#stem side of tumblr

[radfart5]

STEM side of tumblr! What are y'alls favorite programs for creating graphics for posters, such as showing molecular models? I usually use PowerPoint to create my posters, but I dont want to use it to create my visual models :^/

As a grad student, I prefer free materials/programs that university would cover for me! Ty in advance 🥺

[radfart5]

Yes!!! So human cells get specialized by "choosing" which genes are going to be active. All cells have all of your dna!! Its just a matter of whether or not the DNA in the cells is marked to be active or not!!

[chroniclesofachemist]

[beakers-and-telescopes]

OKAY THIS ARTICLE IS SO COOL

I'm going to try to explain this in a comprehensible way, because honestly it's wild to wrap your head around even for me, who has a degree in chemistry. But bear with me.

Okay, so. Solids, right? They are rigid enough to hold their shape, but aside from that they are quite variable. Some solids are hard, others are soft, some are brittle or rubbery or malleable. So what determines these qualities? And what creates the rigid structure that makes a solid a solid? Most people would tell you that it depends on the atoms that make up the solid, and the bonds between those atoms. Rubber is flexible because of the polymers it's made of, steel is strong because of the metallic bonds between its atoms. And this applies to all solids. Or so everybody thought.

A paper published in the journal Nature has discovered that biological materials such as wood, fungi, cotton, hair, and anything else that can respond to the humidity in the environment may be composed of a new class of matter dubbed "hydration solids". That's because the rigidity and solidness of the materials doesn't actually come from the atoms and bonds, but from the water molecules hanging out in between.

So basically, try to imagine a hydration solid as a bunch of balloons taped together to form a giant cube, with the actual balloon part representing the atoms and bonds of the material, and the air filling the balloons as the water in the pores of the solid. What makes this "solid" cube shaped? It's not because of the rubber at all, but the air inside. If you took out all the air from inside the balloons, the structure wouldn't be able to hold its shape.

Ozger Sahin, one of the paper's authors, said

"When we take a walk in the woods, we think of the trees and plants around us as typical solids. This research shows that we should really think of those trees and plants as towers of water holding sugars and proteins in place. It's really water's world."

And the great thing about this discovery (and one of the reasons to support its validity) is that thinking about hydration solids this way makes the math so so so much easier. Before this, if you wanted to calculate how water interacts with organic matter, you would need advanced computer simulations. Now, there are simple equations that you can do in your head. Being able to calculate a material's properties using basic physics principles is a really big deal, because so far we have only been able to do that with gasses (PV=nRT anyone?). Expanding that to a group that encompasses 50-90% of the biological world around us is huge.

[hellsite-proteins]

AlphaFold Nobel Prize!

Hey everyone :) this isn't a structure, but there is some protein news that is pretty relevant to this blog that I felt I had to share. This article gives a nice overview of AI-predicted protein structures and what sorts of things they can do for research. It's not too long, and I recommend taking a look

If you've been seeing my posts for any amount of time, I've absolutely given you a flawed view of how useful AF can be. Experimentally determining protein structures is a demanding and difficult process (I've never done it, but I've learned the overview of how x ray crystallography works, and I can only imagine how much work it would take). AI-generated structures are not going to make structural biology obsolete, but they are massively helpful in making predictions that go on to guide further research.

While in many fields (especially creative areas like art and writing) AI has significant ethical concerns, I feel like this sort of use of AI in science is an overwhelmingly positive thing. The data used to train it is publicly available, and science works by building on the work done by those before us. Furthermore, while AI may not be great at generating new ideas or copying humans, it is very good at sorting large amounts of data and using it to make predictions. It's more akin to very complicated statistics than an attempt at the Turing test, and in this case it is a valuable tool to expand the ways we can do science!

[hellsite-noobteins]

raw input: penis filtered input: PENIS it's just a wibble, not much else to say i think?

stick | cartoon | surface

colored by pLDDT

[learnyouabiology]

Fun Fact: Hognose snakes are dramatic lil guys!

I am particularly fond of the snakes known as hognose snakes, and my reasons are both understandable and correct.

