Quicklinks: 6 – 12 March 2023

Clearly this is quite a bit later than it was supposed to be but, since I had already picked out the links, I decided I would finish it. However, I’m giving up on the weekly quicklinks; they were supposed to help me get some easy writing done in my spare time but they turned out to be a lot more effort and stress than they are worth.

The Japanese name for the wolf also means “great god.”

Did you know the Japanese word "ōkami" is a homonym for “wolf” and “great god”? The last wolf in Japan was killed in 1905, but since the 1990s, there have been groups advocating for reintroducing wolves to help mitigate the damage caused by deer and wild boars. #wolf #funfact pic.twitter.com/qGOsmWBDWM

— Wolf Haven International (@wolfhavenint) March 10, 2023

This article suggests that giving wild animals names, instead of just numbers or other designations, helps reduce the sense that humans are separate from the rest of nature.

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Quicklinks: 06 – 19 February 2023

This time we’re doing two weeks together. Why? I got infected with covid and so all my plans and normal activities have completely gone out the window. It was not a particularly severe case though but it’s still been quite disruptive.

This week we’re starting off with an impressive picture of a snow leopard which was taken in Mongolia.

Best of '22: My favorite shot of the year, finally getting a wild snow leopard not only within decent range (previous viewings were 1-2km away), but in a fantastic setting. It's WILD, the shot isn't faked… and this will probably never happen to me again. 😉

(Western Mongolia) pic.twitter.com/0F9s44qyNb

— Max Waugh (@MaxWaughPhoto) January 11, 2023

Quicklinks: 23-29 January 2023

Let’s start off with a pretty cool cat fact.

Let’s learn a #CaturdayCatFact!

While a cat’s adult canines grow in, they go through a phase where each quadrant of their jaw has TWO CANINES! The adult tooth starts growing in next to the baby tooth, allowing the kitten to never go without the function… https://t.co/C3MbtGtA0x pic.twitter.com/CMuxp8S81r

— Ashley Reynolds – ashinonyx@scholar.social (@ashinonyx) January 29, 2023

AI tools like chatGPT are pretty cool. But they are not exactly reliable and, even worse, it’s difficult to know how reliable they are. When you hear a person you don’t know, you can look into what they do or what qualifications they have. With AI, it’s giving you answers which are a mix of all sorts of information; some true, some false. In the following Twitter thread, you can learn how it can construct that false information.

Why does chatGPT make up fake academic papers?

By now, we know that the chatbot notoriously invents fake academic references. E.g. its answer to the most cited economics paper is completely made-up (see image).

But why? And how does it make them? A THREAD (1/n) 🧵 pic.twitter.com/kyWuc915ZJ

— David Smerdon (@dsmerdon) January 27, 2023

Finally another two books!

After not doing much book reading for most of this year, I can finally extend my 2022 Book List.

Entangled Life: How Fungi Make Our Worlds, Change Our Minds & Shape Our Futures (2020) by Merlin Sheldrake

Written by an author with one of the most amazing names I’ve seen, Entangled Life is all about fungi. There are discussions on how fungi evolved, how they influence plant life, the truffles we eat and how we can use fungi for our own benefits, including one chapter that covers the technologies in The Moralbiont. Sheldrake is so obsessed with fungi that some of the illustrations in the book are even drawn with ink made from a fungus!

Although my interests and the book’s topic overlap quite well, I wasn’t crazy about all aspects of the book; several chapters are written in their own style and not all of them sat well with me. The chapter on truffles takes on the sort of narrative style which can drive a story along but which tends to irritate me as I find it all too convenient. I made a similar criticism about Darwin’s Ghosts a couple of years back. And there are other sections which are so effusive that it feels like he’s trying to make every other paragraph a pale, blue dot moment.

That said, I would still highly recommend the book to anyone with an interest in microbiology. Stylistic quibbles aside, there is a lot of very good and very interesting information in the pages. Most of it I knew of already but there were also plenty of titbits which I had not yet encountered.

Pup Sloots (2020) by Phoenix Xander Artemis

Jumping from fungi to a gay, BDSM, petplay romance might seem like quite a leap but there is actually a microbiology connection between the two; Pup Sloots takes place during the time of coronavirus. More specifically, back in 2020 when things were crazy, no vaccines were available and hard lock-downs were enacted across the world. Despite what I expected, the majority of the, very short, book actually takes place after the lock-down restrictions are lifted.

The story is told through the first-person perspective of an alpha pup who meets someone the night before lock-down restrictions are enacted and who must then wait until they can continue building their romance in person. The entire relationship is built around BDSM dynamics, in particular puppy play, which is a form of role play where the participants act as human dogs. The book describes it all as well as the main character’s thought processes and motivations.

