#just lichenology things

[botanizing]

tfw every specimen you thought was Caloplaca saxicola is just Rusavskia elegans.

(hi I'm alive and I did get into grad school which is why I've been neglecting this blog and will probably continue to do so. but please enjoy this image it took forever to make lmao)

[botanyshitposts]

Well, the lichen test was successful in telling you that it isn't something that turns red when you put that chemical on it, so that's a win. Sort of.

to be honest i didn't realize how funny the lichen chemical spot test concept was until now. like when i was a student my lichenology professor just told us to do it and i was like Aye Aye, but now, like... having read a bit more about the known lichen-specific substances/chemicals, knowing that these specific chemicals number between 850-1,100 currently, knowing not all of these react to known chemicals but some are more common in specific species but don't always occur and have vague or as of yet unknown functions and causes, and finally, understanding that because of this the test boils down to putting known chemicals on unknown chemicals and referencing the reactions, which could be any number of things, with a book.... i'm not saying it's not a useful tool for ID, but i am saying it's really funny.

i think you understand this but listen. a guy walks into a store and is like, i would like to know who that man over there is. the store attendant is like, well if you ask him how hes doing and he tells you about his kids, its bob, he does that a lot i think. the guy goes over and asks and the unknown guy beats him over the head with a chair. we conclude from the test it is not bob, unless it was and he just didnt feel like it that time. in which case maybe it was him

[pyrrhocorax]

my current hetalia wildlife/natural resources au thoughts i have from your resident wildlife biologist: sweden: i have lots of ideas for him but the idea of him being an entomologist is interesting b/c the contrast of "big scary giant guy, but he studies tiny butterflies" is really fun to me. he has a very entomologist personality to me too based on all the entomologists i know so lepidopterist is my current thought. finland: forester. all foresters i know are unhinged in the same exact way he is unhinged. potentially also a fire ecologist?? i think that would be interesting (give me an excuse to learn about fire ecology more) and i think he would enjoy using a flamethrower. iceland: thinking geologist, prob volcanologist? or he studies auks. norway: less sure of him. thinking mainly about fisheries (not sure if marine or freshwater, both are interesting), mycology, lichenology (this is the main one i am thinking about rn), oceanography, or mountain stream hydrology (yes that is a thing) for him. denmark: having the most trouble with him honestly. maybe meteorology, geography (GIS dude??), soil biology?? maybe even human dimensions (i can see him being a good intermediary between the public and natural resources, like park ranger-esque)?? idk if extension agents exist in europe but he'd be good at that i think. estonia: songbird biologist. bander (or ringer you're european). potentially studying migration trends? breeding output of at-risk species? potentially lab mates with austria b/c sharing same field site. he's uncannily good at mimicking bird calls. lithuania: large carnivore biologist that studies in canids (i.e. wolves), mainly does camera trapping but also darts/radio collars them. looking at habitat usage to hopefully boost populations??? latvia: shorebird/rail/stork biologist?? reminds me of a shorebird biologist i know and i think he'd vibe well with water/water adjacent bird work. i also think him studying beavers is fun because beavers are fun! and i think the riga beaver thing back in the day was hysterical lol OR i think him being an aquatic entomologist would be cool he could be a dragonfly guy austria: also a songbird biologist, but looking at vocalizations/song stuff, does a lot more lab work than field work analyzing vocalizations. maybe studying nocturnal vocalizations during migration of birds across different habitats??? potentially lab mates with estonia. america: ungulates. or maybe specifically cervids. respectfully, as an american, we are overly obsessed with deer. could also see him studying salamanders because they are a special kind of person too that fits the american personality well, and america is home to the most salamander diversity in the world so like. yeah. canada: ducks/loons/grebes, raptors (specifically thinking eagles/hawks), weasels (him being so understated but studying wolverines is funny to me), or fisheries? :/ could also see him being a habitat biologist in general, doing modeling stuff for wider scale land changes? i kind of want him to be a prairie conservationist too. england: botanist is my thought for now? he has a "plant research guy who is 3 years into his phd and kind of regretting his life choices" vibe to me. but he's also the world's crustiest birder outside of his work (b/c uk influenced a lot of the current world birding culture) germany: ngl environmental policy analyst seems up his alley and we need more of those who are good. romania: chiropterist. and before you are like "urg don't stereotype the vampire thing pyrr" it's not that. his personality is just very bat biologist. they are a special kind of people, and i say that with affection, as all the bat people i know are fantastic. specifically could see him being also an entomologist studying the interactions between bats/bugs on farmland to see how bat populations help crop production. still thinking on things though!!! welcome to my niche au.

[lichenaday]

In the recesses of my mind I recall reading that lichens are (*suddenly remembers Wikipedia exists* *checks* Yup.) composite organisms. So this means it's not "one thing" -- i.e., one species per colony (for lack of a better word)? Yet it seems pretty clear we can sort them out by how they look, and give each colony (or whatever) a distinct species name? How does this species thing work?

A great question! With a not entirely straightforward answer.

