Time for my annual repost of this banger by Australian artist Denis Lushch. Ever-more relevant with each new horrible year.
Microbial ecologist/carer. NERC IRF and MRF Emerging Leaders Fellow at the University of Exeter in Penryn. I like warming up bacteria, open & reproducible science, making focaccia, and exercise.
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Time for my annual repost of this banger by Australian artist Denis Lushch. Ever-more relevant with each new horrible year.
This is a great cartoon of the illogical narratives I hear refuting climate warming. As I have said many times, it's not "either/or" when it comes to natural variability and human contributions, it's "both/and." Grass grows naturally and it grows differently when you fertilize the lawn....
I hope this is a very niche Simpsons reference.
If someone spoke to a teenager and mentioned suicide thousands of times and told them how to make a suitable noise, then yes action should be taken.
Do you think LLMs and other large broad models could/should be legislated to make them more regulated/predictable. The teenager committing suicide after speaking with chatgpt a lot is horrendous.
Wildlife science is a big one for this too. Paying for work experience and working for free or for a small weekly stipend is distressingly common. Many entry level paid jobs are barely living wage
Severe ME just keeps taking things from us. This trip included the first lunch she has needed to have a meal replacement drink instead of soup. There are no words for her suffering. But here are a few anyway. #pwME #severeME #MECFS padpadpadpad.netlify.app/posts/caring....
Ah sorry! If we wanted to reduce inequality isn't taxing the richest exactly what we should be doing? Although increasing tax on the richest could be selecting for increased pre tax inequality.
This is super interesting. How have relative changes in earnings changes during the same period? Have the richer also got relatively more rich in terms of income, and we're taxing that more? Tried to find data quickly to no avail.
With #eseb2025 coming to a close, it is time to start making plans for 2026. Interested in the interface of evolution 🧬 and ecology 🌳? Come to our #ExE conference hosted by @uniexecec.bsky.social in beautiful #Cornwall. Leave your email address at tinyurl.com/EvolxEcol to join our mailing list!
I know individual cases of both exist, I am interested in the relative importance. I am erring on the side of the latter (maintaining of resistance that evolves elsewhere) but not a huge amount I could find evaluating this. I could also be wrong and unable to find the relevant papers.
Think I might regret asking this, but do we have a handle on whether the wider environment actively selects for AMR that moves into livestock and humans, or whether it mainly acts as a sink for resistance that arises in those areas with higher selection pressures? Papers looking at this appreciated!
On this Severe ME Awareness Day, I present to you my newest exhibition: “In the Absence of Light”. 1/3 www.aquietstorm.me/in-the-absen... #MECFS #SevereME #SevereMEday #pwME #Photography
On Severe ME Awareness day, I try shed some light on the impossible decisions Soph has to make. Do I have energy to communicate today? Unfathomable really. #pwME #severeME #MECFS padpadpadpad.netlify.app/posts/caring....
Feels surreal to say but: I'm hiring! If you are or know anyone interested in looking at the evolution of phage resistance using A. baumannii and natural transformation, then this might be for you www.jobbnorge.no/en/available...
Ah I can wait it's mainly a side project for me so no rush. Think there's good scope to work with BacDive to improve their documentation so would be cool to see how other people do it. Feels like BacDive and phenotyping in general is such an important thing we are no longer making use of enough.
Looks great! I also have been playing with BacDive and it's API using their R package. How did you find it? What took you the most time?
(1/2) Key genetic differences found in people with ME/CFS > Swipe to find out more. These findings reflect the lived experience of thousands of #pwME. Thanks to all our participants & supporters who made this possible! Read a summary of our results: shorturl.at/pgsjk
This was very informative and I agree with all your points. I would also note that a set of preliminary findings is not the same as a publication, be it a preprint or a peer-reviewed publication. This is - cynically - needed for the next set of research questions (and increase funding).
