Out listening

Posted on March 22, 2024 by lembrechtsjonas

Last week, you could find an enthusiastic subset of our team hanging around suspiciously on the campus of the University Hospital in Antwerp, booklets in hand and an ominous device close by.

Ten minutes of just listening and nothing else – science can be highly therapeutic as well

This was the kick-off of a new measurement campaign in the framework of ‘De Oorzaak’, our ongoing large-scale citizen science project on urban soundscapes. Our trip to the hospital allowed us to catch multiple birds with one stone.

First of all, we’re out in the real world capturing sounds. We need a whole lot of different sounds, from all kind of sources, to feed in the AI-models that will automatically detect sound sources in our upcoming large-scale measuring campaign. We listen, the sensor records, and we write down exactly what we hear, greatly facilitating manual labelling of the soundbites afterwards.

This box-with-a-microphone is doing most of the legwork for the project. It has sufficient battery to survive a day without an energy source, allowing us to take it onto a walk into the city.

Second, we are interest in the soundscape on the campus of the university hospital itself. We want to know what sounds patients residing on campus experience, and how that affects their health. And, as we are ecologists at hard, we want to figure out what role a greener hospital campus can play in that regard.

Third, we made use of this trip to start recording bird sounds. We hope to use our extensive sensor network to make a unique spatiotemporal assessment of the distribution of bird sounds in the city. For that, we of course again need to listen to a lot of birds ourselves. Luckily, those were starting to wake up for spring: great tits, blue tits, robins, wrens, ducks, moorhens, even a long-tailed tit: our bird sound dataset is starting to grow!

Finally, we can provide a subjective assessment of that soundscape: how nice was it, how lively, how chaotic? Following standardized terminology, we can create a dataset that links objective sound measurements to our experience of that sound.

Glad this is on a role again, and much more to come!

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Assistant professor in ecological scaling

Posted on March 12, 2024 by lembrechtsjonas

Major milestone: first of May, The 3D Lab is making a big move to Utrecht University in the Netherlands, and it is doing so following my recent appointment as an assistant professor in the Ecology & Biodiversity-group there. Major milestone, indeed, as this means I have left the realm of temporary postdoc positions, and entered the world of long-term academic security (pending tenure, of course).

I’m very honored to be stepping into the role of ‘assistant professor in ecological scaling,’ a unique title that perfectly aligns with my current and future aspirations. Ecological scaling involves delving into ecological mechanisms at a fine resolution and assessing their validity, robustness, and broader applicability on regional or even global scales. This scaling up of ecology has been at the forefront of my work since my first involvement with the Mountain Invasion Research Network (MIREN), back in the days of my master’s thesis in 2012. Through MIREN, our aim is to delve into the factors driving species redistributions in mountainous regions and understand how these dynamics scale up from specific regional settings to the entire spectrum of mountains worldwide.

This switch to the Netherlands marks the end of twelve years of research at the University of Antwerp. Yet, I won’t be cutting all ties, and will keep a strong connection with students and team members staying behind, and will ensure the smooth running of the citizen science trains currently on track.

Scaling up ecology is also a key component of my work with another project dear to my heart: the SoilTemp network. This initiative aims to extend the understanding of microclimate—a phenomenon inherently local in nature—to broader regional and global contexts. These two networks – SoilTemp and MIREN – will therefore remain core pillars of my future work. With the added security of a long-term position, I am eager to finally stop nibbling and start taking full bites out of my long-term vision to explore the intricate mechanisms governing both microclimate dynamics and species redistributions from local to global scale.

However, I am also eager to push the boundaries further, particularly in unraveling the intricate mechanisms driving biodiversity dynamics. To achieve this, I look forward to collaborating with the exceptional expertise in experimental research within the Ecology & Biodiversity group at Utrecht University. Together, we will tackle the issue of ecological scaling both top-down and bottom-up. A lot of room left for future developments in the area of scaling up experimental findings, for sure. To be continued, so stay tuned for the coming few decades…

The biodiversity experimental facilities at Utrecht University provide fantastic opportunities for scaling up of the mechanisms behind microclimate and biodiversity. Here: BioCliVE (https://www.uu.nl/en/research/ecology-and-biodiversity/research/uu-bioclive)

‘Ecological scaling’ to me is the perfect blend of theory and practice. It involves a lot of fundamental ecology, yet with the ultimate goal to save the world. I will also make it a crucial point to build that link from theory to practice and work further on the scaling of ecosystem services and ecological management, the way we have for example been working in our citizen science project ‘CurieuzeNeuzen in de Tuin’.

A fly agaric in a Dutch forest, the fruit of an ectomycorrhizal fungus living in close interaction with the trees surrounding it. I also aim to work further towards understanding these kinds of interactions across scales, to conserve beautiful natural sceneries like this one.