In large part, lichen physiology is shaped by the mycobiont, AKA the fungal constituent of the lichen symbiosis. It makes up the majority of the mass, and is generally thought of as the obligate organism, as many (not all) of the photobionts, AKA the algal/cyanobacterial constituents of the lichen symbiosis, are non-specific or can be found free-living outside of the symbiosis. So when we are talking about scientific names for lichens, those are the names for the lichenized fungus. And when we are talking about genetic testing, we are *usually* talking about genetic delineation of the fungus. BUT. Check out this awesome lichen my lab mate collected in Tenerife:

This is Sticta canariensis--yes, both of them. The one on the right has a green algal photobiont, and the one on the left has a cyanobacterial photobiont. See, for a long time lichenologists thought these were totally different species because, well, look at them! But sometimes they would find them growing out of the same colony! And genetic testing revealed they have the same mycobiont! Just different photobionts! So it is it fair to only classify lichens by their mycobiont when the photobiont can have such a drastic impact on their physiology? Well that’s one of many discussions going on in the field of lichenology at the moment. 

As of right now, DNA sequencing and classification of algae is a difficult and ongoing project in lichenology. Little buggers are difficult to sort by appearance, and it’s a real challenge to successfully extract and amplify their DNA. So we will stick with using the mycobiont for classification for the time being. But in the future? Who knows? 

[itslookingback]

you know whats an actual thing? the intersection between queer theory and mycology / lichenology

its really interesting because it talks about how its really difficult to perceive how a fungus works with its environment, either with tree roots or as part of a lichen etc, when you still have a very binary way of viewing the world. much like how gender, sex and sexuality are constantly sorted into rigid boxes that don’t fit, a fungus is often sorted as an independent individual organism when its so much more than that - its constantly creating relationships with other organisms until there’s literally an ecosystem going on. its much easier to talk about a lichen and how it works as a whole than separating it into its individual components (fungus, algae, yeast, bacteria)

also, there’s a whole thing about the world being mycophobic (afraid of fungi) and how fungi are seen as inherently harmful, strange, literally queer. people used to avoid fungi in science because they are just too complicated to study / taxonomize. i just think the intersection between these two topics is really cool and i think people would be more interested in fungi / lichens if they saw them in a queer, nonbinary view

[microcosmicobservations]

[Note: This is not an advice post. My footsteps are not necessarily the best to follow.]

I have a hard time getting people to understand why I'm in grad school if not to use it to directly advance my career. Realistically the chances of me getting a job related to mycology or lichenology or systematics after I graduate are very slim, and I'm not seriously interested in pursuing a career in academia because my mind and body aren't built for the culture.

So why do it? Before I went back to grad school, I was putting my bachelors degree to use by jumping between seasonal field jobs. There weren't many options for permanent positions. I eventually got a fulltime job at a pharmaceutical testing company, but since I wasn't qualified to do that type of science, I ended up spending most of my time stocking and aliquoting media. With just an bachelors degree, I couldn't find the job I wanted.

So I went back to school, to study what made me happy. I think of grad school as my job. I get paid to do research year-round with funding for up to 5 years, which is more stability than I had before. The best part is, I get access to information and opportunities that I wouldn't if I were studying independently (most of you know very well how hard it is to learn about lichens on your own). I don't necessarily see grad school as a stepping stone to bigger and better jobs - I see it as something that gives me the chance to do what I like right now and get paid for it. I didn't have many job options with a bachelors, and I won't have many job options with a PhD. But right now? I get to learn about awesome things and challenge myself in new ways!

Anyway, this is why I'm not the best person to ask for career advice. :,)

[cedar-glade]

apologies if you've already answered this question a million times already, but how did you go about learning botany? i'd like to but im intimidated by how much information there is to take in and how much i'd have to memorize.

OK TLDR is, get a camera, buy books, memorize apomorphic traits for families, use bonap and I nat, blog and read papers, join societies. and explore herbariums. Im mainly self taught when it comes to field botany.

here is my actual story of why I like botany/ how I got into it to where I am now (trying to figure out sedges, exploring lichenology and bryology) 

I originally got into it, as silly as this sounds, from a tree ID class my freshman year in Highschool. It was just simple leaf collection book, I didn’t do well, but, I didn’t do bad either. Got an 80 on the project. I started looking at things differently after that. I originally was interested in Herpetology and wanted to specialize in that, as any kid growing up in Oklahoma and Ohio would, it was easy to self teach myself about herpetology too at an early age; however, as highschool went on I became more fascinated in habitat preferences, which sparked the switch from zoological herpetology(very basic in concept) to ecological herpetology(complex as all hell). Ended up looking at habitat with a knew mind set and started looking at food and plants a bit different too. After a while I fell in love with botany and ended up at OU for 1.5 years prior to catching a vandalism charge and being suspended for underage consumption on campus( I vandalized a campus police cop car after my friend was detained wrongfully, won’t get into details but I was also drunk at the time.)  I ended up working for a very short time in a lab focusing on PPFD and natural plant stress for a very short time. After being forced to leave I took a year off prior to going to Miami University till the end of 2020. At Miami I was a conservatory worker, which sparked my love for Apocynaceae and Araceae, and I worked in the largest midwestern herbarium too cataloging fungus. I suppose, I started botanizing heavily at OU though, self taught field botany because Stroud's run is insane. At Miami though I learned about Ohio’s botanical impact and it’s many years of excellent public out reach through news letters and bloggers. I learned a lot from going to seminars and societies’ field trips, blogs, and reading tons of papers at this time. The herbarium kinda messed me up though, it gave me the power to access specimens and historic records with relative ease and really boosted my knowledge without to much aid do to just curiosity and the power of uploaded easily searched herbarium specimens online. Dr. Vincent(MU Dr. Moore(MU), Dr. Gladish(MU), Dr. Ballard(OU), Dr. Harding got me into genetics and evolution more or less, and Dr. Keiffer(MU) hooked me up with the Chestnut Foundation and got me hooked on Plant Pathology(my current profession is field pathology). As for the vast majority of my field botany and ecology, it’s self taught, blogging helps you understand concepts better and taking pictures and iding them causes you to memorize species faster than what is normal or natural for the process of learning. Instagram and tumblr are good but their are plenty of older blogspots and word press from pre tumblr that are essentially archives of now professional ecologists field notes from when they just started.