This is a hognose snake:

(They received their name by having the sweetest lil snoot to ever require a boop – image source)

They use these adorable snoots to burrow under sandy soil using a sort of nuzzle-y motion. They then use these burrows as a place to sleep at night, hibernate in the winter, and lay their eggs. 

(you could say they’re into... the Underground Scene! ...ok yeah i’ll show myself out – image source)

Plus, they come in a variety of delightful colours!

We've got brown! Beige! Yellow! Black! Red! Orange! Tan! Kinda greenish! Orange again!

(pretty sneks! – Here’s all the image sources: 1, 2, 3, 4, 5, 6, 7, 8, 9)

And, to be clear, the snakes pictured above are wild snakes. No selective breeding by humans in these noodly bois! At least, not in these specific individuals. probably. I guess a few of them could be escapees... 

But most importantly: These snakes know the true meaning of DRAMA

Hognose snakes are actors, first and foremost. When they feel threatened, the first thing they do is puff out their neck into a hood. 

(like cobras, this hood is made by FLEXING THEIR NECK RIBS. which: gross – image source x)

This superficially makes them look like a cobra, but what they’re actually trying to do is make themselves seem bigger, and therefore scarier. Possibly those dark spots on their neck helps with that! 

Any resemblance to real-life Eurasian cobras, real or fictional, is purely coincidental

Also, it makes its mouth do this:

(Snakes that SCREAAAAAAAM. – image source)

honestly, if I didn’t already know that hognose snakes were harmless, this would ABSOLUTELY make me leave it the hell alone 

But if all of that^ is unsuccessful at scaring away the predator, the hognose snake pulls its signature move: playing dead

If you think that is a lame signature move, then you are wrong, because hognose snakes put EVERYTHING into their performance and I love them for it.

(they’re serious, they’ll do it!  – image source)

((I’m actually going to stick the rest of this under a read-more, bc the pictures of the alive-and-physically-fine hognose snakes do kind of look like a legitimately-dead hognose snake, if you don’t know what to look for. 

So, uh: cw for a snake being too good at pretending to be dead))

Behold: a series of completely healthy, unharmed snakes!!!

(to help with their self-esteem, we ask that you at least pretend to believe that they are dead – image sources 1, 2, 3, 4)

Honestly, the photos don’t do it justice. Here’s my favourite video of the whole wonderous performance: 

But to review:

There's writhing! There's dramatic noises! There's flipping onto their back and opening their mouth wide and letting their tongue hang out! There's excreting a combination of  intentionally smelly substances!!! Truly a master of the art of being left the hell alone (*^▽^*)

(yep. deeeeefinitely dead. not just faking it. nothing worth eating here! – image source)

Personally, my favourite part of this is how they insist on rolling onto their back, even when they are rolled back onto their stomach. 

Seriously, if you try to roll them right-side-up, they will flip back over. It's as though they believe that a good, proper dead snek MUST be on its back, obviously.

(truly fearsome – image source)

Sadly, the hognose snake may have made itself too scary, according to humans.

Out of fear, these snakes are commonly killed on sight 😔. I once heard someone proudly brag about how they’d killed a dozen cobras! In southern Ontario! Where cobras do not live! This is both extremely frustrating and deeply sad.

(safe enough to hold! although maybe don’t, just because this snake IS probably experiencing mortal fear, which is not a good feeling – image source © Dean Stavrides)

So just to highlight: hognose snakes are completely harmless. They’re just pretending to be fearsome!

(not that people should be killing venomous snakes either, imo. Let the danger noodles LIVE THEIR LIVES)

(i is baybee, pls do not hurt me – image source)

And now some bonus facts to help raise us out of that downer:

Hognose snakes are toad specialists! Their favourite food is toads, which is unusual, because toads are poisonous. Hognose snakes deal with this by force of will and also, at least two amino acid substitutions, maybe (Mohammadi et al. 2016). Possibly a few other things help with this, also (Feldman et al. 2016).

(is snek eat toad? or does toad wearing cape of snek? impossible to tell, really – image source)

Also, I have a confession: hognose snakes... are venomous. Technically.

