The 3D lab

Scouting the cliffs of Freÿr

Posted on April 2, 2024 by lembrechtsjonas

On a sunny day in early spring, our team took the car to one of the most monumental locations in Belgium: the cliffs of Freÿr. These beautiful slabs of ‘naked’ limestone of up to 120 meter, overlooking the river Meuse, provide one of the most – if not the absolute most – favourite rock climbing locations in the whole of Belgium.

Overview of ‘les Rochers de Freÿr’ towering over the river Meuse.

With easily a 1000 climbing routes, ranging from the easiest to the hardest, the rock is legendary in Belgium rock climbing milieus. It is there that we headed to for the final scouting for a new – and extremely exciting – global survey: ‘MIREN Rocks’ (more on that – and how to join – here!).

Scouting the area for the perfect survey sites with local guide David

Indeed, as we speak, we finalized the protocol for MIRENs’ global rock survey, using our experience from the cliffs of Freÿr as an example. We checked for routes to sample, estimated variability in orientation, difficulty and botanical diversity and, most importantly, tested out ways to install microclimate sensors on a cliff face.

Microclimate monitoring on the cliffs with the TOMST thermologgers

It’s the latter that perhaps makes me most excited: we can now plug in one of our trusted TOMST loggers – the simpler thermologger one – in a gap in the cliff face, and as such start measuring the true temperatures our cliff plants are experiencing. The ultimate cross-over between my two favourite networks, MIREN and SoilTemp.

The three-layered shield helps reduce the error resulting from direct solar radiation. Nevertheless, it will be hard to get accurate reads of the local temperature due to the extreme radiation absorbed, reflected and emitted by sunbathing cliffs

Now, that protocol is ready for action, also thanks to the extensive contributions by experts from across the globe. As such, the protocol has grown into a true community effort, and we hope it will be a resource for many climbers and ecologists to help us track rock cliff vegetation and the implications of rock climbing on it.

Selecting the optimal climbing routes for our upcoming monitoring

So, take this as a wake-up call: are you an ecologists, botanist or the like, and do you like to climb rocks? Then please join MIREN Rocks! All information can be found here.

Cliff surveys would go fast in some places if you count the number of plants on them – where it not for the issues related with getting up there!

In some spots, the cliffs drop directly into the Meuse

The surrounding Natura 2000-forests were starting to be covered in beautiful spring flowers – here Anemone nemorosa

Posted in Belgium | Tagged Botany, Ecology, Freyr, Hiking, Landscape photography, Microclimate, Nature, Photography, Rock climbing, Rocks | Leave a comment

A new beginning

Posted on March 26, 2024 by lembrechtsjonas

Last week, I spent a delightful day at my soon-to-be new home university in Utrecht. A day packed with discussions on scientific ambitions, teaching plans, and meeting new colleagues and ongoing research in the group. The first tulip of the year made it all feel like an official new beginning.

The real start will have to wait till May 1st, but you bet that I’m already making plenty of exciting new plans in advance!

Posted in Netherlands | Tagged Ecology, Flower photography, Flowers, Nature, Professor, Science | Leave a comment

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!

Posted in Belgium | Tagged Birds, Nature, Noise, Sounds, Soundscapes, UZA | Leave a comment

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!

Posted in Netherlands | Tagged Biodiversity, Ecology, Moving, Science, Tenure track, Utrecht | 4 Comments

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?