Studying | My favourite online courses

I don’t know about you, but I just love doing online courses, especially when they deal in subjects I don’t get to explore in my college courses. Over the years, I tried many different platforms, such as YouTube, Google Digital Garage, Khan Academy, Udemy, and, my favourite, Coursera. As a matter of fact, I discovered Coursera back when they started in 2012; most of the courses I took were on topics of Neuroscience and Molecular Biology. At first, courses and certificates were completely free, but with time, they started offering paid vs. free, as well as many specializations and even some college degree courses. However, many of the courses are still available to watch and do quizzes, just without the certification.

Disclaimer: this post is not sponsored by Coursera.

Synapses, Neurons and Brains – available here

This course, offered by Hebrew University of Jerusalem, is actually the very first course I took, and at the time was one of the rare Neuroscience courses. I have only good memories about this one – it is a good introductory course into the field and the professor explained the curriculum very well. Also, the course mentions real projects that deal with neural networks and brain reconstructions, such as Blue Brain Project. I didn’t mention this previously, but every course also comes with subtitles (in English at least) and transcripts, so you can follow along easier.

The Addicted Brain – available here

The Addicted Brain (by Emory University) is another course appropriate for beginners in this topic – I was initially interested not only because of the topic of addiction, but also because various mechanisms of how drugs interact with the brain were presented. The course also covers the topic of drugs in society, although this part mainly concerns United States of America. Also, I don’t know if this is something that’s important to you, but I followed professor’s narration easily – his voice is calming and he speaks very understandably.

Medical Neuroscience – available here

Medical Neuroscience (by Duke University) is not only the most advanced course of the ones mentioned here, but the most advanced course I ever took. Actually, I started it once or twice before, but dropped out because it required a lot of time and dedication that, at times, I just didn’t have due to my University obligations. This course is really extensive and requires some before-knowledge, but is also very satisfactory when you finish it. The only problem I had with this one is that sometimes I felt that questions in quizzes were asking for details that to me seemed almost overlooked in the videos. However, I felt like this course was quite important for my studies, since I have a strong interest in Neuroscience, but lacked the medicinal perspective.

All quizzes are multiple choice answers, with usually one correct answer (sometimes more correct answers). I vaguely remember some questions where you had to connect some phrases (like 1-d, 2-c, etc) as well, but haven’t came across those recently. Also, the quizzes I did were never timed and you can take one quiz 3 times every eight hours (they keep your highest score).

Coursera also offers financial aid – you can fill out an application where you explain why is the course you’re applying for important to you and why you can’t afford it. So far, I’ve heard of many positive experiences where they gave grants.

There are also two Neuroscience related courses I am planning to take – Human Neuroanatomy (to revise a bit) and Computational Neuroscience, which deals with using Python in Neuroscience research. I would very happily review those for you, in a greater detail, if this is something you’d like to read about!

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What is your opinion on online courses – do you think they’re useful or a waste of time? Did you perhaps take some of the ones I mentioned? If yes, I would love to hear from your!

Short science posts | Anthozoa & nerve cells

Anthozoa (corals & anemones) are interesting animals that live exclusively in seas and oceans. Since they are regarded as sessile organisms, their nervous system is not very advanced. In a previous post, I mentioned that all cnidarians have two diffuse neural nets, and that is true for Anthozoans as well. Multipolar nerve net neurons are connected with synapses, and they also possess sensory cells that are particularly numerous around the mouth and on the tentacles.

One paper investigated traveling of electrical waves in a coral nerve network in coral colonies in genus Palythoa. It was experimentally observed that this electrical wave spreads at the constant speed from the site of simulation. Furthermore, peptidergic neurons (the ones using neuropeptides to communicate) were also noted in Anthozoa.

Did I draw this when I was 5 or 25? – A mystery.