As long as you are interested and start applying what you read, you will learn quickly. Just going out taking photos and making a hobby out of it is a big step.

[mycoblonde]

SONORA FEELS! Today the American and Bryological and Lichenological Society hiked a couple different altitudes at Madera Canyon. I quickly gave into my solo-hiker habits and peeled off to do the long loop. It was hot, no doubt, but the shade of mesquite and oaks and ponderosas was just enough and there was plenty of pretty things to occupy my mind. Here’s Cladonia chlorophaea (probably), a colorful baby Mammillaria cactus, the periwinkle blue neck of the Sonoran collared lizard Crotaphytus nebrius, a red flower I don’t know (@waxwingboheme do you know it?) doing tree pose in a big hat, the huge waxy flower of a giant Mammillaria, another red flower I don’t know (halp?), the most perfect Xanthomendoza lichen I’ve ever seen, and me looking super stoked in my new favorite hiking/fieldwork hat. Thanks for selling this perfect hat to me when I was slightly drunk at a beer festival @rmohats #hiking #tucson #rmohats #arizona #mammillaria #cactus #lichens #lichenology #abls #flowers #desert #sonoradesert #mycoblonde #cladonia (at Madera Canyon, Arizona) https://www.instagram.com/p/B0eoxSBg71x/?igshid=5qwxhncgond0

[geopolicraticus]

Infinitistic Epistemic Expansion

An interesting twentieth century perspective on the expansion of scientific knowledge was provided by Harlow Shapley:

“After seven years of work with large instruments on questions concerning the globular star clusters—their structure, relationships, stellar content—I realized that we were relatively more ignorant about them than when I had started my investigation. I had added more to the unknown than to the known.” (Harlow Shapley, The View from a Distant Star, p. 17)

This is clearly a tendentious way to characterize the results of scientific research. Shapley noted that, “...we were relatively more ignorant about [globular star clusters] than when I had started my investigation,” with relatively being the key term. He did not note that, in absolute terms, his investigations had significantly increased our body of knowledge regarding globular clusters.

Indeed, it was Shapley’s work on globular clusters—specifically, their distribution in relation to the Milky Way—that implied that we are not located in the center of the Milky Way, which became in its turn another Copernican demotion of human centrality in the universe. Mapping globular clusters showed them to be arranged in a roughly spherical shell, from the center of which sphere our observing location of the Milky Way is significantly offset: the study of globular clusters not only yielded knowledge of globular clusters, but also knowledge about Earth and the solar system.

One can regard Shapley’s claim as a humorous way of retaining his epistemic humility; this is the most charitable reading of his claim. A less charitable reading would infer that he regarded his lifework as a failure for having added more to the unknown than to the known, but Shapley would certainly have known that one cannot very well engage in scientific research without expanding the scope of potential objects of knowledge. Indeed, one might even characterize a scientific research program in the Lakatosian sense in terms of the ontology it implies and which it aims to bring to light, so that a proposed expansion of scientific ontology is intrinsic to all research.

Science must pioneer novel objects of knowledge to expand (it must expand the ontology of science), but philosophy can expand parasitically by schematizing the expansion of scientific knowledge, since philosophy can always continue to expand by formulating “the philosophy of x” where the variable x is to be given a value that might be any topic whatever, including topics pioneered by the expansion of science. Quine said that philosophy of science is philosophy enough, and insofar as science continues to expand and produce ever new forms of knowledge, philosophy can also expand as the criticism and elucidation of ever new forms of knowledge. Thus the cipher of “the philosophy of x” can be substituted by any of the special sciences of increasing narrowness. 

Earlier in Reticulate Science I mentioned lichenology, mycotoxicology, and paleomycology as scientific specializations, and the possibility someday of a paleolichenology. There could also be a philosophy of lichenology, a philosophy of mycotoxicology, and a philosophy of paleomycology, so that the expansion of science implies the expansion of philosophy.

