarely use facts to decide what to believe, and why/how scientists should engage with policy). Peter Adler wrote a spirited rebuttal “Response to a post-fact world: in defense of the honest broker“. I responded at the time in the comments. But Meghan’s recent review of the Merchants of Doubt got me thinking about this again. So did an opportunity to shadow my representative in the Maine legislature for a day with my son. During that day I was introduced to one of only two scientists in that body out of 185 people (House + Senate).The two main topics of debate, solar energy fees and legalizing marijuana, both had substantial areas where science could have been informative, but seemed to have little to no impact on the debate, and for that matter the debate seemed to have little to no impact on the actual outcome. Rational discussion of facts is not really how policy gets made. So I want to return to my post-fact world claim that scientists need to become more engaged in policy and Peter’s rebuttal. In particular, I want to suggest that scientists get so muddled in how to relate to policy because we confuse two separate axes.