#or 'cyanobacteria' as google says

[six-of-ravens]

oh so spirulina is. seaweed. ok ok.

[apocalypticvalraven]

Delicious in Dungeon in The Kitchen

So... I was struck by the thought that I kinda wish some food nerd would go through the Dungeon Meshi dishes and analyze them and sort of give a "this is the real world thing they're making" run down.

And then I realized I'm a food nerd that can do research.

So.

We're gonna try this out, starting with Volume 1. I don't promise that I know everything about cooking. I don't promise I'll always be able to make the thing I'm looking at (I am broke, and I don't have my own kitchen). But I can at least look at a dish and figure out what they're doing and how to replicate it, at least sorta.

Dungeon Meshi Volume 1-- Huge Scorpion and Walking Mushroom Hot Pot

The two main components of this dish are the Huge Scorpion and Walking Mushroom.

Walking Mushroom

Looking at the images in the manga, Walking Mushroom seems to just... be a mushroom that can walk around. There are no organs, the interior seems pretty uniform in substance...

Like, literally, that's exactly what sliced mushrooms look like. Senshi cuts the mushroom into ~4" strips (judging by their size next to the small cabbage-like vegetable, and comparing those plants to his hand in the image of him gathering them. I am assuming dwarf hands are roughly the same size as human hands).

There's a variety of edible mushroom that is probably as close as we're going to get to the size of a Walking Mushroom, growing a cap up to 3' wide, but it seems to only grow in termite mounds in a very specific part of the African continent (please forgive my USAmerican, White education leading me to not being able to identify the specific region), so... if you can get that at all, it's probably crazy expensive (as it should be, unless you're literally getting it from the mounds or local markets yourself). Portobello or similar large culinary mushrooms are probably just fine. The Mushroom Feet are literally just mushrooms, so no worries there.

Huge Scorpion

Ok, so... there is a difference between arachnids and crustaceans. As a start, arachnids have book lungs and crustaceans have gills. Arachnid guts are different from crustacean guts, just because of environment. Hell, crustacean limbs grow differently from arachnid limbs.

That said, everything I see in Dungeon Meshi implies that, from a culinary standpoint, Huge Scorpion is a crustacean-

So, really, it's just a big lobster. Take a lobster, cut off its legs, antennae, and the tail fluke, and you're going to see something that looks pretty similar to the huge scorpion in Dungeon Meshi.

Seaweed

Next is seaweed, which... is just a thing, but also kind of an imprecise term, I think. Basically, "seaweed" just refers to any marine algae that is multicellular and macroscopic (big enough to see). Arctic Moss seems to be a real thing which refers to a couple things- the aquatic moss Calliergon giganteum and the terrestrial lichen in the genus of Cladonia, which includes Reindeer Lichen.

Reindeer lichen is edible, in a number of ways, but it's also not seaweed. So we look at Calliergon giganteum. I cannot get an answer as to whether this particular variety of moss is edible. So... fuck it, say Senshi used Reindeer Lichen, at least we know that's edible.

"Star Jelly" is... I don't know. The main result I find when googling it is that it's the sort of general term for various slimes that show up on lawns and other vegetation, etc. Which means it could be anything from amphibian spawning jelly to who the fuck knows what.

However, one thing it could be is a cyanobacteria known as Fat Choy, a commonly used "vegetable" in Chinese Cuisine:

Looks like jelly? Yep. Looks weird enough that you might imagine it comes from a star? Yep. Edible? Yes!

(I mean, maybe don't eat a ton of it, or get it from irreputable sources. At least some Fat Choy contains a toxic amino acid which may or may not have negative health effects, but I'm not a doctor, so all I'm saying is "be aware of this." It's an expensive delicacy, which means that it is a particularly lucrative target for counterfeiters, and China does not have strong, or strongly enforced, food safety laws).

The Hard Stuff

So that leaves "Invertatoes" and "Dried Slime."

Neither of which seem to have a good direct analogue to the real world. Well... sorta.

Invertatoes seems to refer to the plants. The name calls to mind potatoes, and potatoes do indeed grow in the ground and are starchy. It's probably fair to just use any kind of starchy tuber as the "invertatoes." Maybe cassava, since those are large enough that it's at least somewhat believable that "Fantasy Land Cassava" could look like that (although that doesn't fit the "these are normal plants that grow upside down" unless we're being really generous).

The problem is that it's sort of implied that the cabbage-like vegetable seen in the hot pot comes from the same plant, and everything from a potato plant other than the potato itself is toxic. They also don't look like that.

I literally don't know what those cabbage/lettuce-like leafy vegetables are. They're not seaweed, because the two varieties called out definitely don't look like that. They're not, so far as I can tell, the greens of any kind of starchy tuber--

EXCEPT.

So, I was taking one last look at tubers to see if I could find something that seemed to match, and I think Invertatoes could be likened to something similar to chicory. Particularly endives. I never knew endives were related to chicory (ie, "that thing that I'm aware is popular as a coffee substitute in the South, but I don't have much desire to try it, and I wonder if it even has caffeine..."), but, apparently, yeah. Endives are a member of the chicory genus.

So, yeah, lets say that Invertatoes are a sort of fantasy plant similar to the various members of the chicory genus. The trunk can be replicated with chicory root, and the leaves with endives.

That leaves Dried Slime. Dried Slime makes up the noodles in the hot pot, which implies that the noodles are gelatinous, and probably low in gluten. Senshi's explanation of the slime makes me want to think of it as a macro-unicellular lifeform, but... I'm not sure that's accurate.

While it's definitely not an accurate way to describe a jellyfish, I could definitely see a non-biologist describing jellyfish in a way similar to the way Senshi describes the slime. I could also see some fantasy terrestrial jellyfish thing hunting in a similar manner to the slime. Moreover, there are edible varieties of jellyfish, and they're processed in a manner very similar to what Senshi describes for processing slimes. And one way of preparing edible jellyfish is to thinly slice it into noodles.