Nematostella vectensis, also known as starlet sea anemone, is a species of Anthozoa that is known as a model organism – its genome and development have been carefully studied, including its nervous system. In this species, oral and pharyngeal nerve rings have been reported, as well as  longitudinal tracts of neurites (neurites are usually axons or dendrites). These findings would suggest that some groupings of neural cells exist in at least some Anthozoan species after all. Sensory neurons, interneurons, motorneurons, and neurosecretory‐like gland cells were also reported to exist in N. vectensis.

Note: in case I didn’t mention this before, cnidocytes are often considered neural cells because they display mechanosensory properties and calcium dependent neural‐like properties as well.

Literature & more information:
Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
The rise of the starlet sea anemone Nematostella vectensis as a model system to investigate development and regeneration
Cnidarians and the evolutionary origin of the nervous system
Model of traveling waves in a coral nerve network

Short science posts | What is a nerve net?

A nerve net is a type of nervous system that consists of many neurons but there is no brain or cephalization. Nerve nets are found in animals with radial symmetry (Cnidaria) and biradial symmetry (Ctenophora). Despite being called a net, there sometimes exist some groupings of neural cells in some Cnidaria classes, which I will write more about during the next couple of weeks.
Cnidaria are specific due to their specialized organelles, cnidocytes, which they utilize to hunt for food or use for securing itself to a surface. Some cnidocytes contain toxins that can paralyze their prey (the burning sensation you may have felt when touching a sea anemone 😉).
As a rule, Cnidaria have two diffuse nerve nets, one in the epidermal layer and a second one in the gastrodermal layer. In between these two layers is the mesoglea, a layer that functions as sort of a skeleton. The epidermal net consists of bipolar and multipolar nerve cells, while the gastrodermal net is made up of only multipolar cells.

Cerianthus membranaecus (known as cylinder anemone or coloured tube anemone)

Cnidarian nerve systems are fascinating but also quite unexplored. What is known is that nerve cells consist of two types of neurons, sensory neurons that respond to stimuli and motor neurons which ultimately trigger a response. Chemical synapses exist and provide the communication between the neurons. Hormones have also been reported in some cnidarians (steroids, neuropeptides) but it is still not known how exactly these signalling molecules work.

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In the next couple of weeks, I will write a post about every cnidarian class and also ctenophores, focusing on their nervous and sensory systems. If you have any questions or would like me to focus on something, please let me know!

Literature & more information:
Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Endocrine-like Signaling in Cnidarians: Current Understanding and Implications for Ecophysiology
Evolution of sensory structures in basal metazoa

Reading | Blood Work by Holly Tucker

Blood Work: A Tale of Medicine and Murder in the Scientific Revolution by Holly Tucker is a book that I first read almost 10 years ago. I got it as a gift from a dear friend, for my birthday during the time I was a student at School of Medicine (as you can guess, I decided to start anew and switch to Biology). However, this book has always stayed with me, not only because it was the first book of this genre I’ve read – I loved it because I thought it was the perfect mix of history, medicine, and macabre.

Blood Work follows a fascinating tale of the history of human transfusion, something what in today’s world we almost take for granted. Back in high school, we learned all about Rh factor and blood types (and how there is a possibility of A and B parent having an O or AB child) and voluntary blood donations are common occurrence in my country. Despite all this, I never wondered when did the actual blood transfusion procedures start and how did physicians know whose blood to use.

In the book, we follow Jean-Baptiste Denis, a 17th century French physician who administrated first documented transfusion. Since this transfusion included using sheep’s blood, it was called a xenotransfusion, which is a term that describes blood transfusion from one species to another. This experiment was successful, probably due to small amount of transfused blood and, I dare say, luck, since at the time, blood groups and agglutination were not known facts.
Denis’ last transfusion experiment is, however, the one we learn about in a detail – after trying to treat an illness of psychiatric nature, and transferring a large amount of calf blood, his patient dies, and he is accused of murder. Denis was ultimately acquitted (with a true crime worthy twist in the case), but all further transfusions were banned, first by French government, then by English and even the Pope.