(itty bitty little fangs at the veeeeery back of their mouth!  – image source)

They are known as rear-fanged snakes, which means they have fangs aaaall the way at the back of their mouth. The venom they produce seems to be toad-specific, and is considered to be harmless to humans unless you happen to have an allergy but that's the exception rather than the rule

(the two hognose species. They are both baybee, but in different ways actually there might be more than two species but these are the two i’ve actually learned about so ALL WELL   – image source)

Also, hognose snakes are big cowards NOT aggressive and I've never even heard of anyone getting bit by a one (outside of one feeding mishap, which we can all agree was an ACCIDENT). 

The series of events that would need to occur for you to be envenomated are so unlikely and bizarre that I assume you would have to be TRYING to get bit.

This has been Fun Fact Friday, bringing you the forbidden noodly boys to try and keep them a little more safe!

.....................................................................

Sources, because I know me and SO DO YOU:

Averill-Murray, R. C. (2006). Natural history of the western hog-nosed snake (Heterodon nasicus) with notes on envenomation. Sonoran Herpetologist, 19(9), 98-101.

Buchanan, Scott W.; Timm, Brad C.; Cook, Robert P.; Couse, Richard; Hazard, Lisa C. (2017). Spatial ecology and habitat selection of eastern hognose snakes. The Journal of Wildlife Management, 81(3), 509–520. doi:10.1002/jwmg.21218 

CHS: Canadian Herpetological Society https://canadianherpetology.ca/species/species_page.html?cname=Eastern%20Hog-nosed%20Snake

COSEWIC. 2021. COSEWIC assessment and status report on the Eastern Hog-nosed Snake Heterodon platirhinos in Canada. Committee on the Status of Endangered Wildlife in Canada. Ottawa. xi + 45 pp.  https://www.canada.ca/en/environment-climate-change/services/species-risk-public-registry/cosewic-assessments-status-reports/eastern-hog-nosed-snake-2021.html

Cunnington, G. M., & Cebek, J. E. (2005). Mating and nesting behavior of the eastern hognose snake (Heterodon platirhinos) in the northern portion of its range. The American midland naturalist, 154(2), 474-478.

Feldman, C. R., Durso, A. M., Hanifin, C. T., Pfrender, M. E., Ducey, P. K., Stokes, A. N., ... & Brodie Jr, E. D. (2016). Is there more than one way to skin a newt? Convergent toxin resistance in snakes is not due to a common genetic mechanism. Heredity, 116(1), 84-91. 

 Jared, C., Luiz Mailho‐Fontana, P., & Maria Antoniazzi, M. (2021). Differences between poison and venom: An attempt at an integrative biological approach. Acta Zoologica, 102(4), 337-350.

Liu, C., Chen, Y., Zheng, Y., Bo, J., Yang, C., Xu, S., & Zhang, S. (2022). Wear Resistance Improvement of Keeled Structure and Overlapped Distribution of Snake Scales. Journal of Bionic Engineering, 1-11. Citing abstract.

Mohammadi, S., Gompert, Z., Gonzalez, J., Takeuchi, H., Mori, A., & Savitzky, A. H. (2016). Toxin-resistant isoforms of Na+/K+-ATPase in snakes do not closely track dietary specialization on toads. Proceedings of the Royal Society B: Biological Sciences, 283(1842), 20162111. 

 Nature Conservancy of Canada: https://www.natureconservancy.ca/en/what-we-do/resource-centre/featured-species/reptiles-and-amphibians/eastern-hog-nosed-snake.html

Plummer, M. V., & Mills, N. E. (1996). Observations on trailing and mating behaviors in hognose snakes (Heterodon platirhinos). Journal of Herpetology, 30(1), 80-82.

Rouse, Jeremy D.; Willson, Robert J.; Black, Ron; Brooks, Ronald J.  (2011). Movement and Spatial Dispersion of Sistrurus catenatus and Heterodon platirhinos: Implications for Interactions with Roads. Copeia, 2011(3), 443–456. doi:10.1643/ce-09-036     

Seburn, D. 2008. Recovery Strategy for the Eastern Hog-nosed Snake (Heterodon platirhinos) in Canada. Species at Risk Act Recovery Strategy Series. Parks Canada Agency, Ottawa. vi + 24pp.