It’s an interesting book. I really enjoyed the dynamics of the relationship and how everything is described (although I think some of the language which is claimed as being specific to puppy play is really just Lolspeak and common to many internet communities, e.g. using “gib” for “give.”) but it will not be for everyone as it does all build up to explicit sex. That said, my only real hesitation with recommending it would be the length; it is not even 100 pages. However, the psychological aspects of the story are good and it is even educational. If one has any curiosity in that area then one could assuage that curiosity while also helping support a small-scale writer.

Commentary: The Moralbiont

Product concepts made with fungal leather (Image: Mylo)

This is the companion piece to my short story, The Moralbiont. It will discuss some of the references and science from the story. If you have not read the story yet, I would highly advise reading it first.

The conversation between Olivia and her grandfather about his thesis supposedly being covered in cow skin is a reference to a question from the Voight-Kampff test. In the Blade Runner franchise, the Voight-Kampff test is administered to those suspected of being a replicant, a human-like android lacking empathy. By monitoring the physiological responses to questions about shocking or repellent situations, you are able to tell if the subject is a real human or a replicant. I have neither seen Ridley Scott’s classic Blade Runner film nor read the original novel by Philip K. Dick but I did play the 1997 video-game which is where I became aware of the question.

Like my briefcase? Department issue, baby hide. 100% genuine human baby hide.

Short story: The Moralbiont

Earlier this year, I entered the Federation of European Microbiological Societies (FEMS) writing competition. The goal was to write a flash fiction story (not more than 700 words) for the prompt “How Microbiology will Change our Future.” While I did not win, I was very happy to be shortlisted in the top 10 submissions and my story, The Moralbiont, is now available on the FEMS website. Additionally, you will be able to read the story below. As the story was written for a microbiology audience, not everything within may be common knowledge. In a follow-up post I will explain the references, technologies and terms which are important for the story.

ESM 2022 poster: Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

For those that were not able to attend the Ecology of Soil Microorganisms 2022 conference (which ran from 19-23 July in Prague, Czech Republic) I got permission to upload the poster which I presented. Being a scientist can also mean doing a bit of public speaking and graphic design. Below, you will find the abstract and poster.

Patterns of bacterial-fungal co-occurrence in European beech (Fagus sylvatica L.) deadwood

Jason Bosch, Ema Némethová, Vojtěch Tláskal, Vendula Brabcová, Petr Baldrian

Deadwood represents an important nutrient source and microbial habitat in forest ecosystems. Its decomposition is one of the key processes of global carbon turnover considering that European natural forests can contain up to 1200 m³ of deadwood per hectare. This deadwood is primarily decomposed by saprotrophic fungi but bacteria also have a role to play, particularly in the provision of nitrogen. Previous work has shown that the first fungi to become established will physically prevent further colonisation by other fungi. As bacteria and fungi can interact in both synergistic and antagonistic ways, we expect that these fungal zones of control will also influence the bacterial community composition at local scales.

We investigated the patterns of microbial diversity and co-occurrence in 1 cm³ blocks of European beech (Fagus sylvatica L.) deadwood collected from the Žofínský prales National Nature Reserve in the Czech Republic, using 16S and ITS amplicon sequencing. Compared to previously-collected “whole log” communities, the small-scale communities showed less diversity both individually and in combination. By correlating fungal and bacterial species, we were able to expand on previous work which showed that fungi influence bacterial community composition. As small-scale microbial communities collected from the same log can differ dramatically from one another, we advise caution when interpreting “whole log” microbial community data as the results may not reflect the actual interactions which take place in the deadwood.

poster_final_fixedDownload

If you would like to cite the poster, you can use the abstract book citation:

Piché Choquette S., Slaninová Kyselková M., Pospíšek M., Baldrian P. (Eds.), 2022. Ecology of Soil Microorganisms – Book of Abstracts, Prague, June 19 – 23, 2022.

Final papers from my PhD

I am happy to report that the last two papers from my PhD are now available for everyone to read!

Two Is Better Than One: Studying Ustilago bromivora–Brachypodium Compatibility by Using a Hybrid Pathogen

This, along with the U. bromivora genome paper,  is probably the most important paper from my PhD. Those two papers formed the basis of my thesis. Although I did not manage to fully answer the question I set out to answer, this is a paper where most of the experiments, most of the analysis and most of the writing was done by me, so it is special to me. It’s also quite interesting! If you want to know exactly what we learned, you can read the paper itself but I will give you a brief summary of what we were trying to learn.

We knew there were two very closely-related fungal species which could infect different host plants. This told us that although they were very similar, there was something important about them that was different; we wanted to know what that was. Even more exciting, we could create a hybrid between the two fungi that was still able to infect one of the host plants. What I was trying to do was take the hybrid and breed it over and over again with the parent that couldn’t infect while making sure that the hybrid could infect. After enough generations, we should then find the hybrid would be genetically almost identical to the non-infecting parent but with just a tiny bit of the infecting parent inside it. That would tell us what the difference between them was and we could then try to figure out how that part of the genome led to interactions with the plant.