Blood Work doesn’t focus solely on this event – the writer masterfully describes political events of the time, both in France (rivalry with another physician, Henri-Martin de la Martinière, tensions in French Academy of Sciences founded by Louis XIV) and abroad (a competition between French and English Academies), as well as the religious ones (“playing God”, fear that this kind of transfusion could produce some sort of half-human half-animal creature). Furthermore, as Neil Blumberg wrote in his review for Journal of Clinical Investigations, these kinds of experiments were primary conducted due to the belief that transfusion could treat, or even cure,  mental illness, sometimes we now know is not possible.

Lastly, it doesn’t actually matter if you have health and/or science background to find this book interesting, as long as your’re interested in history and historical non-fiction. Blood Work offers a captivating look on the beginnings of one of the most important medical procedures in the world and does it so vividly you almost feel like you’re transported to Paris, in the middle of the scientific revolution.

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I would very much liked to hear your opinion – did you read this book, and if yes, did you like it as much as I did?
Do you have similar book recommendations?  Please let me know in the comments 🙂

Short science posts | Do sponges have a nervous system?

Sponges (phylum Porifera) are sessile multicellular organisms that live predominantly in seas and oceans. They don’t have tissues or organs, and therefore, they don’t actually have a nervous system. However, they do have bipolar and multipolar cells that resemble nerve cells, which are found in the middle, “jelly-like”, layer.
Sequencing of some sponge species showed the presence of many genes associated with neural cells, such as genes that code enzymes for neurotransmitter synthesis and synaptic transmission. It is important to note that these genes have other functions in the organism. It has also been observed that some sponge larvae can respond to outer stimuli and show various “taxis” behaviour – phototaxis (response to light), geotaxis (response to gravity), rheotaxis (response to water current). Phototaxis has been closely studied in species Amphimedon queenslandica (class Demospongiae), a sponge native to Coral Sea.

Aplysina aerophoba, also of class Demospongiae, which can be found in Adriatic Sea.

Potassium channels have been observed in that same species, as well as glutamate, GABA, and NO systems, which have been investigated in Ephydatia muelleri, another species of class Demospongiae. Electrical signalling has been noted in glass sponges (class Hexactinellida). These sponges have bodies comprised of a syncitial tissue and their skeleton is made of silicon dioxide. The scientists were able to measure the action potential (5s long, with 29s refractory period) and deduce this signal relies on potassium and calcium ions.
Some scientists even suggest that sponges used to have a nervous system, but lost it during evolution – they introduced several hypothetical scenarios for this event, proposing that sponges lost their nervous system in order to focus on filtering.

Literature & more information:
Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Evidence for Glutamate, GABA and NO in Coordinating Behaviour in the Sponge, Ephydatia Muelleri (Demospongiae, Spongillidae)

The GABAergic-like System in the Marine Demosponge Chondrilla Nucula
Where is my mind? How sponges and placozoans may have lost neural cell types
Elements of a ‘nervous system’ in sponges

Short science posts | Nervous system evolution

For the next couple of weeks, I would like to write a bit about the evolution of the nervous system, from early nerve cells to the human nervous system and brain evolution. Alongside nervous I will also focus, to a lesser extent, on sensory systems. These posts will be published on my Instagram account, but I decided to publish them on the blog as well.

Mostly, these posts will be about various animals and the nerve systems they have – nerve nets, nerve cords, complete systems. The main process behind this is called cephalization, and it starts with the groupings of nerve cells and ganglia at one end of the body. After some (long) time, this process led to us having a head with sensory organs and a brain inside it.

But when did all of it start? It is kind of hard to say, for even single-celled organisms, such as bacteria, have voltage-gated channels and genes that support the theory of possible synaptic transmission. These channels are potassium (the oldest), calcium, and, rarely, sodium channels as well. Action potentials have been detected in some algae and diatoms, although their function is mostly unclear. In Chlamydomonas (unicellular green algae) on the other hand, potentials were detected in flagellums, which clearly suggest they play the part in the movement of the algae. Action potentials were also recorded in the cilia of some protists, such as Parmecium.