Above all, however, I see this new position as a once-in-a-lifetime opportunity to further expand my role as a mentor. The 3D Lab will continue to evolve into a nurturing environment where aspiring young scientists can learn and thrive as part of a team. While the physical transition to the Netherlands won’t include my team members, our strength in virtual collaboration remains a hallmark of the group. Moreover, I’m committed to leveraging all available resources to enhance opportunities for those working alongside me—a goal that was previously constrained by the uncertainty of my own position.

That mentoring will also expand further as I join the teaching staff for the over 400 biology students in Utrecht. I will take my time – and am extremely grateful for the opportunity – to think critically about what and how we should be teaching the next generation, and if any updates are to be made.

A flower-rich (but species-poor) meadow close to Maastricht, last summer. Ready to turn my gaze to the issues and opportunities of Dutch nature as well

So: are you interested in doing science in the Netherlands, or are eager to forge collaborations on the expansive topics of microclimate, species redistributions, and scaling up ecology, now’s the time to reach out! The opportunities are endless, and I’m excited to explore them together. Let’s embark on this journey of discovery!

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Boosting my R efficiency by 300%: how a robot transformed my coding experience

Posted on February 15, 2024 by lembrechtsjonas

Yes, you read that correctly—300% faster! That’s the remarkable leap in speed I’ve experienced in tackling my most common R programming challenges ever since I enlisted the help of a certain robotic companion to think alongside me.

That companion, as you might have guessed, is none other than ChatGPT. It’s become a trusted ally in various aspects of my research. While its prowess in aiding writing tasks has been widely discussed, I stumbled upon its true strength in assisting with my all-to-common R-isuses.

Let me start with a disclaimer: I consider myself fairly decent in R, but I’m perhaps a bit old-fashioned when it comes to embracing new ideas. My focus tends to be on results, sometimes neglecting code cleanliness or efficiency. These days, I find myself using R much less frequently than during my PhD, mainly for data manipulation, while also doing a lot of debugging of student code.

So, what magic does that friendly robot perform for me?

  • First off, ChatGPT is surprisingly adept at coding. Describe an issue, and it often churns out a correct, clear, and concise solution. For example, filtering a dataset based on specific criteria and then calculating averages across factor levels—a task more proficient R users might do from memory, but one I often find myself looking up the functions for.
  • Sure, I could turn to traditional help files and forums, but with ChatGPT, everything I need is in one place. I can formulate queries easily and get immediate responses, bypassing the need to scour forums or craft elaborate forum posts myself.
  • It gets even better when faced with a series of tasks. ChatGPT remembers previous actions within the same conversation, offering suggestions that build upon each other, simplifying code integration throughout a workflow.
  • When you get a suggestion back from ChatGPT that does not do exactly what you want it to do, you can simply describe where or what is not according to expectations, and ChatGPT immediately provides an alternative. I can even paste error codes directly from R, providing the robot with the context it needs to troubleshoot effectively. This way you can truly get into conversation with the robot, slowly but steadily molding and improving the code into your wishes.
  • If you provide the dataset and column names in your queries – or even snippets of your own code – the R-code generated by ChatGPT uses these names immediately when generating code, making it much easier to see what goes where.
  • Many of the tasks I encounter in R are ones I’ve tackled before. But digging through files to find previous solutions takes time, whereas ChatGPT provides guidance swiftly and efficiently.
  • I’ve noticed my students increasingly relying on ChatGPT as well, empowering them to resolve issues independently, reducing dependency on my assistance and time.

Fabulous, no? To me, this works pretty fluently, and allowed me to effectively speed up some daunting R-tasks, especially regarding data wrangling.

I also see very few drawbacks:

  • One concern is plagiarism, though in coding, this seems less of an issue compared to academic writing. Personally, I’ve borrowed code snippets without explicit credit before, though I do ensure proper attribution for packages used, so that has not changed much by switching to the robot.
  • There is a minor drawback that ChatGPT would not include the most recent developments in R. However, for most general tasks, for example regarding data wrangling, it does have access to everything we need.
  • There’s also the minor drawback of potentially limiting oneself to popular R packages, as ChatGPT may not be well-versed in lesser-known ones. But given my pragmatic approach to coding, as long as I achieve the desired outcomes, this limitation isn’t a major concern to me.

In conclusion, integrating ChatGPT into my coding workflow has streamlined my R programming endeavors, particularly in data wrangling. There might of course be a lot more to say about this, but I thought it might be beneficial to many to at least get the conversation going.

Now, I’m curious—have you used ChatGPT for your coding issues, and if so, what has been your experience? Are there drawbacks that I have – perhaps in my naivety – overlooked?

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PhD defense Jan Clavel

Posted on January 29, 2024 by lembrechtsjonas

Another milestone coming up, as The 3D Lab-member Jan Clavel is making the final preparations for his PhD defense on February 5th!

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Tropical forest understory temperatures

Posted on January 23, 2024 by lembrechtsjonas

New paper in Nature Communications: Ismaeel et al. (2024) Patterns of tropical forest understory temperatures.