Hot Pots

I... think this is using a very specifically Japanese sense of "hot pot" (which makes sense), because in Japan, hot pot can refer to a dish called nabemono, while in general, hot pot refers to a particular kind of dining in China where you get a pot full of boiling stock/broth and a bunch of raw ingredients, and you put the stuff you want into the broth at the table. Nabemono is more of "put a bunch of stuff in a pot, and cook it. Serve it boiling." Which is to say, it's soup.

Senshi puts the scorpion meat and mushroom into a pot on its own, and lets it start boiling-

Then, while it's boiling, he goes and finds other ingredients, coming back with the invertatoes and the slime. The two are prepared simply-

Seasoning isn't included in the ingredients, but I can understand this as a choice for presentation. We do see Senshi add something to the broth after tasting it, and I think it's fair to assume it's one of soy sauce, mirin, fish sauce, or similar. I think it's actually really interesting that we see Senshi add seasoning, but we're not told what it is-

Because... that's cooking. You can follow a recipe, but ultimately, you need to taste your cooking and make your own decisions. Senshi lets the soup cook, tastes the broth, decides it needs something, and gives it a bit of time to let the flavors meld before serving it up.

Dungeon Meshi Lobster and Mushroom Hot Pot

So, we're looking at something like this for the "Huge Scorpion and Walking Mushroom Hot Pot"--

Lobster- ~5 lbs or more (a 1 lb lobster yields about 4 oz of actual meat, which is a single serving), cut into large slices

Portobello- 2 mushrooms large diced, 2 left whole with the caps scored

Reindeer Lichen and Fat Choy- to taste

Chicory Roots- ~1 cup, diced

Endive greens- ~2 cups

Jellyfish, thin sliced- as much as you like

Add lobster and mushrooms to water, and allow to boil. While it comes to a boil, prepare the other ingredients, then add to the water. Let the soup come to a full boil, then reduce heat and simmer for 15 minutes to an hour (can simmer longer, but this will affect the texture of the ingredients. Longer simmering will result in more melding of flavors, but also degraded solid parts).

Taste the broth. It will likely need salt and acid, which could come in a variety of forms, such as kosher salt and lemon juice, soy sauce and mirin/rice vinegar, oyster/fish sauce, or something else. Go with your gut and your taste buds..

[the-tin-dog]

you're projecting, I don't know anything about defending a transphobe, I was just saying that males (inducing myself) where never meant to exist, if anything I'm pro trans because It would be the way of fixing that defect, in fact "The Y chromosome is the most gene-deficient chromosome" or in other words a Genetic disorders so yes to say that the Y chromosome is defective isn't wrong, hell to add on it to you be hard pressed to find any example of testosterone (or masculinity) being a good thing or not toxic in anyway

Right so you’re grossly misunderstanding genetics AND you don’t even know the context of the original conversation. 10/10 great reading comprehension skills there buddy.

Pretty hard to project anything when the entire conversation you decided to stir up (on anon, like a coward), wasn’t about emotions or trauma or any of the possible things that can be projected. It was about genetic science and your Inability to understand a mutation vs a defect. The Y chromosome being the most gene-deficient doesn’t make it defective by nature. It makes it *prone* to deficiencies in a way we don’t fully understand yet (if you actually read the whole article on the number one google search you pulled that quote from you’d know that). The brain isn’t defective because it’s prone to mental illness, the lungs aren’t defective because they’re prone to cancer, the Y chromosome isn’t defective because it’s prone to genetic disease.

Look dude, I don’t need someone too scared to come off anon to spout half-assed genetic misunderstandings that you got from the preview of the first google result that shows up when you search “Y chromosome defective”.

Also “I’m pro trans because it would mean fixing the defect” is literally eugenics rhetoric. Nothing is broken. You can’t “fix” genetics. Fuck off dude. The Y chromosome mutated from other chromosomes. Like literally every other part of genetics. Again, just because we aren’t Photosynthetic Cyanobacteria doesn’t make us defective.

If you knew how to read, you would’ve notice that the full article of that lazily found google preview goes on to say that the Y chromosome is NOT a degenerated X chromosome but one that contains critical survival genes.

Much like Cyanobacteria, or Mitochondria, or Lungs, it evolved into a New Thing. Because mutations and evolution are how new things get made.

[what-plant-metaphor-am-i]

I don’t know if this has been picked up on before, but I am losing my mind over it so I want to share my journey with you. May I present my descent into: Zen’s Algae Report.

It all started when I paused the beginning of episode 14 to see what Zen was writing about and was amazed and highly entertained to find that it seemed to be a report on, of all things, aquatic algae.

This naturally piqued my interest, so, being a loveable-yet-rather-obsessive-scamp with a passion for words and too much time on my hands, I set to work attempting to transcribe what he wrote in that brief scene.

In the transcription I put hyphens (---) wherever the next part was not visible and put asterisks around words I believed to have figured out, though they were partially obscured (Zen’s hand moves in the scene so more words were revealed). Multiple asterisks just mean I have a note about it at the end. 👍

"--- erie could experience one --- severe harmful** algal bloom --- a potential measure of 8.7 on --- the severity index, according --- oceanographic institution.

--- which have different colors *and textures*. Blooms can appear in a variety of colors that depend on the algal species. The aquatic ecosystem and organism --- cyanobacterial blooms, the formal name for the blue-green algae, are the problem here. Their presence means cities and local governments must *spend more* to --- water, puts swimmers in *high concentration*”.***

**this was written as one word - 'severeharmful' - and had me stumped for a while :') I like the thought of this word existing in the ans-verse and the characters using it :D

***after spending too much time rewinding and pausing to see parts of words as zen's hand moves to reveal them, I could make out 'hi --- oncentrat'. I believe it's meant to say 'high concentration' but WHO KNOWS

It was only AFTER typing all this that I found out The Truth.