Of course, the exact evolutionary processes are unknown, and there is a possibility that these organisms acquired the mentioned features later than scientists now assume. It is also possible that some more evolved organisms, such as sponges, subsequently lost some of the features discussed here (more about this in the next week’s post).

Literature & more information:
Habdija et al: Protista-Protozoa, Metazoa-Invertebrata, Alfa, 2011, Zagreb
Bacterial voltage-gated sodium channels (BacNaVs) from the soil, sea, and salt lakes enlighten molecular mechanisms of electrical signaling and pharmacology in the brain and heart
Early evolution of neurons
Deep evolutionary origins of neurobiology
From damage response to action potentials: early evolution of neural and contractile modules in stem eukaryotes

Biology in popular culture – FORTITUDE (season 1)

Couple of weeks ago, as I was driving to classes, I saw a big billboard that showed couple of people and a word “FORTITUDE”. At first, I thought it was some kind of fantasy drama, but after looking it up, it turned out to be crime related TV show starring actors I like. And as a true crime buff who enjoys all crime related content, I decided to watch it. After all, if it stars Christopher Eccleston (the best Doctor Who) and Stanley Tucci, it must be great, right?

Well, not quite –  there are parts of the series that I loved, especially ones regarding biology, despite some of them being naively incorrect. Other parts were not so well executed, but today I want to focus mainly on biology (obviously). Fortitude, the name of the show, is also a name of the imaginary town on an island in polar circle. As it is in small towns, they have a doctor, police force, one hotel, some houses, and many secrets. Oh, and research centre, of course!

Spoilers below!

(skip to the last paragraph for pure Biology)

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Photo by Om Malik on Unsplash


In the first episode, we see a scene where hungry polar bear eats a person. Also, we are introduced to an ambitious post-doc whose research focuses on apex predators; he has a theory that due to environmental changes, predators change their behaviour and develop cannibalistic urges (yes, there was some talk about bear eating another bear). Also, they make a point of making fun of him because he researched that in Britain, where badgers are only the predators. I don’t know why was that supposed to be funny, because I’d rather encounter a wolf than a badger, but I decided to let that one slide. Another story-line follows two children, a boy and a girl, who find a mammoth tooth; this boy later develops mumps-like symptoms and frostbite on his feet (he wandered off); there is also a murder of The Ninth Doctor, and we are led to believe that the murderer was father of the girl who found the mammoth tooth. Why, you may ask? Because he didn’t want to surrender the thawed carcass but sell it to The Ninth. And due to global warming, the carcass has already started to thaw.

Now, that immediately rang a bell; old preserved animal, suspicious disease… Despite some lazy writing, I continued to watch the series, despite not being really satisfied with the direction of it; some of the characters were very well characterized, especially Richard Dormer’s Sheriff, but I generally dislike series where everyone is cheating on everyone with anyone – it feels as if writers think that’s the only way to induce tension and drama. Also, Sheriff’s obsession with one female character was a bit too much – this amount of stalking and re-reading her files is not normal and has no place in adult behaviour. And he’s kind off supposed to be a good guy in the end. I digress, because this post is about biology.

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Hello human, are you tasty?

Photo by Bao Menglong on Unsplash


The aforementioned boy ends up first in the hospital, and then in the research centre where they are developing a method to treat frostbite. Not a lot has been said about this, so I can’t actually comment on it, apart from the fact that he’s being held sedated, in a tank, where it’s not exactly clear how they feed him (I haven’t noticed any openings for infusion pipes). Also, who’s caring for him in the research centre? Someone has to wash him and change him every day, but they made it a point that he’s not supposed to be woken up, due to frostbite pain. So, not exactly biology,  but big mistake anyway.