Not specifically statistics but The Studies Show by @tomchivers.bsky.social and @stuartjritchie.bsky.social is good for covering the scientific process generally. They have a good episode on statistical significance (Episode 23), and the one just out on Retractions is great.
It’s really important for EDI that ECRs and PIs can have open, empathetic discussions about feedback and behaviour, without intimidation. Respect from lab members comes from being able to challenge negative behaviour, and being listened to without discussions becoming a competition.
There's this trope that you have to be so into your PhD topic that you live and breathe it and can't possibly stop thinking about it, so here's your regular reminder that passion is good, but burnout isn't. It's okay and recommended to take breaks, enjoy the weekend, and treat a PhD like a job.
For so long I have told collaborators not to use colours and now there is a way for me to incorporate them if they want to use them. Do I tell them though?
I have irrationally strong hatred of papers that have Results and Discussion before the Methods. It promotes us not reading what people actually did. Without this the Results are basically meaningless! I would ban the practice. If you want to ignore the Methods, at least scroll past them.
I know it is not the point you are making, but if you want a pdf of it just post your email and I will send you one.
Agreed there still needs to be something for the sprinters. The GTs do seem to be getting harder and harder and racing has changed so much. Wonder if traditional sprinters may become a rare commodity for a bit.
In an increasingly difficult science funding landscape, it would probably help me to use these numbers to describe how bad the problem of AMR is, but I just do not have confidence in the methods.
I know peer review is imperfect but it still works to improve clarity of methods and openness about what you did, especially when the reviewers are good! And yet these headline numbers will be widely used and likely influence policy, in part because of how extreme they sound.
Twice they state their methods and results are "highly uncertain", and yet the flagship estimates of economic impacts of AMR through to 2025 only point estimates are provided. It is impossible to judge how good the approach is or how robust the analyses are. Just like the 10m annual deaths stat.
There is a new report out estimating that AMR could cause $2tn a year by 2050, a number which will no doubt end up in grant applications and paper introductions. Having scanned the methods of the report, there is no open code and no statistical analysis section. www.cgdev.org/publication/...
Hello! We're now on #Bluesky! PhULMaR is a PhD lab group for those around the British and Irish Isles studying birds that use the #marine #environment. Currently headed by @bardseyben.bsky.social @dianepavat.bsky.social, we meet online on the last Friday of each month. Get in touch to join!
The Company of Biologists Workshop: Why Are Cells the Size They Are? Thank you to Workshop organisers Dustin Marshall and Craig White. #Workshop #Biology #CellBiology #Cells #Community #Collaboration #Research #Researchers #Academia #Academics
Came straight from Sophs so was unsure how I would do, but enjoyed it. And was surprised that many people - some of which id never met - asked about Soph and said they read my blog. It's always so good to remember how nice many scientists are so thanks everyone.
The Why Are Cells The Size They Are workshop by @biologists.bsky.social was superb. The attendee list was exceptional and whole thing was inspiring. Chose a special conference to be my first for nearly three years.
Thanks Mike I am continuously surprised by the number of people in science seem to read it. It has been very supportive. Hope the GRC went well!
One week left to submit your abstract to @microbiologysociety.org meeting on “Understanding and Predicting Microbial Evolutionary Dynamics” at Liverpool 26-27 November Lots of spaces for ECR talks and posters! microbiologysociety.org/event/societ...
A short visit to Soph's this trip, but still time to have to go through a horrible, gutwrenching lunch with her. We're all trying our best, but it still feels impossible. #severeME #MECFS #pwME 12/07/2025 A greatest hits of despair padpadpadpad.netlify.app/posts/caring...
Hiring/Seeking a *permanent* programmer in ecological modelling at my lab @unibonn.bsky.social. We mechanistically model plant communities, island biogeography, species range dynamics, eco-evolutionary feedbacks, diversity gradients, tropical forests, vascular epiphytes. Pls rt! shorturl.at/Bzzdt
Trying to better document my code and things I do, mainly so future me does not have to go back through bits of old blog posts and ChatGPT to get a solution. If you want to enable non-admin users on a Synology to have ssh access, here is how I did it: padpadpadpad.netlify.app/posts/2025-0...