The first half-word that was at the top of the page was bugging me because I couldn’t figure out the letters. So, being the loveable-yet-slightly-perfectionistic-scamp that I am, I racked my brains over it until I realised it could read as “-ake”. The following word, “erie,” hadn’t made sense at all, so I couldn’t see how I could use it to try to figure out what this “-ake” word before it could be. I decided to google the word “erie” in case it did mean something that I was unaware of. And guess what I found?

“Lake Erie” is apparently the fourth-largest lake (by surface area) of the five Great Lakes in North America. This may be common knowledge to Americans(?) but as a loveable-yet-entirely-European-scamp this was news to me. I was obviously thrilled as this worked for both words and made sense, but I was also surprised that Zen appeared to be writing about a very real, and not ans-verse, American lake. 🤔

I wanted to see just how much of His Algae-Loving Highness Zen’s report was true, so I searched for “lake erie cyanobacterial algae”

After getting over the humiliation of being grammatically corrected, I was thrilled at this confirmation that, yes, Lake Erie does in fact host the infamous cyanobacteria(l) algae from the report! 🎉 but now the question remained: Why the heck did they bother to make this random paragraph about lake algae and translate it into Clarinese??

WELL. I copy and pasted a line from the report along with my previous searches and....

Surprise surprise, an exact same phrase from the report came up in a science news website! (You can imagine I was ricocheting off the walls at this point) Which led to this:

The parts circled in yellow are directly copied into Zen’s report. (It is currently September, hence the apprehensive red addition) Honestly? I couldn’t stop laughing.

(Zen you can’t hand that report in, there’s a little something called ‘copyright’)

So, why did the animation team decide to lift this text from weather.com? What relevance does it have to the story, let alone Zen’s princely duties? Could they have gotten away with it too, if it weren’t for this loveable-yet-meddling-scamp? I cannot say, but if anyone ever finds out more, please do let me know!

I’m going to leave it there, I just needed to get this out of my system, it was certainly a ride. 😂

Something Extra!

An example of a situation where the word ‘severeharmful’ may be used:

Kiki: You fight like an algal bloom.

Mitsuhide: !! D: No need to be so severeharmful!

Zen: Well, actually, if she is comparing you to a cyanobacterial algal bloom then that implies you have a potential measure of 8.7 on the severity index, according to the oceanographic institution.

Mitsuhide:

Zen: Which would mean you fight pretty well, I guess.

Mitsuhide: *turns to Kiki with question marks for eyes*

Kiki: Precisely, I thought that was an obvious reference, given the green-blue shade of your hair, the exact colour of certain cyanobacterial algal blooms.

Mitsuhide: WHERE DID ALL OF THIS ALGAE KNOWLEDGE COME FROM

*shirayuki sneezes somewhere*

[mercurialbadger]

Metabolic engineering of Green Dudes Part 2

The next article, by popular demand, covers the limonene synthesis.

When you search for ‘limonene biosynthesis‘ either in PubMed or in Google Scholar, the two articles that pop out first are a review on advances in production of limonene in a huge variety of organisms and a research article on prototyping metabolic pathways in vitro before putting them into the cell.

They are both kinda hard to read, even if they are good.

The other article showcases how even good journals sometimes publish things that would be more fitting into an advertising email than in a research journal. In this case, authors are pushing forward their neural network, while diminishing the importance of actual human ingenuity in these sorts of things.

So, for today’s journal club we chose this article for its elegant approach and important insights.

Engineering of cyanobacteria for the photosynthetic production of limonene from CO2

Let’s start with the abstract!

Isoprenoids, major secondary metabolites in many organisms, are utilized in various applications. We constructed a model photosynthetic production system for limonene, a volatile isoprenoid, using a unicellular cyanobacterium that expresses the plant limonene synthase. This system produces limonene photosynthetically at a nearly constant rate and that can be efficiently recovered using a gas-stripping method. This production does not affect the growth of the cyanobacteria and is markedly enhanced by overexpression of three enzymes in the intrinsic pathway to provide the precursor of limonene, geranyl pyrophosphate. The photosynthetic production of limonene in our system is more or less sustained from the linear to stationary phase of cyanobacterial growth for up to one month.

Writing is considerably worse here than in the previous article, so, like, the first sentence says basically nothing.

The second sentence tries to catch up as a result of this, and ends up rushed. They constructed model system for producing limonene in a photosynthetic bacterial system by using an enzyme found in plants.

spoiler: the photosynthetic bacterial system here is Synechocystis sp. PCC 6803 again

limonene is a valuable compound actually! Known for giving pines and oranges their distinct flavour, it also found use in cleaning industry as a renewable solvent for removing highly hydrophobic dirt, machine oil and bad odor. Being a nearly saturated aliphatic (meaning that it has no aromatic nuclei) hydrocarbon, it also can be used as fuel.

The next sentence mostly repeats the previous points, except it offhandedly points to researchers making a gas-stripping device that continuously extracts limonene from the culture.

Now, we should note that limonene in plants is an antimicrobial and antifungal compound. Does it affect our microbial culture? The next sentence says ‘no’.

This lack of strain on cells is then demonstrated as the culture kept producing limonene for a month.

The main text is written slightly better, so it's going to be a bit easier.

So, let’s move to introduction.