It may seem a bit ridiculous to speculate on a possible philosophy of paleolichenology, and indeed I can remember an exchange of letters with a friend many years ago—back in the day when people wrote letters on paper and sent them through the mail—in which my correspondent maintained the unlikelihood of philosophy having anything interesting to say about cell biology (or, contrariwise, the unlikelihood of cell biology having any philosophical implications). This probably was my point of view for many years, but having seen the growing sophistication of philosophy of science, and of philosophical inquiries into scientific specializations, I am ready again to argue for the relevance of philosophy even of the most minute and detailed research.

Also earlier in Reticulate Science I asked above the fate of disciplines tied to science, like big history, and whether they share the fate of science as science evolves over the longue durée, and perhaps over cosmological scales of time, if there is any being capable of doing science that can endure over cosmological scales of time. We can clearly see the possibility of philosophy following the development of reticulated history of science, with philosophies not only of the increasingly narrow specializations, but also philosophies of the interdisciplinary studies that attempt to converge on the big picture. Even philosophy merely as philosophy of science in the Quinean mould can continue to expand and diversify as science expands and diversifies. 

As we saw with the concept of the reticulate structure of science, the development of science not only involves new and narrower specializations, but also new and broader interdisciplinary approaches to knowledge, which not only present philosophy with novel objects of knowledge, but also the interesting methodological problems of previously independent sciences each approaching empirical evidence in their own way, now working together in an interdisciplinary context and attempting to converge upon one and the same object of knowledge.

And when philosophy is applied to those disciplines with only a problematic relationship to the paradigm of empirical science—the examples I previously gave were mathematics and history—philosophy as philosophy of science passes imperceptibly beyond the strict bounds of science, but in doing so its development is consistent with its past as philosophy of science. In this way, philosophy can again grow back into its ancient role as the science of science. 

One of the most gratifyingly clear definitions of philosophy of which I know is that of R. G. Collingwood from his paper “Philosophy of History” (1930), which begins, “Philosophy is thinking about the world as a whole.” In the next section of the paper, Collingwood writes, “‘The philosophy of something’ is a legitimate phrase only when the ‘something’ in question is no mere fragment of the world, but is an aspect of the world as a whole—a universal and necessary characteristic of things.” Then in the third section, Collingwood turns to philosophy of history specifically, and argues for the universal and necessary human interest in history as the basis for the legitimacy of a philosophy of history, whereas, according to Collingwood, there can be no philosophy of horse-racing, which does not possess this universal and necessary human interest (I’m not sure that I agree with this, but leave that aside for the time being).

Collingwood’s definition of philosophy and what can legitimately serve as a philosophy of something has important implications for the parasitic expansion of philosophy as enabled by the expansion of science. I don’t think there is any question but that philosophy of science is a legitimate philosophical undertaking and possesses the same universal and necessary characteristics that Collingwood identified in the philosophy of history. Could a philosophy of paleolichenology also possess the same universal and necessary characteristics? Would paleolichenology be, “…pregnant with philosophical truths that [the philosopher] cannot learn from another source”?

Certainly science does not cease to be science as it focuses on a narrow specialization, but do narrower specializations involve any particular insight into the world not offered by science simpliciter? Suppose we take this question and apply it reflexively to history. There is history simpliciter, which is presumptively the object of the philosophy of history, but are there (or should there be), philosophies of specialized subdisciplines within history? Hegel divided history into original history, reflective history, and philosophic history. Nietzsche divided history into the monumental, the antiquarian, and the critical. As divisions in history drawn by philosophers, all of these strike me as being of philosophical interest. Hegel further subdivided reflective history into universal history, pragmatic history, critical history, and specialized history. With the latter we have arrived at the more familiar decompositions of history into domains like art history, political history, environmental history, and so on. Here we are presented with the same difficulty as we saw with the relationship of science simpliciter to its specialized subdisciplines: the relationship of history (and philosophy of history) to its specialized subdisciplines. History does not cease to be history when it is focused on a narrow subdivision, but do these reveal what cannot be learned from another source?

I would say that, both in the cases of science and history, there are instances when a narrow focus reveals insights not otherwise obtained, but this is not invariably the case. Thus whether a given subdivision of a discipline can reveal new insights can only be determined by studying the subdivision to determine its relative fruitfulness for philosophical investigation.

Just as we do not know if the subdivision of science into further specializations can be carried on indefinitely, or whether it must eventually come to a halt, so too we do not know if the expansion of scientific knowledge will continue indefinitely, or whether the expansion of knowledge will continue to drive the further expansion of the unknown that had distressed Shapley. Science could be exhausted when the empirical world has been studied to its limit, and in the finite cosmos defined by the consequences of the big bang, this is a very real possibility. But if our universe is part of a larger and more extensive cosmological system, and the big bang is but our big bang—one big bang among many—then there would seem to be no limit to the expansion of scientific knowledge because there would be no limit to the universe; there would always be further reaches of the empirical world not yet studied.

However, even contemplating the infinitude of the universe, science might still be exhausted if the uniformity of nature—a fundamental presupposition of science—holds at the largest scales. If studying a part of the universe reveals to us the nature of the whole, and the nature of reality is purely iterative, then even an infinitistic universe could be exhausted for scientific knowledge. However, it would not be exhausted for experience. If a conscious being could sustain and perpetuate itself in an infinite universe, it could travel infinitely in the cosmos without experiencing any perfect repetition of experience, and this in itself could be the datum of some science. I would hesitate to call this datum psychology, as we do not know if an infinitely old being would have anything like what we call a psychology, even if it constitutes a form of conscious cognition. Whatever this lived experience would be, if could be self-reflexively the source of unending scientific knowledge.