🚨New blog post 🚨 A short post about some of the questions you might want to ask yourself before you decide which IDE to use! Link: nrennie.rbind.io/blog/how-cho... #RStats #Python #VSCode
Just want to follow up that I implemented steps using some of your filtering advice, autocycler and recommended post steps, and pgap for annotation and it worked great. Thanks for your help.
We ran a randomized controlled trial to see how much AI coding tools speed up experienced open-source developers. The results surprised us: Developers thought they were 20% faster with AI tools, but they were actually 19% slower when they had access to AI than when they didn't.
New Independent Fellowship position in Microbiology to launch your lab in our department @johninnescentre.bsky.social (UK). We are conducting a broad search in the area of plant-associated microbial interactions. Message me if you have any questions. Apply here: www.jic.ac.uk/vacancies/in...
If LLMs help us ecologists write more unit tests and checks it will definitely be a good thing.
Writing a quarto help document and want to allow people to easy collaborate on it, what would be the best method. Is it still GitHub pushing and pulling? Is there a smoother, more interactive way @michelnivard.bsky.social @andrew.heiss.phd?
Bioinformatic hive mind: Has anyone got a paper/primer that describes how to go about choosing sequencing depth/amount of sequencing for metagenomics? E.g. things to think about, pros and cons of fewer, more in depth samples vs more, shallower sequencing. Maybe @blekhman.bsky.social knows of one?
Thanks for your quick reply! Your walkthrough here: www.atcc.org/resources/te... is great! We have an assembly from the sequencing service we used but interested in doing it ourselves as well. Sharing/standardising best practice between groups seems like its missing a little.
Hi @bioinformer.bsky.social I am putting together my own genome assembly pipeline based on your teams ATCC protocol, is it better to have less coverage but all high quality short reads or more coverage but some lower quality? Any other advice? Thinking of trying auto- and unicycler to compare.
In about a week we (Biological Sciences @ Monash Uni in Melbourne, Australia) will be opening a search for 3 (!!!) permanent academic positions (40% research, 40% teaching, 20% service) at Lecturer/Senior Lecturer. 1 Genomics, 2 Ecology. Please share, email me, DM, follow, send carrier pigeons…
Imagine being bedbound during a heatwave and not being able to do very anything to help yourself. There is no escape for Soph. #severeME #MECFS #pwME 21/06/2025 The stress of heatwaves. padpadpadpad.netlify.app/posts/caring...
👇 genuinely don’t understand why people are unable to comprehend “don’t get AI to do something for you if you can’t understand whether it has produced the wrong answer”.
Lil intro to our early-stage rayyanR R package, from the first day of #ESMARConf2025 (youtu.be/dmcTZ-0eC18?...). Please beta test it and find its inevitable bugs/missing features so I can fix them/incorporate them (you can help us if you like!) 🙏 @ecehh.org @eshackathon.bsky.social #medlibs
So I've really got to ask Sam Altman: where is this singularity? Is exponential intelligence in the room with us now? Because everything is still looking very linear to me
So happy to be part of @cp-trendsecolevo.bsky.social 's ongoing Disability in Ecology and Evolution series! It's great to see serious conversation around our experiences & how we can make the field better for us all www.cell.com/trends/ecolo...
These are great, but it might be useful to distinguish between parents, parent carers, and carers as although similar, they have large differences too. I was trying to read any profiles about Parent Carer/Carers but most profiles seem to be about managing parenting with academia.
I never, ever want to hear again that women are too emotional to be leaders.
I talked to 15 teachers/professors about how AI and ChatGPT is ruining their lives: www.404media.co/teachers-are...
It was the weekend we had been dreading - the return of the Wychwood music festival made Soph worse last year. And... it was fine. Never thought I would be relieved Soph was just THIS awful. 01/06/2025 A paradoxical weekend. #severeME #pwME #MECFS padpadpadpad.netlify.app/posts/caring...