Fun fact also, while limonene is a monoterpene, it is still of isoprenoid biosynthetic nature. All sterols, including steroid hormones, such as cortisol, testosterone or estradiol, are triterpenes, i.e. also isoprenoids! Meaning that they can be produced entirely within the isoprenoid pathway. However, aside from making them from petroleum, plant sources are very slow to grow. Marker degradation process, for example, one that revolutionized the steroid chemical synthesis and allowed HRT to even exist for both cis and trans people, uses yams as a plant material for example.

So, of course people tried to make them in the genetically engineered organisms. And of course they started from E. coli and yeast to do it, but, then again, heterotrophic organisms live by turning organic matter into CO2, making organic matter using them is not very rational.

So, they chose a cyanobacterium for it, and used the most studied one.

So, the results are written in a very dry way. Thus, it is imperative that we look at figures. This is a metabolic pathway.

You probably remember the G3P and pyruvate from the previous article, and you might remember that phytol and carotenoids are structural moieties in the light-harvesting systems of photosynthetic organisms. Specifically, phytol is a part of chlorophylls, and carotenoids are these super-active antioxidants that give carrots their color and allow you to see at all. So, like, everything from Calvin cycle (it's the CO2 fixation cycle) and the lower right corner has to occur in the chassis organism no matter what.

Calvin cycle is when you use the carbon you got by affixing it to the ribulose to make more ribulose to affix carbon to. It's literally it. It might be called after Some Guy, but it's nothing conceptually hard. Just moving carbons around like in those children's problems of "how do you measure 5 liters of water having only a 3-liter and 1-liter bucket?"

The arrow pointing to limonene starts at GPP, standing for geranyl pyrophosphate. GPP is made by combining two "activated isoprene" blocks (DMAPP and IPP) , hence the name "isoprenoids". Isoprene is an old name for a gas that you get if you decay natural rubber, which is also an isoprenoid. It has two double carbon-carbon bonds, so it can be 'activated' by pyrophosphate group in two ways as a result. Limonene synthase is a 'magic enzyme' here, which takes the intermediate product of what is called 'primary metabolism' (you will die a lot if you do not do it) into a 'secondary metabolite' (everything else).

Well, Figure 2 is a biologist's version of those "this is going to be so tasty!!!" pictures on the culinary blogs where they post the gray dough in the least appetizing light spread thin on the ugliest dish in existence.

Of note: Cm^R and Km^R signify cassetes of antibiotic resistance to chloramphenicol and kanamycin. They can be used as selective markers, letting the strain that has it survive in the presence of said antibiotic.

Ptrc is a trc promoter. It is strong, making lots of protein. And constitutive, meaning it works always.

6xHis-tag is. Hm, it's a bit of satanic magic actually. If you put six pentagram-like amino acids (protein constituents) in a row, they will be able to bind nickel or cobalt ions, both named after demons (Nick and kobold respectively).

The second colorful sausage shows that they also expressed a cassete of usual isoprenoid pathway enzymes under a strong promoter, but like. It doesn't matter, just as insertion sites (blue arrows on a string) do not really matter. Now, for the black and white part of the figure. The pic labeled (B) is "PCR analysis of the integration of the limonene synthase using the primers 2031-9 and 2031-12". Which means that they amplified using Polymerase Chain Reaction a select part of the bacterial genome, which should contain their insert, and this part became bigger after the insertion, confirming that the insertion really happened. In the pic labeled (C) they confirm that their insert makes protein and that this protein is not immediately degraded by the cell. Pic labeled (D) sucks ass, so I am not commenting on it. So, now we know that their construction makes protein in Synechocystis, but is this protein functional?

I have absolutely no idea why they didn't put this result into the previous figure. They basically just show that an ion of the weight of limonene appears at the retention time of limonene, and is absent in the wild type strain. Whatever.

But there are many other ions here! How do we isolate limonene from this mess? And they solve it very elegantly, but also completely undersell the ingenuity of the approach. Air that we breathe is actually not very polar. Oxygen and nitrogen are monoelemental gases, carbon dioxide is perfectly symmetrical, argon is a noble gas. This means that the non-polar compounds like limonene actually would prefer to be in the air than in the water solution!

So the authors connect the air output of the culture to the cold trap (cold trap is a vessel on the path of gas that is cold and traps wanted/unwanted things by being too cold for them to be in gaseous phase) filled with octane. And all the limonene goes to the cold trap and does not poison the algae. This is genius, but also they really tried to make it look the worst way possible.

Hip Dadaist(@hypdadaist) — WHY ARE SCIENCE PAPERS LIKE THIS???

You take the stupidest and the craziest people that can still be functional, put them into an underfunded institution on the diet of deadlines, and pay them on the basis of how much papers they write. I am actually surprized that we as civilization lasted that long since the fall of the Soviet Union.

The other two figures are basically "number go up", so commenting on them seems pointless.

Discussion also sucks, aside from the calculation that they used 2.5% of cell isoprenoid synthesis by sloppily putting an unmodified enzyme under the "eh, it's going to be fine anyway" promoter. The coding sequence for the enzyme was isolated from the backyard japanese catnip their lab neighbor studied.

This is really cool because of THINK OF THE POSSIBILITIES, but also it seems like authors despaired at some point.

Like, there is probably some science fan out in the wild that will be like "you can make saturated hydrocarbons in your backyard with just sun, air and fertilizer????" and there are scientists that are like, "yeah, yeah, the clean energy ready to go whenever, we've all seen it".

That’s it for now!

Questions?