Also, at one point, their only doctor is almost murdered (by her own daughter who developed symptoms similar to the boy and then died due to heart failure) and they have to preform a lumbar puncture on the boy. Again, why you may ask? Well, during the autopsy of  murderous daughter, the post-doc and his veterinary boss discovered some molecules;  some anti-bodies and IgE. And immediately they developed the theory that this was some different kind of disease that turns people into murderers. Which wouldn’t been such problems, apart that IgE’s are the common antibodies that could indicated allergy of some sort? And in their research lab, they don’t have electronic microscopes, which are used to see viruses? A mess. That’s the only word I can use to describe this plot jumps, a big headache-inducing mess. However, let’s go back to the lumbar puncture. Doctor, I presume general practitioner, is incapable of helping, since she’s basically on her death-bed. So a post-doc and his boss decide to do the lumbar puncture, because why not? (Hint: NO.) They do it perfectly, but before it, they ask the boy’s mother for permission, because lumbar puncture is painful. (Hint: It’s not! Headache that comes after is painful, but the puncture itself doesn’t actually hurt. Source: been there, done that.) Anyway, boy’s spinal fluid doesn’t show presence of whatever thing they were looking for, which de facto labels him a murderer of The Ninth Doctor (excuse me?), despite having positive anti-bodies in his blood, which indicated that he might have had that mysterious disease. My only comment is, no, it doesn’t work like that, and please everyone stop thinking that you understand immunology, especially when we have specialized doctors who spend their lives learning about our immune system.

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Photo by Joyce McCown on Unsplash


Anyway, back to the mammoth carcass, and the rest of mammoths that are thawing on this island. I would just like to say that there are also some Russians involved in the whole story (they work in a mine), the Governor wants to make an ice hotel on a glacier (I’m not kidding – on. a. glacier.), and literally everyone has a secret and/or secret agenda.
Well, before mammoths, let’s talk about one thing they got right, and that’s IgE – it gives us immunity to various parasites. And as it turns out, the mammoths were infected, just not with a virus, but parasitic wasp. Basically, larvae survived in mammoths, and were now making humans their hosts – since they were as old as mammoths, the humans didn’t actually have some real defenses against them. This is also definitely confirmed after post-doc finds some live wasps in the doctor (he then sets the whole room on fire, in order not to get infected or allow the wasps to find new hosts – yes, he survives).

Ichneumonidae, also known as Darwin wasps, are indeed parasitic wasps with 25 000 described species. Honestly, I think they were a very good choice for the main bad guys in the series, and were quite well described. Basically, these wasps reproduce in a bit gruesome way – they lay their eggs into a living host, which is then eaten by newly-formed larvae. Apart from this family, there also exists another similar wasp, called Emerald cockroach wasp (Ampulex compressa). This wasp, of the family Ampulicidae, injects cockroaches with it’s eggs; the peculiarity is that the wasp also injects the cockroach with the toxin directly in thoracic and cerebral ganglia, which prevents cockroach to move, effectively turning it into a zombie. It was explained that this is what happened in the Fortitude as well, the wasp larvae have taken control of human bodies, and they turned on people closest to them, when they felt threatened.

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Excuse me Sir, do you have time to help me search for cockroaches? (this is NOT an emerald wasp)

Photo by Wolfgang Hasselmann on Unsplash


All in all, I wouldn’t call Fortitude’s first season exceptionally bad, but I wouldn’t exactly call it good. They had some excellent moments, and the mammoth-wasp story-line was, in my opinion, on point, but was often overshadowed by multiple story-lines that don’t necessary bring anything to the overall plot. If you want to watch something that doesn’t require a lot of thinking, and can overlook some of the obvious biological mistakes, I would recommend it. However, I think it’s time that filmmakers educate themselves, or ask for help, when tackling topics they don’t quite understand.
(I read on Wikipedia that the writer did consult a parasitologist, which is probably why that part of the story functioned well; I don’t know why they didn’t do it for the other aspects of biology in the show.)