Schwartz, V. & D. Golden (2002). Field Guide to Reptiles and Amphibians of New Jersey. New Jersey Division of Fish and Wildlife

VHS: Virginia herpetological society http://www.virginiaherpetologicalsociety.com/reptiles/snakes/eastern-hog-nosed-snake/eastern_hognose_snake.php#:~:text=Heterodon%20is%20derived%20from%20the%20Greek%20words%20heteros,meaning%20%22broad%20or%20flat%22%20and%20rhinos%20meaning%20%22snout%22

Young, R. A. (1992). Effects of Duvernoy's gland secretions from the eastern hognose snake, Heterodon platirhinos, on smooth muscle and neuromuscular junction. Toxicon, 30(7), 775-779. https://doi.org/10.1016/0041-0101(92)90013-U

Young, B. A., & Morain, M. (2003). Vertical burrowing in the Saharan sand vipers (Cerastes). Copeia, 2003(1), 131-137.

SARA: threatened https://www.canada.ca/en/environment-climate-change/services/species-risk-public-registry.html

[disthene-al2sio5]

You ever feel emotional over a mountain ?

I give you :

Sainte Victoire, my beloved 😔i would die for you, sweetheart.

The Sainte Victoire is a mountain next to Aix en Provence in the South East of France, where i grew up.

I took the first picture during my last afternoon hike with my mom before i left the south of France after high school. The second picture was taken this christmas out of my train window.

I'm very emotionally attached to it, it's my childhood mountain. I could see it from my high school and from my village everyday. Now i only see her at christmas.

It's mostly jurassic limestone.

Those maps are from Rockd on the left and info-terre on the right (si ya des français qui passent par là allez voir info-terre il y a la carte géologique de la France plus plein d'autres cartes)

I think it's most famous for having been painted by Paul Cézanne so here are some of his paintings

(i had the second painting as a postcard and i put it on the wall of my dorm when i left the south)

English wiki :

Wiki français :

[troythecatfish]

Here's an interesting question: why has western feminism failed so much at achieving gender equality in STEM careers, meanwhile Iran and many other Muslim countries that are considered to be repressive to women's rights have been so successful at it?

Communist countries of the 20th century were also very successful at getting women into STEM careers, which is why even to this day, after the fall of communism in those countries, roughly half of scientists in Russia and Eastern European countries are women, so this isn't just a Muslim thing. It seems that liberal feminism has failed at getting women into STEM careers, especially in areas like engineering which is a total sausage fest.

Also, this is a good counterpoint to the Jordan Peterson/James Damore argument of women supposedly just being innately less interested in STEM careers because of their biology or whatever.

Clearly that's not the case since many countries around the world have already achieved gender equality in STEM careers, so this is really just a failure of the liberal west, not a result of women's innate biology like the Jordan Petersons and James Damores of the world suggest.

Sources:

1st slide: https://www.forbes.com/sites/amyguttman/

2015/12/09/set-to-take-over-tech-70-of-irans-science-and-engineering-students-are-women/? sh=69f2111f44de

2nd-3rd slides: https://qz.com/1223067/iran-and-saudi-arabia-lead-when-it-comes-to-women-in-science#:~:text=The%20West%20is%20way%20behind, Science%20like%20a%20girl.&text=In%20|ran %2C%20nearly%2070%25%20of,than%20in%20an y%20other%20country.

4th slide: https://thehill.com/changing-america/ opinion/481684-how-iranian-immigrants-can-be-role-models-for-diversity-in-stem/amp/

https://thehill.com/changing-america/

[anulithots]

In preparation for the Bio fanfic I want to do.

It shall be my summer project. I'll finish LotFF, and write a bio fanfic, hyperfixate on Link Click, and get back into reading. Keeping it simple and fun. hehehe

okay side tangent what I meant is that:

It would be so. much. fun. to try to make this with other people. the biology people. the infodumping and brainstorming that could take place it would be wonderous.