[tremella-mesenterica]

ahh hi, i just wanted to say that ive just changed my blogs name bc its not dedicated to sso anymore (even tho i still will be posting some sso related content!!) so id be weird to have my ocs name in the url.

so say goodbye to sasha beeblanket, hello to my fav fungi, commonly called witches butter!! funfact about this name, apparently there also are cyanobacteria called very similar (witchs butter)(nostoc) and theyr SO COOL LIKE SRSLY GOOGLE IT. some of its other names r spit of moon or a fallen star, like bruh, those names r amazing eh and its so so funny bc even tho the names r pretty cute the colonies of many species of those looks like snot jjkhsadasd

anywayz my point is hello im the same person, just want my main to be more personal. hope thats ok and if ur here for sso content only feel free to unfollow!! luv u i wish uall a nice day ur amazing and loved and the universe exist for u

[bassprideshops]

I’m your host, Barney Barnacle

Welcome to my fish blog! I made this space so I can talk about fish as much as I want. And I want to a lot. 

Thank you to @bouvardia-against-bourgeoisie for the fantastic icon, I love you.

Fish identifications

I post pictures of fish that myself or a fellow field crew member took during the field season in Southeast Alaska with the identification we gave it OR my own updated ID, if we got it wrong in the field. The books I have to ID at home are Coastal Fish Identification California to Alaska by Paul Humann and Ned Deloach and Pacific Northwest Sculpins, the ultimate pdf guide. I’ll definitely make separate posts about both of these because it’s what they deserve. I also use the Goog.

I put a Serotonin Rating under every ID of a fish I’ve caught. This indicates the amount of joy I experience upon catching and interacting with this specific species. 

Invertebrate identifications

Fish are number one. But everything else is number two. I’m far from an expert, but I have Guide to Marine Invertebrates by Daniel W. Gotshall. And Google.

Literally just whatever I want

Sometimes I just get really passionate about rockfish. Or the fact that nudibranchs who “photosynthesize” are actually just hosts for cyanobacteria. While they get nutrients from the bacteria, they are not actually photosynthesizing themselves. 

Please send:

Fish and invertebrate submissions

If you have a cool picture that you want me to post, say less. ID, no ID, impossible to ID, send them all. I would be absolutely honored to ID your picture for you. Again, I’m not an expert, but I have Some resources and knowledge. 

[macgyvermedical]

Thanks to the Grass Pea: A “Seeds + Permafrost + Feather” Review

Listen.

Listen.

That’s the sound of them messing with me.

Like, when season 4 comes out its going to be perfectly scientifically accurate and it’s going to come out that they’ve just been messing with me specifically this whole time. Just me. Just Ross. Just to get my reaction. They’re going to hire someone to knock on my door, slow clap for a few minutes, and leave.

It’s going to be really embarrassing.

Anyway.

Despite the lengths they go to not name the poison (literally they just call it “the poison” a lot), this was no ordinary handwavy science ep. Someone sunk time and energy into this. Not for the general public, oh no, but for people who wanted to dig in deep. People like me who were willing and really wanted to know what the hell was going on and what was at stake.

Watching this episode and digging into it on google afterwards was was like a little scavenger hunt for me. It was actually super fun ‘cause you know how much of a poison nerd I am, and I’m always up for a challenge when knowledge of a new poison is on the line!

The episode centers around the race to track down the seeds for a kind of pea plant, found otherwise only in North Korea, that supposedly contains a weaponizable chemical agent. There’s a lot of twists and turns and it turns out the seeds themselves mean nothing to the plot, but they’re still interesting and deserve some bandwidth.

I started with two clues:

Clue one was the name of the seeds:

Pisum amortium. Not to brag, but I google a lot of poisons and I was a little surprised I’d never heard of this plant. Honestly, being a legume I was kind of expecting it to be a cyanide. But cyanide is everywhere- why go to the trouble to steal these particular peas when cyanide is pretty cheap and abundant elswhere?

However, as you might imagine, it didn’t take me too very long to find out Pisum amortium wasn’t a real plant. The only things that came up in the google search were texts referring to the garden pea, Pisum sativum, in archeobotany and paleonutrition. Don’t ask me why other mentions of the garden pea didn’t come up, because none of the 10 or so articles have any mention of the word “amortium” in them at all (and literally it was just images of abstracts, no other search results). Which I found... odd.

But I put that aside. I had another clue to look into:

I kinda applaud the person who made this printout. There’s a lot to talk about in it. Let’s start at the bottom: the title in the bottom text box reads “6-Fluroro-L-Tryptophan -- L-BMAA”.  Now, accounting for what I can only assume are purposeful misspellings (though I got a few results that indicate it might be a correct spelling in Norwegian), “6-fluoro-L-tryptophan” and “L-BMAA” are real things. Different things, but real things.

Tryptophan is an essential amino acid, meaning we can’t make it ourselves and need to ingest it from food in order to survive. Our bodies use it to make the neurotransmitter/hormones serotonin and melatonin. It’s found in most animal-based food sources like meat, fish, and dairy, but is also present in brown rice and soybeans. 6-fluoro-L-tryptophan is a form of tryptophan that contains an atom of fluorine on one of its carbon rings (the “6″ and “L” just refer to the placement of various parts of this molecule). The fluorine on the molecule makes it so instead of helping create serotonin and melatonin, it inhibits their creation.

Now, that sounds bad, but as far as I can tell its effects have never been studied in humans. It is listed as an irritant and pretty standard PPE (N95 masks, gloves, etc...) is recommended to handle it. Even if humans *were* exposed to it in a meaningful way, it appears to have a relatively short half-life: when rats were injected with it, they had some disruptions in their sleep-wake cycle for about 3 hours, but that was pretty much it.

Like, yes, it’s a neurotoxin, but its *probably* not going to kill anyone. Going to the trouble of adequately distributing it is like a Doofinshmirtz-level evil scheme of “muahahaha I’m going to make everyone irritable and sleep-deprived for like 3 hours with my grump-n-ator and you can’t stop me Perry the Platypus!” <-- evil!scientific re-enactment.

The structure at the top of the page is indeed a form of fluorotryptophan, but with a hydrogen moved that makes it probably unstable? It’s been a while since I took organic chemistry, but I think this was probably just done for obscuring-the-science reasons.

