Francois Keck

Scientists no Longer Find Twitter Professionally Useful, and have Switched to Bluesky Synopsis. Social media has become widely used by the scientific community for a variety of professional uses, including networking and public outreach. For

Looks like the science community has found a home.
academic.oup.com/icb/article-...

A chart showing how LLMs can be used for different tasks in academia. Tasks are distributed along two axis (fails-works and evil-good).

I finally made that scandalous chart.
#AcademicSky #LLM #ChatGPT

In our latest paper in PNAS, we ask: How can scientific progress be accelerated to meet the urgent challenges of the Anthropocene? We point to significant barriers in forecasting & prediction efforts for the biosphere 🧵👇 🧪🌎🦋 1/n www.pnas.org/doi/10.1073/...
#ScienceTwitter #Ecology #Anthropocene

In my opinion, Zenodo is the safest option. But CRAN offers a sort of long-term persistence: the sources of a package remain available even after it has been archived.

👋 I’m back with some project updates: ecosystem function, Europe-wide experiments, policy papers, a global biodiversity synthesis… and most exciting of all — a new baby💥 Big year and its not even🎄yet😉

Huge thanks to amazing collaborators for keeping projects moving and published! 1/8

In massive #collaborative #effort, we assembled published & unpublished #fish 🐟 #eDNA 🧬 metabarcoding datasets, covering ~2000 sampling sites/>100 river systems globally. 🐟 🐠 🐡 🌐 🌍

Now results out in 2 #parallel #preprints @biorxiv-ecology.bsky.social

#aquatic #biodiversity #meta-analysis
1/6🧵

If doughnuts are coming back into fashion, let me bring this one back. #rstats #ShowYourStripes #ShowYourTorus

We just launched the Kickstarter campaign of MicroMates, a card game that brings the hidden world of microorganisms to life in a fun, colorful, and scientifically inspired way. Please back us up and spread the word! micromates.se

RNG version — with_rng_version Change the RNG version and restore it afterwards.

You can try with_rng_version from withr.
withr.r-lib.org/reference/wi...

On my way to #gfoe2025 @gfoesoc.bsky.social annual ecology conference in Würzburg www.gfoe-conference.de 🌳 🐟 🔬 🧪 🦀 🦋 🐝

Very much looking forward to catch up with my German & International #Ecology colleagues, please DM for a meeting/chat!

Want to learn to write fast R code—and support Ukraine while doing it?
Join my workshop Thursday, August 28th 6-8 pm CEST!

We’ll cover profiling & benchmarking, and take a tour of fast packages like data.table, collapse, Rcpp and more...

With plenty of code examples & hands-on practice!

#rstats

Thick black line is the centerline of the Beni River in Bolivia. Circles that are tangent to the centerline represent the radius of curvature ag the location. Smaller circles = higher curvatures.

In this version the circles are colored according to the curvature; brighter colors = higher curvatures.

I have been experimenting with different ways of visualizing the curvature of meandering rivers. Plotting curvature in the context of the meanders themselves helps QC-ing the curvature data ⚒️🧪

From literature to biodiversity data: mining arthropod organismal traits with machine learning The fields of taxonomy and biodiversity research have witnessed an exponential growth in published literature. This vast corpus of articles holds information on the diverse biological traits of organi...

A Workflow for Annotating #Arthropod Organismal Traits bdj.pensoft.net/article/1530... #biology #evolution #taxonomy #textmining

Graphical abstract of the publication

Impressive quantitative synthesis led by Rebecca Oester on the cascading effects of land cover change on aquatic detrital food webs.
Now out in @globalchangebio.bsky.social 💧 🌐

🔗 doi.org/10.1111/gcb....

How clear and simple data visualizations bring the climate crisis home Climate change is a slow-moving disaster. We need graphics that capture both its pace and its impact.

Data visualizations are some of the most powerful tools in a climate science communicator’s playbook. However, designing visuals that are clear to the public and policy makers is not a straightforward task, writes @rachitdubey.bsky.social .

So, what works?