SO! Gently tagging some people, please let me know if you're interested, but NOT forced whatsoever also this is a vague idea right now. (in terms of organizing this). I do not know what I'm doing...but I'll figure it out. (Also apologies if this is too forward after not interacting a ton... however... BIOLOGY AND SLEEP DEPRIVATION IS TEMPORARILY OVERRIDING MY SHY-NESS)

@osbob-the-existent @neurospicy-salsa @bonesbeetle @pansexual-exoplanet

ALso also, to any other biology-interested creatures who stumble across this post, feel free to let me know if you want to be included!!! <3 <3 <3 <3

[stemandleafdiagram]

PLUTO NEWS!!!! FROM TODAY!!!!

well technically it's about Charon which is Pluto's biggest moon which is half its size.... so it counts

carbon dioxide and hydrogen peroxide have been detected on detected for the first time traces of carbon dioxide and hydrogen peroxide on Charon's surface!!! hell yeah james webb telescope

for reference, water ice, ammonia, and organic materials were detected on the moon beforehand and scientists couldn't get much further than that

look at this fella

[terrarium-of-mistakes]

...Im such a stem nerd. Like without even considering my interests

I have the weird fashion sense. And the ability to completely own it.

For example, today, at school, I came to school wearing my sneakers (teal), with black legging/socks (texture is leggings, but they are socks) covering my knees, and blue jorts that reach my knees as well (the socks & jorts meet). As for my top half, I have a red t-shirt, with a brown hoodie, green fingerless gloves, and a black paper boy cap. Oh and pinned to the top of the cap, there is a decently big white paper crane, with each fold outlined in black. That is not a normal piece of my outfit.

The crane is there because I came to school with a bucket of tiny cranes to give to the drama department (no, I am not in drama) for a haunted house

You want to know the most ridiculous part??? The part that seals the deal? THE ONLY PERSON WHO TOOK A DOUBLE TAKE WAS MY SISTER

I CAME TO SCHOOL WITH A FUCKING BIRD ON MY HEAD & NO ONE THOUGHT IT ODD

NO ONE

...also I wrote a little thing about ∝ in AP Physics:

"Is it a fish or proportional? Why not both? A proportional fish"

[chroniclesofachemist]

You know what? I'm sick of it.

I'm sick and tired of pretending I don't want to float in

✨Cherenkov radiation✨

Look at that shit, it's perfect. I bet it feels amazing on the skin and organs. I bet it revitalises the pores. I bet it tastes incredible.

Don't listen to authorities, look at that colour, nothing that pretty could be bad for you.

I want the forbidden swim.

[beakers-and-telescopes]

Slime Molds and Intelligence

Okay, despite going into a biology related field, I only just learned about slime molds, and hang on, because it gets WILD.

This guy in the picture is called Physarum polycephalum, one of the more commonly studied types of slime mold. It was originally thought to be a fungus, though we now know it to actually be a type of protist (a sort of catch-all group for any eukaryotic organism that isn't a plant, animal, or a fungus). As protists go, it's pretty smart. It is very good at finding the most efficient way to get to a food source, or multiple food sources. In fact, placing a slime mold on a map with food sources at all of the major cities can give a pretty good idea of an efficient transportation system. Here is a slime mold growing over a map of Tokyo compared to the actual Tokyo railway system:

Pretty good, right? Though they don't have eyes, ears, or noses, the slime molds are able to sense objects at a distance kind of like a spider using tiny differences in tension and vibrations to sense a fly caught in its web. Instead of a spiderweb, though, this organism relies on proteins called TRP channels. The slime mold can then make decisions about where it wants to grow. In one experiment, a slime mold was put in a petri dish with one glass disk on one side and 3 glass disks on the other side. Even though the disks weren't a food source, the slime mold chose to grow towards and investigate the side with 3 disks over 70% of the time.

Even more impressive is that these organisms have some sense of time. If you blow cold air on them every hour on the hour, they'll start to shrink away in anticipation when before the air hits after only 3 hours.

Now, I hear you say, this is cool and all, but like, I can do all those things too. The slime mold isn't special...

To which I would like to point out that you have a significant advantage over the slime mold, seeing as you have a brain.

Yeah, these protists can accomplish all of the things I just talked about, and they just... don't have any sort of neural architecture whatsoever? They don't even have brain cells, let alone the structures that should allow them to process sensory information and make decisions because of it. Nothing that should give them a sense of time. Scientists literally have no idea how this thing is able to "think'. But however it does, it is sure to be a form of cognition that is completely and utterly different from anything that we're familiar with.