But let’s put that aside for a moment too.

It’s hard to see in this screenshot, but the text in the lowest text box doesn’t talk about 6-fluoro-L-tryptophan at all, but it does talk about BMAA (the “L” usually isn’t used in the abbreviation). This is where it starts to get interesting. BMAA, or beta-Methylamino-L-alanine is in fact also an amino acid and neurotoxin, and what they’re probably talking the most about in this episode.

BMAA is produced by cyanobacteria, so plants and other things that naturally have cyanobacteria in them (cycads, certain ferns, and lichens) or animals that eat them or are routinely exposed to cyanobacteria (flying foxes, some sharks), can have toxic levels of BMAA in their flesh and can cause problems when eaten by humans. The presence of BMAA specifically causes protein misfolding in the brain, and leads to so-called “tangle diseases” (like, the proteins are all tangled) like Alzheimer’s, Parkinson’s, ALS, PSP, and Lewy-body disease. There are certain regions in the world (most notably Guam) where the food supply has historically had a lot of BMAA naturally occurring in it, and therefore has also historically had a relatively high prevalence of tangle diseases.

Now, you might think you know where I’m going with this, but BMAA is not found in any kind of peas- not even super region-specific ones. Fortunately, wikipedia came in clutch for me by recommending I look into a similar neurotoxin called Oxalyldiaminopropionic acid or ODAP.

When consumed, ODAP causes paralysis of the lower body called “neurolathyrism.” The primary source of dietary ODAP comes from, wait for it... a plant called “Lathryus sativus” or grass pea (see above). The grass pea is an important plant in many parts of the world because it is seen as an insurance crop- it survives droughts and floods when other crops die off. It’s high protein content allows people to live off of it as a temporary staple food. There are other varieties of ODAP-containing Lathryus peas used in traditional Greek and Spanish cuisine, to the point where they have a Protected Designation of Origin.

But... poison? The picture below is a famous Goya print called “Thanks to the Grass Pea.” The title is a clever slant on both the fact that the depicted individuals were kept alive by the pea, only to slowly become paralyzed from it. 

The truth of the matter is, though, if you’re not relying on grass peas as a single food source for more than 3 months at a time, neolathyrism is pretty difficult to get. This doesn’t mean you couldn’t potentially extract enough ODAP to harm someone acutely or add it to the water supply in large enough amounts over a long enough time to cause neurolathyrism in a widespread way that would really confuse public health professionals, but its value as a chemical weapon is pretty low unless you’re really into delayed gratification.

But what if you mixed a fluorotryptophan and ODAP together?

Alas, this is, I’m sorry to say, kind of where the trail went cold for me on the poison front. They’re both mild neurotoxins but they work in really different ways and nothing I read talks about them having ever crossed paths in a research capacity.

Assuming the trail goes no further, I think it’s safe to say that the poison in the episode was based on ODAP. ODAP is *like* the episode’s poison BMAA, and comes from a plant that’s *like* the pea featured in the episode, which is related to a pea that also contains a lower level of ODAP that, while present in many parts of the world, is at least legally protected as an export from a very specific geographic region (that region is part of Spain, but still). Its a little less exciting than a dangerous chemical-weapon-making-pea from North Korea, but you gotta dial up the drama somehow.

Phew. Its almost like they really didn’t want someone to track all that down.

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[joyfuldelusionchaosvaliant]

Science and Chemistry Classes

What does myelin actually do?

- John Hewitt , Medical Xpress

Students of physiology are invariably taught that the primary function of myelin is to insulate nerves. In particular, to make action potentials more efficient by increasing the thickness of the membrane and thereby decreasing its electric capacitance. But this crude idea—this analogy, really—can't be correct. Despite the protestations of dogmatic neuroscientists, neurons aren't electric devices, at least not in the sense of electrons flowing in wires.

Sure, there appear to be plenty of electron currents flowing through and between proteins in the inner membranes of mitochondria deep inside of neurons (some say up to 50 amps for the whole body), but these currents have nothing to do with action potential propagation. Spikes are multifaceted biophysical disturbances in the axons. They clearly do have an ionic component in the form of assorted flows of sodium, potassium, chloride, calcium, and potentially even protons, through channels and pumps; however, electrons are not the bearer of any current or conductance here.

In the current issue of the Royal Society's Open Biology, Alessandro Morelli et al. present intriguing evidence that myelin sheaths with concentric multilamellar structures possess similar bioenergetics to cyanobacterial thylakoids. In addition to a host of eclectic molecular refinements held in common, both structures also share the apparent function of feeding nutrients, potentially including ATP-synthase-derived ATP, into the central heart of a complex multilamellar structure. No one is claiming myelin itself was derived from thylakoids membranes, as that would seem taxonometrically impossible, only that these observations may comprise an enlightening example of convergent evolution to fulfill some fundamentally similar task.

Beyond gross structure and ATP generation, there are other clues to this common underlying function. For example, tightly packed concentric lipids reliably appear as nature's optimal construction for dissolving and sequestering the largest amount of gas in a particular volume. Lipids, particularly neutral lipids, can hold about five times as much gas as water. In this case, the cyanobacteria would be most interested in dissolving CO2 for carb construction, and nitogen for fixation, while myelin would no doubt be seeking O2. Brain tissues do not have the luxury (as do other high-respiring tissues like muscle) of having a high-affinity myoglobin to snatch away O2 from circulating hemoglobin.