Do you want FE colleges too (years 12 and 13)? This looks so great btw congratulations.
Trump administration cuts to NSF will result in more than 200,000 FEWER people per year involved in basic science, training, and education - what should have been the next generation of US scientists. This isn't even eating your seed corn, it is setting your seed corn on fire and salting the earth.
📣Post-doc opportunity in thermal ecology & species interactions with Arnaud Sentis at INRAE Aix-en-Provence, France. 🌡️Explore how antagonistic interactions shape thermal tolerance in freshwater organisms. 📆 Start: Nov. 2025 | Duration: 2 years 📩 Sept. 8, 2025 Info 👉 www.inrae.fr/en/news/erc-... 🌐🧪🌍
The pundits have only interpreted public opinion, in various ways. The point, however, is to change it.
New study in #Nature reveals the 'Gollum effect': nearly half of surveyed scientists report territorial behaviors—data hoarding, gatekeeping—mostly during #PhD. Early-career researchers bear the brunt; 1 in 5 left academia as a result. www.nature.com/articles/d41... 🧪
Patients with severe #MECFS need hope in the form of evidence-based interventions, not opinions @binitakane.bsky.social @daltmann.bsky.social @putrinolab.bsky.social @sunny-rae1.bsky.social @davidjoffe64.bsky.social @ahandvanish.bsky.social www.bmj.com/content/389/...
Agree completely. Many of us try and do training to teach ourselves how to be good PIs, but it is not mandatory so the people who do it are self selective of nice people trying to be better. It is hard to pick up the ones who do not think they need it/do not want to do it.
From experience very few senior PIs (almost all men) fully appreciate the amount of luck that has gone into their success. Myself probably included. It is reinforced by the scramble for funding which forces us to big ourselves up, but many of us end up believing our own bullshit.
Just back from a short Soph visit. I try discuss the difficulties of planning visits a little bit and how it impact work and life. 19/05/2025 There and back again and the dreaded chat about dates. #severeME #MECFS #pwME padpadpadpad.netlify.app/posts/caring....
This looks amazing!
Just out in PNAS! www.pnas.org/doi/10.1073/... "The evolution of thermal performance curves in response to rising temperatures across the model genus yeast". Beautiful work using experimental evolution forecasting climate impacts on biodiversity by Jennifer Molinet @jennifermolinet.bsky.social
Ah thanks for the heads up. I suppose I will stick with the rstanarm survival branch. Although marginaleffects might support output rstanarm::stan_surv (although I do not not know enough to know if stan_surv() output is different to stan_glm() to the point they are not compatible).
This looks amazing. Does this work when using coxme (e.g. accounting for random effects. In my research we sometimes have multiple replicates of the same treatment and want an overall treatment effect).
A must read
Interested in phages ? Want to work as team that will isolate, genome sequence and charachterise 1000s of phage to build a biobank . Come work with me and Martha Clokie at Leicester jobs.le.ac.uk/vacancies/va...
Today is #WorldMEDay. Soph has not got out of her bed for over a year. There are hundreds of people like her in the UK, and many thousands more who are not as severe, but still suffer everyday. We can change this.
I got hit by some rather sudden and extreme financial hardship so if anyone is in need of remote wetlab contract research, strictly BSL1, do let me know. Currently scrambling for gigs. Plant, Bacterial, Archaeal Non-model Bioeng Custom Lab Hardware Turn Key Genetic Design Please repost for reach 💚
A general brain dump about worrying about keeping Soph cool in the heat, and the despair and numbing involved in realising I can no longer understand Soph most of the time. 28/04/2025 The haze of losing things we take for granted. #severeME #MECFS #pwME padpadpadpad.netlify.app/posts/caring....
These all look amazing! Super cool stuff.
