# Redesign of the Jungle Rhythms webpage

I decided to redesign the webpage of the Jungle Rhythms project. The previous web page only served as a portal to the Zooniverse citizen science project. The project is finished, and so a place to host more content, such as details on the dataset and visualizations was needed. I alos copied over old blog posts from my personal blog to aggregate those on this new website as well.

# Finalizing Jungle Rhythms processing

In the run-up to the ATBC 2018 meeting I’ve finally sat down and crunched through the final processing of the Jungle Rhythms dataset. I can now accurately convert all the citizen science annotations to coordinates on a grid and finally, estimates of tropical tree phenology. In total, while omitting ‘empty’ years, the project now has gathered phenology observations of 16417 site years of data, across 1237 species.

# The unseen taxes on post-docs

It is tax season in most countries. As most law abiding citizens post-docs pay taxes on their wages. However, there are many unseen taxes in a post-docs life. Most of them go undocumented.

## The Health tax

Most academic institutes provide health coverage for post-doc positions (although not guaranteed). But do not be fooled, even with coverage you do pay extra if not monetary, with your health. Mobility often makes it difficult to get reimbursed after leaving the country and legal disputes regarding medical bills are all but impossible.

Short term (international) contracts often result in the fact that no meaningful relationship with a family doctor can be established. The lack of familiar setting is a hurdle when looking for medical advice, especially concerning mental health issues. Furthermore, it often leaves you with a fragmented medical history which negatively influences diagnosis.

Finally, given the short term nature of most contracts it is hard to convince institutes and PIs to invest in policies which only pay of in the long term. For example, simple interventions such as ergonomic office chairs, standing desks which have huge short and long term benefits are often overlooked. These requests are often ignored as post-docs aren’t around long enough to benefit from it (at this location) or fight for it.

## The Exchange Rate tax

Although most post-docs are not motivated by money, it might be prudent to consider the exchange rate between where you earn your wages and where you hope to end up. For example, the exchange rate of the dollar to the euro varied up to 20% percent points over the last 5 years. In short, when moving between countries you lose a substantial amount of earning potential on your savings not necessarily offset by higher wages in the country of origin. Obviously, if you are lucky this might also works in your favour.

## The Career tax

It is often cited that scientists who worked abroad have a broader network and more international collaborators, and higher impact work. However, this mobility comes at a price. What you gain in international contacts you often lose in terms of local (political) influence. Leaving a country means you leave the local watercooler talk and employability that comes with it. Although science pretends to be unbiased, supposedly hiring the best candidate, it often hires the most available one (known quantity). If you are not at the watercooler, you are not a known quantity nor available. Unless you return within a short time frame (1-2 years) consider your chances of being employed or appointed a permanent position to diminish.

## Compounding factors

All these taxes are compounded by additional factors and multiply their severity (cost). I’ve written this from my personal perspective, but I can imagine that having a family, being disabled or suffering from a (chronic) illness will increase the Administration tax and all others substantially. As a cis-gender white male I’m not going to write extensively about this, due to a lack of personal experience. However, looking at the racial/gender dynamics in the US I often wondered how people manage their anxiety with respect to these issues. So there is a serious Racial / Gender tax as well.

# On multi-disciplinary research, context and navel gazing

I recently came across the publication titled:  “A global geography of synchrony for terrestrial vegetation” by Defriez and Reuman.  The paper discusses the synchrony of terrestrial vegetation as measured through cyclical patterns in the enhanced vegetation index (EVI) using a systematic analysis of the concordance of time series across the earth surface.

The paper looks at cyclical events in vegetation indices (i.e. vegetation growth) and some reference to phenology, i.e. the study of recurrent life cycle events, and it’s ecological implications would have been in place if not necessary. Sadly, no direct reference to phenology was made in the text while only two references directly mention phenology in their title.

Instead the focus of the paper was on the metric “synchrony” and the concept of the Moran effect. The Moran effect can be seen as Tobler’s first law of geography,  which postulates that “everything is related to everything else, but near things are more related than distant things “ with a time component added. For example, on a landscape level, most trees (of the same species) in a particular area will leaf out around the same time of year. Deviations from these patterns of synchrony therefore inform you about local abiotic or biotic changes in the landscape and through time, and the related species responses.  (Note, that framing this without touching on real life ecological context or phenology is rather hard).