It may be interesting to compare coronal sections of cetacean brain with that of the human in light of the vastly thinner and more convoluted cetacean cortex that has evolved under the selective pressure of oxygen deprived conditions. Cetacean cortex may likely contain a large preponderance of large deep layer projection neurons relative to their thin upper layers in order to maximize the number of axons available for producing white matter. A cursory look at dolphin brains on Google images does not support this one way or the other, however a more exhaustive accounting could be illuminating. Similarly, the spermaceti of the sperm whale, which presumabkly beamshapes and focuses ingoing or outgoing echolocation signals, may moonlight in an oxygen nourishing capacity. Their wax par excellence, i.e. cetyl palmitate is a C16 fatty acid that esterifies an alcohol and may be deal for absorbing oxygen. Curiously, concentric multilamellar structures are also produced in the lung surfactant, the crucial element for good O2 absorption by the pulmonary alveoli. The outermost layer of pulmonary epithelial cells also have similar lamellar body formations.

In order to overcome the negatively charged repulsive forces of phospholipids in multilamellar structures, nature seems to have unanimously gone with galactolipids. These lipids, which have galactose as their sugar group, are a favorite among plant membrane lipids, where they substitute for phospholipids presumably to conserve phosphate for other essential processes. Galactolipids make up about 70 percent of the lipids in the cyanobacteria thylakoids, up to 80 percent in plant thylakoids, and about 30 percent in myelin. Myelin galactolipids have also been shown to be essential for proper formation of the nodes of Ranvier.

Another commonality with thylakoids is a close homology in the protein sequences of non-selective ion channels in thylakoids with the ubiquitous, voltage-dependent anion channels (VDAC) abundantly expressed in mitochondria and other membranous structures. In myelin, the VDAC can potentially tetramerize into complexes which would form a central pore approximately 1.3 nm in diameter, roughly the same size as the thylakoid ion-channel pore. In the green unicellular alga Chlamydomonas reinhardtii, these channels connect the thylakoid stacks to an essential structure called the pyrenoid. Bicarbonate, NADPH and ATP are all conducted through pores to the central pyrenoid to feed the Calvin–Benson cycle.

A very high concentration of the enzyme RuBisCo is required for CO2 incorporation into organic compounds. While being the most abundant protein in our entire biosphere, RuBisCo displays only modest catalytic efficiency. This is the likely reason that the dense nuclei of RuBusCo complexes which form carboxysome are found deep within the centers of concentric lamellar structures. To transport CO2 to the business end of the thylakoids, carbonic anhydrase is required to form a bicarbonate intermediate, much as it is in us. Carbonic anhydrase is essential in mitochondria to convert Krebs cycle derived CO2 into bicarbonate. Another place where carbonic anhydrase is found is the myelin sheath, suggesting a metabolic role in handling this gaseous species.

Mitochondria contain expansive membrane compartments known as cristae. Normally these elements form parallel stacks sporadically connected to the outer membrane by tubular cristae junctions. Under certain circumstances, these cristae can completely reconfigure themselves into concentric, onion-like membranes. Many manipulations, both natural and artificial, cause mitochondria to adopt concentric cristae, including alterations in ATP-synthase expression. Some time ago, a few researchers suggested that myelin acts like a mitochondrion. A theoretical objection to this concept later claimed that if an errant ATP-ase should find its may into myelin, at best, it could only operate in reverse to break down ATP.

These author's calculations for the proton motive force across the myelin membrane were based on known values for pH and the membrane potential of the oligodendrocyte, and a few assumptions about the underlying configuration and polarity of the ATPsynthase in the membrane. Theoretical proofs of metabolic this-or-thats, like the amount of energy required by neurons, are notoriously difficult—nature invariably surprises with how much it can do with so little. For example, the same researchers throwing shade on the myelin hypothesis have also made noble attempts to calculate the energy requirements for spiking axons. While many stealth energy sources are also available to the axon, like vesicle-attached ATP generators in the form of GADPH, axons do a lot more than spike. In fact, spiking may be relatively easy compared to more physical processes like transport and growth.

Peter Mitchell, of Nobel fame, introduced the concept of H+-motive force (typically around 250 mV), which would be constituted by the transmembrane electrical potential difference (Δψ) plus the pH difference between the two aqueous phases (ΔpH). However, in talking to Alessandro, an extant pioneer tangibly connected to that bountiful era, and still quite active today, it quickly becomes apparent that all may not be well in chemiosmotic land. It has been observed that the biological membrane surface is separated from the bulk aqueous phase by ordered water molecules representing an electrostatic barrier, which for H+ ranges around 120 meV. Any calculation of the value of pmf across different surfaces is therefore far from straightforward when the actual biology is considered.

The nature of free protons in and around membranes is similarly difficult to intuit. A particularly high proton concentration probably wouldn't be very healthy for membranes. With better techniques, physical variables in structures like mitochondria can now be measured with greater spatial and temporal accuracy, often with astounding results. Temperatures deep inside the matrix literally blaze, calcium sparks fire, and mitochondrial membrane potentials slew about within an order of magnitude of the speed of the spikes of the parent axon itself.

In order to overcome the negatively charged repulsive forces of phospholipids in multilamellar structures, nature seems to have unanimously gone with galactolipids. These lipids, which have galactose as their sugar group, are a favorite among plant membrane lipids, where they substitute for phospholipids presumably to conserve phosphate for other essential processes. Galactolipids make up about 70 percent of the lipids in the cyanobacteria thylakoids, up to 80 percent in plant thylakoids, and about 30 percent in myelin. Myelin galactolipids have also been shown to be essential for proper formation of the nodes of Ranvier.

Another commonality with thylakoids is a close homology in the protein sequences of non-selective ion channels in thylakoids with the ubiquitous, voltage-dependent anion channels (VDAC) abundantly expressed in mitochondria and other membranous structures. In myelin, the VDAC can potentially tetramerize into complexes which would form a central pore approximately 1.3 nm in diameter, roughly the same size as the thylakoid ion-channel pore. In the green unicellular alga Chlamydomonas reinhardtii, these channels connect the thylakoid stacks to an essential structure called the pyrenoid. Bicarbonate, NADPH and ATP are all conducted through pores to the central pyrenoid to feed the Calvin–Benson cycle.