Our new paper, led by Andrew Burton-Jones, argues English-only science is unfair, costly and may no longer be necessary. With AI translation tools advancing rapidly, we ask what truly multilingual science could look like and how we might get there.
doi.org/10.3127/ajis...
#languagebarriers
1/4

Most of the internet used to be like this. This is actually the default, it took companies enclosing the internet and adding weird, soul-killing incentives to make people behave the way they do now. In a way, there is truly nothing special about Wikipedia except that it survived longer.

Sorry, that's not glamorous, but start by taking a serious course on linear modeling with applications in #rstats.

Yet another synthesis challenging the idea of systematic biotic homogenisation

Thanks for reporting for evolution. I agree that aggregating by paper is also important to get an idea of the absolute usage.

So, has this reached us yet? Yes, it did. I did a quick #rstats analysis of the literature in ecology. 📊
🔗 See my new blog post: www.pieceofk.fr/the-rise-of-...

Apply now: #PhD #position “Advancing environmental DNA (#eDNA) approaches to future-proof #environmental #monitoring of #aquatic #ecosystems” 🧬 🔎 🦐 🧪 🐟 (4 years position)

➡️ apply.refline.ch/673277/1268/...

Thanks for sharing to suitable candidates! @eawag.bsky.social

Phylosignal, 500 citations later My first R package, phylosignal, that I started more than a decade ago, has just passed its 500th citation. So I decided to take a little time to celebrate (we definitely don’t celebrate enough). I…

Phylosignal celebrates its 500 citations! 📦🎉

I've written a short blog post to celebrate and reflect on this 10-year old #rstats project. 👨‍💻

www.pieceofk.fr/phylosignal-...

Stripe plots showing the changes of multiple socio-economic and earth system trends in the Anthropocene.

I'm taking advantage of this #showyourstripes day to repost this graphic I once published on “the other site”.
There's climate change and then there's all the other issues. Human activities are profoundly reshaping our planet in multiple dimensions.

In a synthesis of over 3000 population trends in the Wadden Sea, we show a substantial reorganization of biodiversity with over 38% of populations undergoing significant change (i.e., increases or decreases), identify winners and losers and critical time points of change! dx.doi.org/10.1111/gcb....

A Metadata Checklist and Data Formatting Guidelines to Make eDNA FAIR (Findable, Accessible, Interoperable, and Reusable) Environmental DNA (eDNA) has emerged as a transformative tool for biodiversity monitoring and species detection, yet inconsistent metadata practices hinder data interoperability and reuse. To address...

🚨 Out now in #EnvironmentalDNA led by #MiwaTakahashi: Results of a huge, global effort to facilitate the publication of raw and processed #eDNA data & ensure that dataset we are currently generating, adhere to the #FAIR principles & won't be lost. @gbif.org, #ENA,
doi.org/10.1002/edn3...

Important stuff discussed here.

Ecological and evolutionary consequences of changing seasonality Climate change and other anthropogenic drivers alter seasonal regimes across freshwater, terrestrial, and marine biomes. Seasonal patterns affect ecological and evolutionary processes at different eco...

If you think the seasons are feeling… different, you may be right.
Our new review in Science (@science.org) shows that Earth’s changing rhythms could have major and underestimated consequences for life on Earth. 🌍🧵
www.science.org/doi/10.1126/...

Utilizing aquatic environmental DNA to address global biodiversity targets - Nature Reviews Biodiversity Aquatic eDNA-based technologies offer the potential for universal and standardized biodiversity monitoring. In this Perspective, Altermatt et al. discuss how these technologies can help to achiev...

In our May issue: Perspective led by Florian Altermatt discussing how to bring aquatic eDNA collection and data management in line with the Kunming-Montreal Global #Biodiversity Framework. 🧪🌎
Web link: go.nature.com/4mv2h4W
Readcube: rdcu.be/eh0uC

Careful design of Large Language Model pipelines enables expert-level retrieval of evidence-based information from syntheses and databases Wise use of evidence to support efficient conservation action is key to tackling biodiversity loss with limited time and resources. Evidence syntheses provide key recommendations for conservation deci...

We trained 10 large language models with 6 retrieval strategies then compared all of these with our experts with access to literature. Well-trained LLMs won! General LLMs without extra training are likely to perform poorly and misinform decision-makers
journals.plos.org/plosone/arti...