Provided this oversight of any mention of the phenology or any larger ecological context I decided to write a very polite rebuttal using a key statement made in the paper:  “… However, our new result that geographies of synchrony in temperature and precipitation are important correlates of the geography of EVI synchrony, while true, does not follow automatically from the earlier knowledge.” The latter statement is false - and the many phenology models in existence prove this (if you want to read the literature that is). There are cases where synchrony is an interesting study topic, but most of these cases are lost at the scale on which the analysis is executed.

Sadly, my comment was not well received by the Global Ecology and Biogeography editors and I quote:  “ Critique letters need to be novel enough and interesting enough to attract readers attention at the same level as an original paper. I don’t feel that debate over whether a one sentence claim to novelty was exaggerated or not rises to that level. Especially as they go on to qualify that statement.” Aside from the point that comments only seems welcome if they generate readers not when they are factually correct (so far for peer review), I used this one sentence a problem emblematic to the whole paper to pitch my argument. A subtlety not picked up by the editors, which seemingly have an equally narrow frame of mind as the authors.

Today’s research is multi-disciplinary and failing to acknowledge this by not reading widely and referring to previous research and providing context puts the author at fault.  The editors pointedly refer to the fact that the authors qualify the statement,  sadly doing so within a very narrow context of bio-geography and landscape ecology and navel-gazing on a technical discussion surrounding the Moran effect. Research never happens in isolation. Yet the authors fails to bridge fields, ignores previous findings, adding little to the research community without this proper context (overall a rather impressive feat).

Aside from the lack of ecological context the paper does not address the fact that the analysis is dealing with land surface dynamics, not terrestrial vegetation. The EVI signal as aggregated by the authors combines multiple land cover types, ranging from urban areas, over crop fields with their distinct growing cycles (if not in rotation), over barren areas. Lumping these together at a 1 degree scale (~100x100 km) is questionable at best. Patterns derived are thus tainted by the proportion of land cover type(s) which make up a 1 degree grid cell used in the analysis. Thus, patterns are representative of the terrestrial land surface, not terrestrial vegetation. The latter greatly impacts, if not discredits, any further analysis and direct attribution to vegetation changes.

Finally, the lesson I have learned from this is that when writing a comment on a paper you need to utterly destroy the previous authors.  Do not leave a piece standing. Surely, being considerate and constructive will not “attract a sufficient readership” to merit publication.

# Why scientists should learn from Aaron Swartz. part 2: on standards and frameworks

Instead of the -let's just build something that works- attitude that made the Web (and Internet) such a roaring success, they brought the formalizing mindset of mathematicians and the institutional structures of academics and defense contractors. ... With them has come academic research and government grants and corporate R&D and the whole apparatus of people and institutions that scream -pipedream-. And instead of spending time building things, they've convinced people interested in these ideas that the first thing we need to do is write standards.

In an excerpt of A Programmable Web, Aaron Swartz argues against the bureaucracy which slowed progress toward a semantic web. The Web and the data which resides on it, scientific or not, has been characterized by being used, re-used, cut, re-mixed, copied and mashed-up. This fast, transparent sharing of data is what made the Web and revolutionized how we think about data.

A common misconception in academia is that all standards and frameworks need to be defined up front, therefore creating rigid structures. This leads to publications which posit that a community is in dire need of a new standard or “framework”. Yet, all too often these works overlook easier more flexible solutions which build on existing infrastructure and more agile community driven movements.  At times they even lead to more fragmentation (obligatory XKCD comic below).

As Aaron carefully observed: “To engineers, this is absurd from the start – standards are things you write after you’ve got something working, not before!”

Although I acknowledge that standards are important, within the context of data use and re-use this carries less weight and data accessibility is the limiting factor. In this day and age, if the service isn’t created and carried by the user community, as a software package or larger initiative, chances are that there is little need for such a service (standard, or framework). Unless demonstrated to work first, diverting money to a service no-one wants or needs seems wasteful.

Creating well documented application program interfaces (APIs) to (ecological) data would go a long way in facilitating interoperability without the added cost of supporting a new aggregating platforms or standards (and the various committee members that come with it). Or, talk is cheap and fast and easy access through APIs and ad-hoc integration often trumps institutional frameworks and standardization.