A very high concentration of the enzyme RuBisCo is required for CO2 incorporation into organic compounds. While being the most abundant protein in our entire biosphere, RuBisCo displays only modest catalytic efficiency. This is the likely reason that the dense nuclei of RuBusCo complexes which form carboxysome are found deep within the centers of concentric lamellar structures. To transport CO2 to the business end of the thylakoids, carbonic anhydrase is required to form a bicarbonate intermediate, much as it is in us. Carbonic anhydrase is essential in mitochondria to convert Krebs cycle derived CO2 into bicarbonate. Another place where carbonic anhydrase is found is the myelin sheath, suggesting a metabolic role in handling this gaseous species.

Mitochondria contain expansive membrane compartments known as cristae. Normally these elements form parallel stacks sporadically connected to the outer membrane by tubular cristae junctions. Under certain circumstances, these cristae can completely reconfigure themselves into concentric, onion-like membranes. Many manipulations, both natural and artificial, cause mitochondria to adopt concentric cristae, including alterations in ATP-synthase expression. Some time ago, a few researchers suggested that myelin acts like a mitochondrion. A theoretical objection to this concept later claimed that if an errant ATP-ase should find its may into myelin, at best, it could only operate in reverse to break down ATP.

These author's calculations for the proton motive force across the myelin membrane were based on known values for pH and the membrane potential of the oligodendrocyte, and a few assumptions about the underlying configuration and polarity of the ATPsynthase in the membrane. Theoretical proofs of metabolic this-or-thats, like the amount of energy required by neurons, are notoriously difficult—nature invariably surprises with how much it can do with so little. For example, the same researchers throwing shade on the myelin hypothesis have also made noble attempts to calculate the energy requirements for spiking axons. While many stealth energy sources are also available to the axon, like vesicle-attached ATP generators in the form of GADPH, axons do a lot more than spike. In fact, spiking may be relatively easy compared to more physical processes like transport and growth.

Peter Mitchell, of Nobel fame, introduced the concept of H+-motive force (typically around 250 mV), which would be constituted by the transmembrane electrical potential difference (Δψ) plus the pH difference between the two aqueous phases (ΔpH). However, in talking to Alessandro, an extant pioneer tangibly connected to that bountiful era, and still quite active today, it quickly becomes apparent that all may not be well in chemiosmotic land. It has been observed that the biological membrane surface is separated from the bulk aqueous phase by ordered water molecules representing an electrostatic barrier, which for H+ ranges around 120 meV. Any calculation of the value of pmf across different surfaces is therefore far from straightforward when the actual biology is considered.

The nature of free protons in and around membranes is similarly difficult to intuit. A particularly high proton concentration probably wouldn't be very healthy for membranes. With better techniques, physical variables in structures like mitochondria can now be measured with greater spatial and temporal accuracy, often with astounding results. Temperatures deep inside the matrix literally blaze, calcium sparks fire, and mitochondrial membrane potentials slew about within an order of magnitude of the speed of the spikes of the parent axon itself.

Dr. Alessandro Morelli

[maple-keenes]

This is a ramble free card! Use this to ramble whenever you want about anything you want to ramble about! (Pass it on)

dkfajhadlk. okay so. it literally doesn’t fit with anything else about my personality (ie, writing, drawing, loves d&d, theater kid, loves languages, wants to do something with linguistics) but i fucking LOVE biology. i think it’s fascinating.

you know what i especially love???? TAXONOMY. did you know that the only rules concerning the species name of an animal are that it a) has to be in latin or something approximating latin, and b) can’t be offensive to any person or group of people. and the second rule was only added on because the guy who came up with the system we still use to classify organisms today used to name plants he thought were ugly after his enemies!!! carl linnaeus was That Bitch!!! 

you know what this means???? biologists can name their discoveries pretty much fucking anything. there’s a genus of beetles known as the gelae genus. the fucking jelly genus. that’s how you pronounce that!!!

there’s the gelae rol beetle, the gelae donut beetle, the gelae baen beetle, and so on!!! these are all real-ass animals!!! 

also, there’s no rules against swearing in your taxa of an animal!! so many animals have “fuck” as part of their Actual Scientific Name!!! because you can!

you know what else is super fucking cool??? protists! they were originally considered plants, but they were too similar to animals! also, they’re not bacteria or fungi or anything!!! they’re just this single-celled motherfuckers who were too special to be plants!!!

if i asked you what algae is, you would say plant, right? WRONG!!! it’s a protist!!! it’s not genetically similar enough to plants to be a plant!!! 

you know what else is a protist? fucking cyanobacteria. you know what those motherfuckers actually are? BACTERIA!!! but they’re the only species of bacteria that can do photosynthesis so biologists had to be like, “whoops, guess they’re a protist now!” they break all of the rules of protists!!! they should be in a totally different domain!!! but they’re not and it’s great!!!!

what do you think lichen is? a PLANT? you’ve been fooled!!! tricked!!! lichen isn’t even a single organism!!! it’s TWO!!! 

lichen is a combination of certain types of fungi and algae or cyanobacteria!!! it’s called a mycorrhizal relationship!!! isn’t that a cool word???? it’s a super fancy symbiotic relationship that allows for algae to get nutrients it normally wouldn’t be able to outside of water!!!

google calls lichen a plant!!! HA!!! fooled!!! it’s not!! it’s a combination of protists and fungi!!! 

thanks for coming to remi’s biology corner, please feel free to ask me any questions and i’ll probably not answer it and instead yell at you about fungi. thanks