It’s a thing we do at SoilTemp: create microclimate maps over large extents for all to use. We have done this before for soil temperature at the global scale (with 1 km resolution), and have done so for European forest understory temperatures at a breathtaking 25-m resolution.

And now we do that again! This time, for an area that has long been undersampled, but that is extremely important for global biodiversity and ecosystem functioning: tropical forests. As is the case for European forests, we can expect substantial temperature buffering under tropical forest canopies. How much, that has always been hard to say.

A microclimate sensor in the tropical rainforest of Congo, one of the many that allowed mapping forest understory microclimate across the pantropics. Pic: Matti Barthel

Not anymore, as we are proud to introduce a new paper in Nature Communications: patterns of tropical forest understory temperatures. The big thing: we created maps of tropical forest understory temperatures at a resolution of just a few tens of meters for all tropical forests, in South America, Africa, and Oceania!

As expected, forest understories were on average cooler (1.58°C, to be precise) than macroclimatic temperatures, and they were also buffered more (1.72°C lower diurnal – day/night – variation) than macroclimate.

We found significant spatiotemporal variation in daily temperature offsets in tropical forest understories in South America (left), Africa (middle) and Oceania (right).

Importantly, however, these averages hide significant spatiotemporal variation in that buffering, driven by patterns in macroclimate, vegetation structure, and topography. This variation holds some important information for understanding of these important ecosystems. For example, temperature buffering is stronger in regions with a distinct dry season. Although reduced rainfall is usually associated with higher temperatures, deep-rooting tropical species can for a long time still access water reserves and keep up their ‘airconditioning’ function, effectively creating a larger difference between understory and free-air temperatures.

The former works as long as these droughts remain within reasonable limits, of course, as climate change might very well push these forests over a threshold, making them lose their airconditioning function and rapidly increasing understory microclimatic temperatures. But that’s a story for another day.

An interesting observation for me is the fact that offsets across these tropical forests are usually not so large. On a daily basis, forest understory temperatures were often less than 1°C cooler than macroclimatic temperatures outside the forests. This was especially true in Indonesia, for example, but large swaths of South American and African rainforests are showing surprisingly small offset values as well.

This phenomenon can be attributed partially to the contrast between daily maximums (which tend to be cooler in forests) and minimums (warmer within forests). However, there might be other contributing factors at play. The high humidity prevalent in tropical regions is likely another significant influencer, dampening the intensity of microclimatic differences.

Nevertheless, despite these seemingly small variations, the consistent stability of temperatures throughout the year results in a cumulative effect. Over time, these incremental differences in temperature do add up, significantly impacting the overall energy input within the ecosystem.

The marked disparities and the crucial spatial diversity present across the pantropical regions underscore the significance of the maps we’ve crafted. These visual representations hold immense importance for anyone delving into the intricate workings of tropical forest understories, spanning from deciphering species distributions to comprehending litter decomposition dynamics. The relevance of such high-resolution microclimate products has already been elegantly demonstrated in understanding the distribution patterns of European forest understory plants. It’s only a matter of time before their paramount significance in tropical ecosystems is similarly illuminated.

The maps are freely available here! For now, at a 300 m-resolution, while we figure out a good way to share the 30-m resolution files open access. The latter are currently available upon request.

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Following plants in the crags: MIREN rock face survey

Posted on January 23, 2024 by lembrechtsjonas

Join the new MIREN rock face survey

With long-term monitoring campaigns focussing on mountain roads and trails, and divergences to railroads and rivers, we are happy to announce that MIREN wants to tackle another – perhaps more unusual – linear disturbance in a new, global survey: rock climbing!

Rock climbing is in many respects similar to mountain roads and trails, with routes serving as linear disturbances and dispersal corridors across elevation gradients, with significant effects on the local vegetation. Nevertheless, cliff vegetation, and the influence of rock climbing on it, is pretty unique: rock faces often cover strong microclimatic gradients, resulting in a unique vegetation of species at either the warm or cool edge of their distribution. 
This unique vegetation often consists of (locally) rare species with very patchy distribution, and the passage of climbing routes over their habitat might thus have substantial impact. To map that impact, and its interaction with the effects of microclimate and climate change on species redistributions, we launch this new MIREN rock face survey, and you are welcome to join!

Wilder Kaiser, Austria – by Sarane Coen

Through the MIREN rock face survey we want to learn about global similarities and interregional differences between rock faces. To do this, we will set up permanent vegetation monitoring plots on and adjacent to existing rock climbing routes to monitor local plant species richness and community composition. Wherever possible, we will also measure rock face microclimate in comparison with the microclimate in the environment.

If you are interested in monitoring the vegetation on and along one or a few rock climbing routes in the upcoming summer, express your interest via this form. We are currently developing a standardized protocol that can be applied with minimal effort on any rock climbing route across the globe. If you want to be involved in finalizing that methodology, you can inform us through the same form!

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