In so far as an infinitely old being continuing to have experiences constitutes a history, the possibility of ongoing scientific knowledge at this extreme, at this farthest edge of knowledge, would be historical knowledge. This is similar to my line of reasoning a few years ago when I wrote Who will read the Encyclopedia Galactica? In this essay I imagined Dyson’s eternal intelligence with nothing to work upon after the cessation of most physical processes other than the historical records of the earlier history of the universe. Thus Dyson’s eternal intelligence is essentially an historian. Now I see that the experience of the eternal intelligence itself could be an object of knowledge, meaning that the history that it could contemplate could include its own history, this being a further exemplification of infinitistic historiography. In this case, the known could increase exponentially even as the unknown continues to increase exponentially, and so on, world without end.

Harlow Shapley

[lycomorpha]

So... I'm drawing video game botany right now...

This post is about plants and games. And OK, I’m me, so there’s lichen and fungi in here too. But broadly speaking, welcome to something about botany – because that’s where most of my own art is going right now. (Well, and some work art too, but look on the bright side inverte-friends… At least I’m not drawing chordates lol!) Tbh I’m making this post so I can point at something when anyone asks why the whole entire fuck I’m suddenly drawing plants, fungi, and lichen associated with particular video games. (I have limited spoons so I only wanna explain things once, don’t judge me.)

Assassin’s Creed Valhalla (Ubisoft) - Eivor investigating regional flora. It’s a little known fact that Eivor is well into her botany (incl mycology and lichenology)

The coronavirus pandemic lockdowns have been stressful for all of us, and for lots of different reasons. For me, the work I’m getting is a lot more sporadic, and it’s hard to plan ahead for any length of time. I don’t know what I’ll be doing in 6 weeks’ time, let alone 6 months. I feel like I can’t start much because I don’t know what I’ll be doing when, or for how long. I know lots of people are in the same situation, and that I’m lucky to have relatively safe housing etc, but yk… It still sucks. And I’ve got the same worries as many folks do about family and friends, accessing healthcare for chronic conditions during all the mayhem, etc. So, my regular vanilla anxiety/depressive disorders have been supplemented by a new and [checks notes] ‘exciting’ flavour of pandemic-induced worry.

But in this pandemic-anxiety-void, video game botany has sorta stepped in to make me feel a bit more stable. & Yes, it’s lichenology and mycology too & not just those limelight-hogging vascular plants (don’t @ me myco-people.)

There’s a lotta nice lichen in ACV. I’m just saying.

Playing video games isn’t something I talk about a lot online. But FWIW, I love open world RPG games with lots of natural environmental features. I play on a PC shared with my lovely other half, and we play the same games taking turns to drive, and talking a lot about the worlds we find ourselves in. I enjoy thinking about how plants and animals in game worlds relate to the real world. I love to ponder which aspects of wildlife closely resemble reality and, where there are differences, whether they’re an artifact or accident, or if they’re deliberate e.g. to facilitate an interaction. Some differences between real-world species and video game representations seem incidental, but others have an obvious practical benefit. Take poison dart frogs in Shadow of the Tomb Raider. In reality, many of these frogs are smaller than they appear in the game, but a player needs to be able to spot them and interact with them. So, it’s easy to think of a reason why that difference in scale might occur – having a creature be the size of Lara Croft’s thumbnail ain’t gonna help me find the chuffing thing while playing. Where fictional species exist, I also like to consider why they might have specific biological features and if/how that makes them suited to the world they appear in.

Anyway, at some point during the pandemic this all spilled over, and I started drawing all this video game botanical shit, because it made me less stressed out. (& You have to admit… It is somewhat on brand for the only fan art I’ve done to be fungi, lichen, and plants.)

Medicinal Valley’s blush from Horizon Zero Dawn (Guerilla Games)

I am not sure why, but it’s become my personal pandemic thing. Maybe it’s because video games have been my main source of trees/lichen/plants/bugs/etc to look at during lockdown when I can’t go out much. Although chronic illness/spoonie life keeps me in more than most anyway so idk… Maybe it’s because some of these species are comfortingly familiar; currently I’m playing Assassin’s Creed Valhalla, and given I live in England I can relate to what most of the fungi, lichen, plants, and trees in that game look like in real life… Because they’re literally right outside my door!

Since Horizon Zero Dawn came out for PC I also got into that, and with my beloved friend Dr Maria Christodoulou I’ve started thinking about the fictional species of plants found there. All the useable plants in Horizon Zero dawn seem to be based on extant species, so we have a starting point to think about each one. I’m a visual artist and a former pharmacologist. Maria is a botanist and a biostatistician. We can use a variety of expertise to question how the species we know today might have adapted, and what a fictional species might need to survive in a post-apocalyptic habitat where it could potentially be stomped on by machines, as well as eaten by humans and other animals. It’s a perfect Sunday project because it breaks into nice discrete chunks; we can think about each plant and its different features one at a time. It doesn’t have to be done to any particular timescale either - games aren’t going to suddenly disappear if paid work gets hairy and weekends get lost in it for a few weeks.

