Category: science

It’s possible that I just bought a slime mold (Physarum polycephalum) kit that’s intended for a classroom size of 30 students, and I’m planning on livestreaming its progress over the next few weeks. This is my gift to you (funded by my friends who were enticed by respite from current events).

I will probably livestream on my YouTube, unless someone tells me it would be better to do it elsewhere. (I’m also planning on doing my first unboxing video, which is hilarious because I will be unboxing slime mold.)

Hello friends, I just discovered a lady lichenologist, Annie Lorrain Smith, from the early 1900′s. From her Wikipedia:

Scott found work for Lorrain-Smith at the British Museum to curate Anton de Bary’s collection of slides of microscopical fungi, but she had to be paid from a special fund because women could not officially be employed there. She soon was responsible for identifying most of the fungi which arrived to the museum. She identified and reported on newly collected fungi, arriving from abroad as well as from the UK, and worked in the museum’s cryptogamic herbarium. She published various papers from 1895 to 1920.

Smith led a lichen survey of Clare Island, which was outside Clew Bay in Ireland, in 1910 and 1911. The Clare Island Survey involved not only Irish but also several European scientists who were all looking at different aspects of the island’s natural history. The team were credited with the first project aimed at characterising a particular biogeographic area. In 1921 Smith wrote the illustrated Handbook of British Lichens which was a key to all known British lichens. In the same year Lichens was published and was quickly established as a classic text.

microcosmicobservations:

Paul Stamets is great in that he has made mycology a little more accessible to laypeople, BUT please understand that the man is a snake oil salesman who presents his own half-baked theories as scientific truths. It’s unfortunate that there aren’t better resources out there for non-scientists to learn more about mycology, especially if you’re interested in learning about fungi that aren’t mushrooms. I hope to change that, someday, when I am not being consumed alive by grad school, but in the meantime here’s a list of decent intro to mycology books (which are relatively technical but don’t let that scare you).

Some of you have asked me to explain, and I’m proud of you for doing so because I wouldn’t expect you to take my word more than anyone else.

Paul Stamets is clearly a smart person, and his passion for mycology is intoxicating, but it’s important to keep in mind that at his roots he is a businessman.

My problems with Stamets boil down to the scientific method and how to decipher scientific results. I do believe that science is something that should be broadly accessible to everyone, regardless of whether or not they passed through the ivory towers. HOWEVER if you are going to do science and then bring your results into the public’s eye (in his case, via TED Talks, books, movies, etc.), even try to SELL your results as some miracle cure, you must do more rigorous science. When people’s health is relying on the robustness of your methods, you must do more rigorous science. Science is messy. Sometimes things that have worked in one condition, never work in any other condition (see this paper debunking one of his claims). Stamets inflates his results and then tries to sell them as a product. There is no accountability. His products and claims aren’t evaluated by the FDA.

I don’t want to be a gatekeeper. I am thrilled that Stamets has gotten so many people interested in mycology, but he’s gotten them interested in the pseudoscience rather than the actual science.

He’s a sensationalist and romanticizes the way fungi work. If Stamets has brought you over to the beauty and wonders of mycology – welcome! This is such a fascinating realm to enter, even if you’re not a scientist! You belong here, and you deserve to get joy from this as a hobby.

Great news, everyone. Scientific papers do eventually get published and aren’t caught in a cycle of peer review and edits for eternity! The paper I started working on a little over a year ago has been published.

(I originally wrote this up to share my research with my non-scientific friends and family and realized it fits well within the scope of my blog so here you go)

In most phylogenetic studies, the ultimate goal is to construct a tree that accurately reflects evolutionary relationships between species. We used to do this by entirely comparing anatomy, but once DNA sequencing was introduced, things were revealed to be more complicated than we could have anticipated. In the beginnings of DNA sequencing, we were pretty limited in how much we could sequence. People would sequence a single gene and be pretty pumped about their phylogenetic tree. But with advances in sequencing, we learned that the phylogenetic tree created from a single gene merely reflects the history of that gene, not necessarily the species themselves – each gene has its own evolutionary history. So folks were like, okay, we’ll just get a few more genes and maybe a phylogenetic signal will emerge, a consensus between gene trees, thus giving us the true species tree.