So, what do you think? Should we focus more on biology being correctly represented in popular media? Did you watch Fortitude – if yes, what did you think about it? Let me know in the comments below! 🙂

Biology in popular culture – neuroscience & movies

Hello everyone, and welcome to my new post! Yes, I’ve decided to try and write more often, and this time I will do a bit of self-promotion. As you may, or may not, know, I love watching movies – I think they are great past-time and I find them relaxing. Lately, I have had some troubles concentrating for more than an hour, but for now I would like to think that’s because I wasn’t choosing good movies to begin with. What does that have anything to do with neuroscience?

 

gyruslogo


Well, apart from writing this blog, I also write and edit for Gyrus Journal. Gyrus is student journal of neuroscience, where we write review articles about different topics: basic neuroscience, neurology, neurosurgery, and psychiatry. I have written some articles, and if you stumble across them, don’t judge me too hard – they are meant to teach us how to search databases, cite, and write in English, since our mother-tongue is Croatian. I feel very fortunate to be a part of this journal, since it helped me a lot in understanding of many scientific terms in English language, primary language of science; it also helped me to learn how to communicate with my authors, as well as how to dissect a topic I’m supposed to write/edit about. Of course, we also have reviewers, wonderful professors and scientists from University of Zagreb, who do the last editing before publication. (I would just like to say that we didn’t have reviewers from the very beginning, hence why some of the earlier articles perhaps lack in quality.) Lately, we have been struggling a bit with latest editions, but started to publish articles online – you can access them all on the link above. You can also follow us on Facebook page as well as Twitter!

A cover photo of the Gyrus Journal; light pink stylized brain surrounded by Gyrus logo and topics
A cover photo of Gyrus Journal


In Gyrus Journal, you will also find shorter articles and movie&book reviews, where title of this post finally comes in play! So far, I have written five movie reviews, with three still waiting to be published. For my first one, I picked the obvious choice: Memento (2000) by Christopher Nolan. Apart from being one of my favourite movies in general, I think it truthfully portrays anterograde amnesia.

In addition to portraying Leonard’s fragile mental state that makes us question not only his current objectives, but also whether his recollections of past are reliable, or simply figments of his imagination and almost fatalistic wishes, Memento is different in comparison with other films of similar genre, simply because it truthfully portrays the slow agony of losing the principal neurobiological process – a human memory.

You can access the full text here: Gyrus11-Memento

The second review I did was about movie that might not seem so obvious, but was quite intriguing: Side Effects (2013) starring Rooney Mara and Catherine Zeta-Jones. This movie also has a crime aspects but it deals with the psychiatric illness, for which we don’t know, until the very end, if it’s real or faked.

You can access the full text here: Gyrus12-Side-effects

Although dealing with semi-real thesis, the question still remains how the movie influenced real world cases. Did it help with recognizing the ones feigning the illness, or just put extra strain on the patients dealing with the illness that is already under deep historical stigma? Regardless of being the rather entertaining thriller, we are left wondering whether the movie deepened the negative view of the various psychiatric illnesses in the general public.

Three, still unpublished, reviews are:

  • 100 Minutes of Glory (in Croatian) – a biopic about famous Croatian painter Slava Raškaj, who was born deaf, suffered from depression, and lived her last days in Psychiatric hospital “Vrapče”. In Croatian, title of the movie is also a wordplay on Croatian word “slava”, her name; it’s literal translation to English is “glory”
  • A Different Brain – famed documentary by Loius Theroux; it follows four patients who suffered through some sort of traumatic brain injury and consequences it brings
  • Still Alice – movie that earned Julianne Moore an Academy Award for Best Actress, Still Alice is a touching but often times difficult story about a woman with early onset Alzheimer’s Disease

What about you? Do you like watching movies – which ones are your favourite? If you watched any of these, please tell me what you think! I would love to discuss movies with you & I’m really interested what you watch in your free time 🙂

RTŠB 2019 – biospeleology field trip – PART 2

I hope you liked part 1 of my biospeleology field trip in Slovenia, because here is part 2! Here I write about other days & share the rest of my experiences.