Sketch & finished drawing of one of the interactable fungi from AC Valhalla

So, I guess I’ll be drawing/posting about fungi, plants, and lichen I recognise in AC Valhalla at some point. I’ll also be sharing work I make with Maria to create field notes and sketches of the medicinal plants in Horizon Zero Dawn, from the perspective of people in the different human tribes in the game. And while it’s not my usual bug-fest, you can bet your butts the moment I get the *merest hint* of an opportunity to shoehorn insects into the discussion, I will be all over it. Anyway, thassit. Please take care of yourselves and each other as much as you can right now, and expect some botany soon xx

[lichenloglichenblog]

How a Guy From a Montana Trailer Park Overturned 150 Years of Biology

We here at the lichenloglichenblog encourage you to read this.

Biology textbooks tell us that lichens are alliances between two organisms—a fungus and an alga. They are wrong.

ED YONG, JUL 21, 2016 SCIENCE

In 1995, if you had told Toby Spribille that he’d eventually overthrow a scientific idea that’s been the stuff of textbooks for 150 years, he would have laughed at you. Back then, his life seemed constrained to a very different path. He was raised in a Montana trailer park, and home-schooled by what he now describes as a “fundamentalist cult.” At a young age, he fell in love with science, but had no way of feeding that love. He longed to break away from his roots and get a proper education.

At 19, he got a job at a local forestry service. Within a few years, he had earned enough to leave home. His meager savings and non-existent grades meant that no American university would take him, so Spribille looked to Europe.

Thanks to his family background, he could speak German, and he had heard that many universities there charged no tuition fees. His missing qualifications were still a problem, but one that the University of Gottingen decided to overlook. “They said that under exceptional circumstances, they could enroll a few people every year without transcripts,” says Spribille. “That was the bottleneck of my life.”

Throughout his undergraduate and postgraduate work, Spribille became an expert on the organisms that had grabbed his attention during his time in the Montana forests—lichens.

You’ve seen lichens before, but unlike Spribille, you may have ignored them. They grow on logs, cling to bark, smother stones. At first glance, they look messy and undeserving of attention. On closer inspection, they are astonishingly beautiful. They can look like flecks of peeling paint, or coralline branches, or dustings of powder, or lettuce-like fronds, or wriggling worms, or cups that a pixie might drink from. They’re also extremely tough. They grow in the most inhospitable parts of the planet, where no plant or animal can survive.

Lichens have an important place in biology. In the 1860s, scientists thought that they were plants. But in 1868, a Swiss botanist named Simon Schwendener revealed that they’re composite organisms, consisting of fungi that live in partnership with microscopic algae. This “dual hypothesis” was met with indignation: it went against the impetus to put living things in clear and discrete buckets. The backlash only collapsed when Schwendener and others, with good microscopes and careful hands, managed to tease the two partners apart.

Schwendener wrongly thought that the fungus had “enslaved” the alga, but others showed that the two cooperate. The alga uses sunlight to make nutrients for the fungus, while the fungus provides minerals, water, and shelter. This kind of mutually beneficial relationship was unheard of, and required a new word. Two Germans, Albert Frank and Anton de Bary, provided the perfect one—symbiosis, from the Greek for ‘together’ and ‘living’.

“That was the eureka moment. That’s when I leaned back in my chair.”

When we think about the microbes that influence the health of humans and other animals, the algae that provide coral reefs with energy, the mitochondria that power our cells, the gut bacteria that allow cows to digest their food, or the probiotic products that line supermarket shelves—all of that can be traced to the birth of the symbiosis as a concept. And symbiosis, in turn, began with lichens.

In the 150 years since Schwendener, biologists have tried in vain to grow lichens in laboratories. Whenever they artificially united the fungus and the alga, the two partners would never fully recreate their natural structures. It was as if something was missing—and Spribille might have discovered it.

He has shown that largest and most species-rich group of lichens are not alliances between two organisms, as every scientist since Schwendener has claimed. Instead, they’re alliances between three. All this time, a second type of fungus has been hiding in plain view.  

“There’s been over 140 years of microscopy,” says Spribille. “The idea that there’s something so fundamental that people have been missing is stunning.”  

The path to this discovery began in 2011, when Spribille, now armed with a doctorate, returned to Montana. He joined the lab of symbiosis specialist John McCutcheon, who convinced him to supplement his formidable natural history skills with some know-how in modern genetics.

The duo started studying two local lichens that are common in local forests and hang from branches like unruly wigs. One is yellow because it makes a strong poison called vulpinic acid; the other lacks this toxin and is dark brown. They clearly look different, and had been classified as separate species for almost a century. But recent studies had suggested that they’re actually the same fungus, partnered with the same alga. So why are they different?

