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.

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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.

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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.

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.

Photos from Prague

I’m ashamed at how little I have written this year, even though I have had several ideas for blog posts. To help assuage some of my guilt, I will share a few photographs I have taken.

I’m rather lucky to be living near the Krč forest where I can, regularly, go walking. At the beginning of the year it was still winter and most of the trees were bare.

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2022 Book List

We’re now in mid-March and I still haven’t written down my thoughts on the two books I read in January. A lot has been going on recently but, the longer I take to write these down, the worse my recollections become.

2021 Book List
2020 Book List
2019 Book List
2018 Book List
2017 Book List

06/11/2022 Added Entangled Life and Pup Sloots.

The Philosopher and the Wolf (2008) by Mark Rowlands

In this book, Rowlands shares several of his experiences moving between countries and building a career in philosophy, all while raising a wolf. The anecdotes about Brenin, the wolf, invariably serve as the starting point for some sort of philosophical digression. While several of these digressions are indeed interesting, I was seldom convinced by his arguments (see my blog post on what makes a person evil for an example).

I would’ve preferred much more of a focus on the stories involving Brenin, but those that are there do provide some fascinating insights on animal behaviour and training. While not all of the methods will probably be approved of by everyone, Rowlands does make the point that wolves and dogs are quite different and, from the stories he gives, he managed to have a wolf which was much better behaved than many dogs. It’s also clear that he cared deeply for Brenin, and his other dogs, and, especially towards the end, many of the stories were quite emotional.

If you were planning to read The Philosopher and the Wolf to hear about what is like to have a wolf as a pet, you will probably be disappointed. I’d estimate that that about two thirds of the book are given over to his philosophical musings which, if nothing else, at least serve as food for thought. I can’t say that I agreed with most of them but I did still enjoy the book and think it is worth reading.

A Christmas Carol (1843) by Charles Dickens

There’s really little to say about this one. It’s an old story and, if you have any contact with Western culture, you have likely seen an adaption, homage or parody of this. I am, of course, familiar with the story but not the original work. In fact, I think this is my first time reading Dickens’ own words. I have no complaints but, given how well-known the story is, there were no real surprises.

What was special was that I was reading a copy which, I believe, had been my maternal grandmother’s. I can’t recall the exact printing date of the book but it was around 80-90 years old. While not as old as the story itself, it’s still quite a bit of history and all of the people who originally bought and read it are now dead. Yet the book is still there, can still be read and provides a tangible link to the past. Plus, a physical book has no battery issues or file type compatibility problems.

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.

A literary return to the Namib Desert

I managed to finish off two more books for my 2021 Book List. It’s still fewer than I had hoped for this year but it’s better than nothing.

The Sheltering Desert (1956, translated 1957) by Henno Martin

This is a memoir which recounts the story of two German geologists stationed in South West Africa, now Namibia, which I bought during my trip to the Namib Desert. When WWII broke out, they wanted no part in it, nor did they wish to be interned by the police, so they resolved to hide out in the Namib Desert until it was all over. The pair of scientists and their dog travelled into the desert and remained there for two years until malnutrition forced them to abandon their plan.

Along with the descriptions of life in the desert are several philosophical musings on human society, evolution and the nature of man. A lot of it feels quite dated but I really enjoyed the discussions on the similarities and differences between humans and non-human animals. Even back then, many people living in cities and towns had little actual contact with wild, or even tame, animals; meaning no familiarity. Martin observed that, after time in the desert, with only the wild animals as their neighbours, they began to see the complexity in their behaviour and recognise the animals as being as unique as other people.

As the pair are scientists, the story is more than just a tale of survival. Scientific curiosity is evident in many observations and trips which include one to investigate why the rocks of a distant mountain were so white. If you’re at all interested in outdoor activities or the Namib, I think it will make for a great read.

Why Vegan? (2020) by Peter Singer

Why Vegan? is a collection of essays by the controversial, utilitarian philosopher Peter Singer. I had already read his classic book Animal Liberation but only after already becoming a vegetarian. These essays also revolve around the topic of animals and diet and span several decades, the earliest from 1973 and the most-recent from 2020. It’s a quick read, with some essays being incredibly short, but a very important topic.

Singer’s ethical approach is about avoiding causing unnecessary suffering, so several essays discuss cruelty in farming. In his introduction he does note that several practices documented in older works, such as Animal Liberation, have now been outlawed but not all problems have been fixed. In an essay from 2006 on chicken farming, he describes how many chickens are still kept in cramped conditions, standing in their own filth, where some starve to death and many others are boiled, alive and conscious, due to failures of the stunning system and manual oversight. These are things we ought to know if we are to be informed consumers.