Day 5

The day started with making some spreadsheets and entering coordinates for various water springs. After that, we visited the Rivčja jama again, but unfortunately we found no Proteus (or anything else for that matter) in our traps. However, we found a very narrow entrance to the other part of the cave, aaaaand I got stuck. Like properly can’t-move-in-any-direction stuck. Most of you who never visited a cave probably wonder what kind of feeling that was. I don’t have a straight answer for that, since it’s more a range of emotions being experienced all at once; I wouldn’t describe it neither as panic nor fear, although parts of that were present. It was more a desperation that I’m not strong enough to wiggle out, mixed with frustration and adrenaline rush. I didn’t feel claustrophobia, but that feeling might sometimes be present as well. In the end, I managed to drag myself up that hole, and enter another part of the cave. Tjaša went even further, to my amazement, but I stayed back with Ester & Eva and collected as many pieces of another fox skeleton I could. This was was almost hole, but I only took few limb bones, skull, jaw bones, and vertebrate. *expect a video about it soon
After this ordeal, we went back to swimming in beautiful Krka and went back to school for quasi picnic (a barbecue on the school meadow).

cave
Inside of the cave


Day 6

Day six was day off; Bruno, Paula, and me went to Ljubljana and visited huge mall complex. Why? Because they have Whoop!, a trampoline park. In our defense, we were not the only adults there. After an hour, we went on our merry way to Burger King, and then a bit of shopping around. The most important thing I bought were hiking shoes. Paula helped me choose a pair (she specializes in orientation running, so knows a great deal about it), and they are pretty neat. But why Emina, why didn’t you already have ones? Well… That’s a long story, but I never had to walk this much before, and didn’t have to constantly change from my boots to rubber ones. So yes, before buying this pair, made for walking around in the forest, I wore my black combat shoes, with metal caps. One boot weighs almost 1 kg, so you can imagine how easy I suddenly walked everywhere. Just a note, specialized shoes exist for a reason.

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Wasp spider, Argiope bruennichi, in the grass


Day 7

On this particular day, I was on duty. I already wrote what that means, and it was exactly like that – preparing breakfast and making lunch&dinner. Nothing interesting happened, after my group returned we talked a little bit where they went, some determination of specimens happened, and we also had another lecture, about climate strike.


Day 8

This day was special because we were joined by Teo. I think he was Ester’s mentor for her Master’s thesis, but I’m not sure. In any case, Teo is an achieved biospeleologist and obviously knows a lot. First cave we visited, Jama pod Gradom, was nice, but I honestly don’t remember much, apart from the fact that we were walking around for kilometer or two, before realizing we parked in front of it. The second one, Blatna jama v Šici, was, to me, quite a difficult one. We spent more than 2 hours inside, climbed up, and down, and up and down, we crawled, and had to use the before-installed rope in order to pass some sections (not with equipment, just good old hold-the-rope and walk really closely to the rock). Well, the fact these were old lead to the unfortunate fact that Bruno fell in the water, after part of the rope tore. I wish I caught it on the video, but, by then, my camera was already completely out. We did caught quite a lot of Proteus, and I honestly didn’t realize how big they can sometimes be. *I have to check, but if the footage is salvageable, you can expect some kind of video
In the evening, I did some more determination with Anja & Tjaša.

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Did you know spiders can also live in the caves?


Day 9

First cave (Vodna jama pod Zijalom) was flooded, so we were hanging out in the front, trying to catch some more Niphargus (them) or taking videos (me). Then, we went back to Velika jama pod Trebnjem, the first one we visited and where we laid traps for infamous Leptodirus. Unfortunately, we found nothing, every trap was empty. Of course, we went back, and then some of us went looking for bats with bat group. This catch-mark-release activity has taken place a bit further from the school, near the small pond. The pond which also connected to a cave system, but had no entrance big enough for us to go in. So, two wild-life cameras were put up, as the word from the village was that at night, Proteus came out to play, um feed? Swim? Enjoy the moonlight? I’m still not sure, but next day I was told that they were captured on video. All-together, 23 bats were caught, with 10 different species being noted, which is a lot. Like huge, because when we first started, the bat group was optimistic with the estimate of “maybe 10 bats, and maybe 3 species”. I didn’t handle any bat, because 1. I don’t know how and 2. I have a perfectly rational fear of rabies.