To find out, Spribille analyzed which genes the two lichens were activating. He found no differences. Then, he realized that he was searching too narrowly. Lichenologists all thought that the fungi in the partnership belonged to a group called the ascomycetes—so Spribille had only searched for ascomycete genes. Almost on a whim, he broadened his search to the entire fungal kingdom, and found something bizarre. A lot of the genes that were activated in the lichens belonged to a fungus from an entirely different group—the basidiomycetes. “That didn’t look right,” says McCutcheon. “It took a lot of time to figure out.”

At first, the duo figured that a basidiomycete fungus was growing on the lichens. Perhaps it was just a contaminant, a speck of microbial fluff that had landed on the specimens. Or it might have been a pathogen, a fungus that was infecting the lichens and causing disease. It might simply have been a false alarm. (Such things happen: genetic algorithms have misidentified plague bacteria on the New York subway, platypuses in Virginia tomato fields, and seals in Vietnamese forests.)

But when Spribille removed all the basidiomycete genes from his data, everything that related to the presence of vulpinic acid also disappeared. “That was the eureka moment,” he says. “That’s when I leaned back in my chair.” That’s when he began to suspect that the basidiomycete was actually part of the lichens—present in both types, but especially abundant in the yellow toxic one.

“Toby took huge risks for many years. And he changed the field.”

And not just in these two types, either. Throughout his career, Spribille had collected some 45,000 samples of lichens. He began screening these, from many different lineages and continents. And in almost all the macrolichens—the world’s most species-rich group—he found the genes of basidiomycete fungi. They were everywhere. Now, he needed to see them with his own eyes.

Down a microscope, a lichen looks like a loaf of ciabatta: it has a stiff, dense crust surrounding a spongy, loose interior. The alga is embedded in the thick crust. The familiar ascomycete fungus is there too, but it branches inwards, creating the spongy interior. And the basidiomycetes? They’re in the outermost part of the crust, surrounding the other two partners. “They’re everywhere in that outer layer,” says Spribille.

Despite their seemingly obvious location, it took around five years to find them. They’re embedded in a matrix of sugars, as if someone had plastered over them. To see them, Spribille bought laundry detergent from Wal-Mart and used it to very carefully strip that matrix away.

And even when the basidiomycetes were exposed, they weren’t easy to identify. They look exactly like a cross-section from one of the ascomycete branches. Unless you know what you’re looking for, there’s no reason why you’d think there are two fungi there, rather than one—which is why no one realised for 150 years. Spribille only worked out what was happening by labeling each of the three partners with different fluorescent molecules, which glowed red, green, and blue respectively. Only then did the trinity become clear.

“The findings overthrow the two-organism paradigm,” says Sarah Watkinson from the University of Oxford. “Textbook definitions of lichens may have to be revised.”

“It makes lichens all the more remarkable,” adds Nick Talbot from the University of Exeter. “We now see that they require two different kinds of fungi and an algal species. If the right combination meet together on a rock or twig, then a lichen will form, and this will result in the large and complex plant-like organisms that we see on trees and rocks very commonly.  The mechanism by which this symbiotic association occurs is completely unknown and remains a real mystery.”

Based on the locations of the two fungi, it’s possible that the basidiomycete influences the growth of the other fungus, inducing it to create the lichen’s stiff crust. Perhaps by using all three partners, lichenologists will finally be able to grow these organisms in the lab.

In the Montana lichens that Spribille studied, the basidiomycete obviously goes hand-in-hand with vulpinic acid. But is it eating the acid, manufacturing it, or unlocking the ability to make it in the other fungus? If it’s the latter, “the implications go beyond lichenology,” says Watkinson. Lichens are alluring targets for ‘bioprospectors’, who scour nature for substances that might be medically useful to us. And new basidiomycetes are part of an entirely new group, separated from their closest known relatives by 200 million years ago. All kinds of beneficial chemicals might lie within their cells.

“But really, we don’t know what they do,” says McCutcheon. “And given their existence, we don’t really know what the ascomycetes do, either.” Everything that’s been attributed to them might actually be due to the other fungus. Many of the fundamentals of lichenology will need to be checked, and perhaps re-written. “Toby took huge risks for many years,” says McCutcheon. “And he changed the field.”

But he didn’t work alone, Watkinson notes. His discovery wouldn’t have been possible without the entire team, who combined their individual expertise in natural history, genomics, microscopy, and more. That’s a theme that resonates throughout the history of symbiosis research—it takes an alliance of researchers to uncover nature’s most intimate partnerships.

This part is from Lichenloglichenblog:

Lichen on!

[botanizing]

Categorizing the Uncategorizable

(or, the divine is stored in the infinite mystery of life on earth)

I swear this is about lichen genomics but it’s not not about gender

Recently I was asked “What do you think of species described only from DNA?” That is to say, species not morphologically distinguishable from others but when tested genetically, show up with results different enough that some people have decided they count as a different entity.

Over and over again in my (short) career as a biologist I keep running across the question “What is a species, really?” It doesn’t seem like something that would be the subject of ongoing debate. We should be able to tell the difference between different types of creatures, right? Even if they look similar, if they can’t breed and produce fertile offspring, they are not considered to be the same species. This works for most vertebrates, as far as I know, but a brief glance at botany makes everything infinitely more complicated. Different species of plants are absolutely capable of interbreeding and producing fertile hybrids (that’s how we get so many fun cultivars to grow in our gardens). And by the time one considers lichens, the concept of “species” is more of a vague suggestion, or a shorthand we’ve all agreed to use while acknowledging its drawbacks.