Then there’s my project. We sequenced 962 gene regions – surely such an absurd amount of genes that would tell us a relatively clear story of evolutionary history? But it hasn’t. It’s an absolute mess. There is a profound amount of disagreement between all of the genes, each telling a conflicting story about what happened in the past. And I am fascinated with this mess. I looked into this group of species because we suspected hybridization, and this mess of gene histories further supports that – maybe the reason there are so many mixed signals is because we’re not getting genes that have stayed with a single species throughout time, maybe they’ve have been passed between species.

Anyway, I am super super pumped. I’ve wrapped up the project for the purposes of the class I’m doing it for, but I am absolutely going to push further. This is so much more exciting to me than a clean and tidy phylogenetic tree!

I just realized I can have the Kitten Academy livestream running on my second monitor while I read scientific literature, and if that isn’t life hacks I don’t know what is

Hi! I have a question about lychen taxonomy and nomenclature, and the more I read the more confusing it seams to be. Are each species of lychens one species of algae and one of fungi or can there be many of both in one lychen? How does it work, do you identify all the different species of mycibionts and phytobionts or do you do it as a whole new thing?

This is a great question, and honestly the more I learn about lichens the more confusing they are. Here is a figure from Toby Spribille’s 2018 paper “Relative symbiont input and the lichen symbiotic outcome”:

Column A was the original view on lichens and why we originally decided to name lichens after the mycobiont – we thought that each lichen was made of a distinct fungus but photobionts were promiscuous. Column B describes what we’ve found with molecular studies looking at the mycobiont – the fungus can be promiscuous too! And column C is the hypothesis that Spribille puts forward in the paper, which I tend to agree with too – that lichens are a big ol’ mess, and there’s more going on than we’ve yet to really investigate.

However, in spite of all of this, lichenologists still tend to identify lichens based solely on the primary mycobiont and/or morphological characters (in plain English: how it looks). I think we’re at a crossroads right now where we’re realizing things are a lot more complicated than we originally thought, so where do we go from there? How do we define the lichen species? Or is that even reasonable, given that they’re a collection of bionts that can change based on where it’s growing or other conditions?

I was always a bit worried because it seemed like my one strength as a scientist was remembering scientific names and being able to ID plants/mushrooms/lichens with relative ease, which is a helpful skill but not necessarily sought after. Now, however, I have uncovered another superpower thanks to my advisor encouraging me to go down rabbit holes: being able to dig deep into the literature and efficiently synthesize knowledge on a topic I know next to nothing about. I am so excited to share my new knowledge with all of ya’ll!

This blog will be in a bit of a lull for the foreseeable future – I rarely get out for photo hikes these days (not necessarily because I’m too busy but because Utah is not really for me – I prefer meandering not climbing mountains), but I spend a tremendous amount of time reading scientific papers so that I can set up my research projects. My goal is to create a bridge between my research and non-scientists. I believe that lichens are one of the coolest things on the planet, and I refuse to keep my findings inaccessible within the ivory towers. Everything I learn is something I hope for you to learn too. But it will take a bit for me to get to the point where I am organized in my deliverance of knowledge (I’m always open to spontaneous questions on Tumblr though, especially if I am looking for a break/distraction).

My chronic illness has been flared up bad, and today I am trying to understand sexual reproduction in lichens when my brain is an absolute fog. And let me tell you, trying to understand reproduction in a composite species in which only one biont reproduces sexually but wouldn’t be able to form reproductive parts if it weren’t for their other bionts, where species can be sexual or asexual or both or seem like they’re always asexual but then you find this random population that’s sexual, where we apparently haven’t made much effort into investigating what causes it to be sexually reproductive in the first place (maybe because it’s too hard to observe in the lab?)…trying to understand this – not just understand it but think critically about it – when I have two or three functioning brain cells at the moment is quite a challenge.

I love lichens, and I am deeply passionate about my research, but sometimes I regret not choosing a more straightforward organism to study.