If someone has never thought much about the practice of eating animals, because it is usually an unquestioned aspect of human society, then this collection will serve as a good introduction to the topic. This collection doesn’t go deep into details (I would recommend something like A Plea for the Animals to expand on the topic.) but it raises many of the questions and concerns which everyone should keep in mind. Regardless of the answers we eventually settle on, this is a pressing topic which we must think hard about and not allow the suffering of our fellow creatures to be hidden behind the veils of tradition and ignorance.

Updating my blogroll

The blogroll is on the main page of my blog and links to various other sites that I consider worth reading. The sites which were on there were from many years ago and included several which I no longer read. When I noticed that, I saw that it was time to update it. Here’s a new list of blogs which are worth reading. Go check them out.

Animal Emotions

Animal Emotions is written by Marc Bekoff, Professor Emeritus of Ecology and Evolutionary Biology at the University of Colorado, Boulder, United States and co-founder of the Jane Goodall Institute of Ethologists for the Ethical Treatment of Animals (ethology being the study of animal behaviour). The blog deals with various aspects of animal behaviour, welfare and ethics.

The Bowman Lab

This is the blog for the laboratory of Jeff Bowman from the Scripps Institution of Oceanography in the US. This is a blog that I started following more recently to get a wider view of microbial ecology. The Bowman lab works on different aspects of microbial ecology with many posts focussing on analytical tools as well as marine and polar microbial ecology.

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Rocks, (metaphorical) souls and His Dark Materials

Additions to my 2021 Book List.

Life at Rock Surfaces (2021) edited by Burkhard Büdel and Thomas Friedl

This is quite different to the other books I’ve been reading, both because it’s aimed at academics and because it’s not mine. I was lent a copy of the book by Pedro, my friend and colleague, who was an author of one of the chapters. Each chapter focusses on a different aspect of life, mostly microbial, at rock surfaces. Some of the chapters make for interesting reading on organisms living in quite an extreme habitat and some, like a taxonomy guide, are not chapters that lend themselves to normal reading.

As it’s aimed at an academic audience, it’s not really accessible unless you have a fair bit of familiarity with the field. Each chapter is written by a different set of authors and so the quality and style of writing varies wildly from chapter-to-chapter. The best chapters are fairly easy to read and follow but others are a slog. Part of this is due to the content of the chapters but, often, it is poor academic writing that is opaque or unnecessarily stilted. For example, there was one chapter written by a single author that repeatedly used phrases such as “The author hypothesises …” instead of “I think …” The former isn’t a more scientific way of writing; it’s stilted, it’s awkward and is the sort of thing that leads to multiple articles about why scientific writing needs to change.

Science in the Soul (2017) by Richard Dawkins

This is a collection of Dawkin’s essays and speeches from across the years. There is a lot of good content with a wide range of subjects, including science, religion, politics, humour and even a few eulogies. I had read probably about four of them before but that didn’t matter because it was still worthwhile reading them again. Out of the whole collection, there only a handful which I did not enjoy, which is a pleasant return to normality after Outgrowing God.

Despite the breadth of topics, there is an impressive depth of insight which one only gets from spending decades immersed in science. Dawkins’ clarity when writing and the knowledge beneath his writing is a welcome change from so much of the shallow and misguided thinking which is commonly seen today. Indeed, several chapters touch on issues which are still debated, even though they probably should’ve been settled many years ago. Dawkins is probably the best modern science writer and I can highly recommend this book.

His Dark Materials: The Amber Spyglass (2000) by Philip Pullman

The Amber Spyglass is the final book of the His Dark Materials trilogy and it is a great conclusion. I won’t say I am entirely happy with the way that everything ended, but I can see why it ended that way. I won’t say much of what happens to avoid spoilers, but I will say that it is a brilliant story, set in vivid worlds and overflowing with imagination.

I really enjoyed seeing some scientific musings in this book. During the story, the characters travel between different worlds and, in one of them, evolution followed a very different path. It’s not in any way a scientific book but it did a really cool job of pondering a different path of evolution and showing the interplay between different organisms as well as their environment. That was really cool.

The entire trilogy was well-written but I have to be clear how addictive and easy-to-read it is. There are good books that I’ve enjoyed reading but, when I finished a chapter, I was ready to stop. All of the His Dark Materials books are those wonderful sort where, after I finished a chapter, I just wanted to keep going. I thoroughly enjoyed it, highly recommend it and think I might need to look into the BBC series to see how it compares.