 


Day 10

No caves today! I switched, and spent the day with amphibian group. And since it was the last day, we mostly chilled. We did try to visit one pond, but it turned out it doesn’t exist. The second one was actually really close to the cave I visited previously (Pekel pri Kopanju), and there we found quite a lot of frogs (all stages) and salamanders. Honestly, they looked really cute too! Afterwards, we went to Krka for quite a long time (*and quite a nice footage!). For dinner we actually had a whole dinner&party, but I had to miss that one due to migraine.


Last day was un-adventurous, we packed, ate a lot at McDonalds, and finally arrived home. And I’m looking forward to going again.
I would like to say a big thank you to Ester, Tjaša, Anja, Eva, Teo, and Živa, as well as our organizers.

Biology & informatics &… olms?

Last Friday (8th of November) I was fortunate enough to hold a workshop (with Bruno) called “Little workshop of Bioinformatics” – the title is a bit wild, but we purposefully chose an “exotic” name in order to arouse curiosity.
This workshop, held in House of Velebit in Krasno, is actually a continuation of a two workshops we already held (one in a City Museum Samobor and another one at my old primary school) and which we designed to introduce school children of all ages to primary concepts of molecular biology & genetics. Of course, kids in 7th and 8th grade were already familiar with it.

We first designed the workshops, with the help of our mentor Dalibor Paar, associate professor at Department of Physics, Faculty of Science, and were nominated for Rector’s Awards in 2019.

Where is the informatics part, you ask? In the using of micro:bits, cute and small mini computers that are easily programmable in Python or JavaScript (we chose Python). Bruno wrote a very elegant code and I designed the rest of the workshop: ciphers to de-code, phenotypes, core of the workshop… In terms of design, my BFF Ivana generously lend her drawing skills and we were all set.

fbt


How the workshop works?
First, I introduce students to basic concepts of the molecular biology: what is DNA, what is a protein, and that DNA codes for proteins. This part, depending on the ages (and attention) of children can last up to 15 minutes, then the fun begins. Every kid gets a cipher, which consists of four or five lines, each of those consists of nine differently coloured arrows that can point in one of four directions: up, down, left or right. micro:bits have motion sensors that pick up in which directions they are pointed and display one of the four letters: A, C, T or G. We also coded for a second program, in which kids enter those letters (DNA bases) and they show three letters that represent a very short amino-acid sequence (in this example, a protein). When they are finished with this part, we give them another paper, where they are supposed to find what is encoded by their protein (blue or green eyes, blonde or red hair…).
For the workshop in Krasno, we switched things up a bit, and our “proteins” encoded for different characteristics of two different olm subspecies: a pink one and a black one.
This might seem a bit complicated in theory, but in practice, children picked up everything really fast 🙂

Olms & micro:bits!
Olms & micro:bits!


So, how many of you have heard of olms, or proteus? And how many of you knew there is a black subspecies? 🙂
Olms (Proteus anguinus) are amphibians (like frogs), they are completely aquatic and live in dinaric caves. Noted sightings include Italy, Slovenia, Croatia, and Bosnia and Herzegovina. They have elongated bodies, external branchiae, and no eyes. The black subspecies (Proteus anguinus parkelj) is, well, black, and has eyes. The other notable difference is that pink olm lives in colder waters (up to 11° C). Another interesting fact is its name in Croatian: “čovječja ribica”, which roughly translates to “human fish”.

I think the name is appropriate, and you?