Lichens are always already at least two species – a fungus and a photosynthetic partner (green algae or cyanobacteria) – combined into one “body” that looks unlike either partner would if grown separately. They are recognizable entities, a whole that is more than the sum of its parts, but the parts are always visible in cross section, or in the genomic data. And this is without even mentioning the myriad species of other fungi and bacteria simmering in the lichenological stew. The lichenological community decided to use the Latin name of the fungal component to refer to the whole lichen, since the fungus makes up the majority of the biomass and seemed to determine the morphology while the photosynthetic partner was more or less along for the ride. The same species of alga is also known to partner with different fungi to form different lichens, which was taken as evidence of its relative non-selectiveness versus the fungal partner’s specificity (something that has more recently been called into question). Regardless of one’s stance on the fungi-centric model, we can all agree that the idea that one genome=one species does not apply to lichens.

So why do we call lichens “species” anyway? Well, what else would we call them? They are distinct entities that live and reproduce and play particular roles in an ecosystem. They can be identified by their distinctive morphological features. And when so much work in biology relies upon knowing “what lives where”, we need to have a name for the “what”. So, we’ve given imperfect names to capture some aspect of our infinitely interconnected world. This is something we need to do, for the sake of communication.

But just like words can never quite capture elusive and complex feelings, grouping a set of organisms together and calling them a Latin binomial will never quite express the reality. We are only human, after all, and as much as we learn about the world around us, we are limited in the scope of what we can understand. I don’t think we will ever unravel every mystery in the natural world, and that’s not a bad thing. The more we learn, the more questions we have. What I’m getting at is that we can never have an omniscient view of every single biological interaction ever. We research and study and we get an approximation. It might be a very good approximation that answers our questions and contributes to our body of knowledge, but it is still an approximation impacted by the limits of our perception and our implicit biases.

The way I see it, using our human perspective to apply categories to the natural world is always a functional endeavor. We do not name lichens because we think this is what the lichen would call itself, or even what god would call the lichen. We name them because we are interested in them and we need something to call them when we talk to other humans. Endangered species lists are just that – lists of species. We wouldn’t be able to protect rare lichens without assigning them a species and putting them on the list. There will always be exceptions, and edges, and individuals that don’t quite fit. Evolution is always happening; we see populations that are not quite different enough to be their own species, but we can tell that one day, thousands or millions of years from now, maybe they will be. What do we name these? Perhaps a subspecies or a variety, perhaps not. The important thing is not that we’ve discovered the One Truth of the Universe, but that we are close enough to accomplish what we need to accomplish.

But are DNA sequences enough to define a species? I think not. We must consider again not what a species is, but why we describe species. We do not describe species for the sake of making up a name for a slightly different DNA sequence, we do it to categorize an entity we are interested in. If two lichens look the same, contain the same chemicals, and fill the same ecological niche, are they really different? And if they are, are they different enough to matter?

This is not an indictment of the act of naming species, or a call to stop trying to study and understand what appears unknown and unknowable. It is simply an encouragement to think more critically about categories and why we categorize. Why is it important to tell these two things apart? In what context would it become important? What would it look like to treat them the same? How much more can we learn from thinking consciously and openmindedly about what we mean when we say “this is a species”?

[botanyshitposts]

What is the most cursed thing you’ve come across?

dude i come across cursed things like once a week, more than that if im in a specific swing of hyperfixtating on a very niche subject. this entire blog is just the cursed underbelly of botany and occasionally mycology and lichenology. whenever i say something on here ‘makes me uncomfortable/scares me’, what i actually mean is that i was flooded with an intense amount of serotonin from learning about it to the point where my breath kind of caught in my chest for a second and i was forced to reflect on how fucking bizarre this entire kingdom is in the grand scheme of our existence, after which my three brain cells compressed my feelings down by just stamping ‘cursed’ across it like the mythbusters mythbusting stamp and posting it here

other than that, i have a test over secretory structures and leaves tomorrow in plant anatomy and im ruminating over the fact that gingkos have internal mucilage cavities between some of the venation in their leaves. theyre kind of hard to see even under a microscope, but if the leaf is stained right, once you know what you’re looking for it’s like ‘oh. what the hell’. anyway we looked at it in lab and it was on the practice practical and during the review session friday i was like, ‘hey, what are those even for?’ because you know, like, one would think that aside from being an incredibly prehistoric plant with a very distinctive leaf shape there really wouldn’t be any reason for them to have like....weird mucus cavities in their leaves (as normal leaves don’t? why would you need mucus?), but my professor was just like. ¯\_(ツ)_/¯. so yeah thats pretty cursed 

[botanizing]

hoping I don't get in trouble for accidentally hoarding a Swedish Bryoria specimen in my basement for two years...

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welcome to the Peltigera Zone™... it's where I realize 99% of the green Peltigeras I photographed are all aphthosa

[botanizing]

don’t even talk to me about understory vegetation of you’re not going to ID your lichens to species, Robert