We're in a really bad spot with supposedly reputable journals regularly publishing dodgy stuff that expert/stats review should easily catch. So expert review isn't happening consistently, for reasons we all understand in our bones. It's a dream for malicious actors who can shop "papers" as needed.
How did the #COVID-19 pandemic shape scientific productivity? Stephanie Meirmans, @maurineneiman.bsky.social, Shalene Singh-Shepherd @royalsocietypublishing.org and I crunched the submission and acceptance data for 25 journals in #Ecology&Evolution: doi.org/10.1098/rspb... @uniexecec.bsky.social
How did we get from "Do not use Wikipedia as a source" to "ask hallucinating chatbot everything"?
Emile Michels' first PhD paper published today. Amplification of Borrelia in ticks at pheasant-release sites – an intriguing example how non-native species can increase zoonotic disease risk through spillback. @uniexecec.bsky.social onlinelibrary.wiley.com/doi/10.1111/...
Our family cat growing up was called Zico as she walked in as a kitten just as he missed a penalty in 1990. Great name for a top cat. I vote for Wazza. Or Pippo.
Fully funded QUARTILES DLA PhD opportunity supervised by @micecoevo.bsky.social and @lancasterlt.bsky.social at @uniofaberdeen.bsky.social Apply now, deadline 30th April! UK/Home applicants only www.findaphd.com/phds/project...
Lifetime reproductive success (LRS) is a key metric in evolutionary biology and ecology. But what counts as a success? And whose successes do we count? @sevans.bsky.social doesn't shy away from the big questions in this new paper just out in @journal-evo.bsky.social: academic.oup.com/evolut/artic...
“People with ME, their carers and families are saying: how can you deliver a plan with no money assigned to it?” Rosie Barrett on @bbcspotlight.bsky.social (Clip via @abrokenbattery.bsky.social)
Point taken.
If the UK government doesn't bring in regressive new student visa changes we could get quite a lot of new international student demand though.
The move has caused Soph to crash. Feels like the tight rope we walk is ever more precarious. And yet there are uplifting moments amongst the despair. 07/04/2025 Looking through the keyhole its still bright inside. #severeME #MECFS #pwME padpadpadpad.netlify.app/posts/caring....
Biggest commitment to a 3 second joke I've ever seen
This does look awesome, but the lack of useable code is a little disappointing if we want this to be available for a wide number of researchers.
The core trilma here remains the same - the govt needs to accept one of three things: high student migration, higher domestic student fees (or higher taxes to fund universities) or university bankruptcies. Those are the only options, given where we are. Pick one.
A tricky thing about modern society is that no one has any idea when they don’t die. Like, the number of lives saved by controlling air pollution in America is probably over 200,000 per year, but the number of people who think their life was saved by controlling air pollution is zero.
Dating Bacteria is hard due to the lack of maxima. Assuming aerobes likely postdated the GOE gave us better resolved ages, but also surprised us, but not Dr Dayhoff, showing O2 use predated its atmospheric rise by 900 Mys and helped oxygenic photosynthesis to evolve. www.science.org/doi/10.1126/...
Minimum wage for a 9-5 full time job (40 hours a week) is, as of yesterday, (I think) £25,396 a year for anyone over 21, so a pay of £23-£28k does not seem great.
When you sit with a griever, your work is to be with them where they are, not drag them out where you are more comfortable.
Many scientists celebrate @alcs.co.uk day, but can someone explain to me where the money goes if we do not claim it. The whole thing does not feel very within the spirit of open science.
What an awful start to the year. People with (very) severe ME need modern life to stand still sometimes and it doesn’t. I can barely - if at all - understand Soph atm and its gutwrenching. 💔 18/03/2025 It feels like we’re drowning. #severeME #MECFS #pwME padpadpadpad.netlify.app/posts/caring....
Hi Alfredo! Looks fabulous. In Figure 2, it seems like your mean estimates do not capture the distribution of the data overly well, with the means and CIs being inflated. Do your methods try to account for that in any way?
