Aaargh…. One of the side affects of writing is the constant need of noise. I’m not joking. If it is too silent, I can’t sit still. It reminds of the entrance exams to high school and university. So I listen music and I have to sing along of course from time to time. Everything seems normal so far, what’s so wrong about this you might say.

I’m singing in KOREAN! After watching that many dramas and half the available episodes of Running Man, I made my way to K-Pop. I would find the songs I liked from drama soundtracks but I have never actually googled group names until a few weeks ago.

It all started with the episode of the running man where BigBang was the guest. They looked interesting so I read about them at wiki. My jaw dropped at their success at such a young age. Wow. Just wow. One thing led to another, I decided to watch all the episodes of Running Man. Came across Choi Siwon, hmm he looks cute. Another wiki search, met with Super Junior. My jaw again dropped, how they can maintain a 8-12 member (I lost the count after 6) boy band. I can not get along with 6 of my siblings, they perform together? And they have some catchy songs on top.

So know my list is crowded with Super Junior and BigBang songs. Expanding to 2PM. I am not only listening but actually singing along. I spent 7 years in Sweden and didn’t go beyond saying tack. Me who for one reason or another didn’t learn Swedish is desperately trying to sing along in Korean…

I don’t know when I will finish all the writing but looks like I’ll learn Korean along the way 🙂

Pulatise Tinnitus Cure Found

I have been quite during the conference and after. I would have kept quite if it wasn’t for this kick-ass correlation analysis. The data you are about to see is revolutionary. I have been visiting doctors, trying to get to the bottom of this tinnitus problem. I literally want to stab my ears – only the right one to be honest- pretty much every night. But something magical happened during LA. It might be a certain religious magic, more on that at a later time, or it might be related to the temperature. You see in LA, 48h after landing, I was cured of tinnitus. The constant signal was there but I am quite used to that bitch by now. The latest nightmare… pulsatile tinnitus.

It was quite magical. Day after day, I had good night sleep and nothing was playing in my ears. I didn’t get to taste full silence but it wasn’t thumping/buzzing. There were no drums. I thought maybe it is because I get quite tired during the day and pass out so I don’t get the chance to hear it. But I came back to Stockholm for 4-5 days… nothing… It’s like… nothing. I was finally free of it. Unbelievable…

Until it came back couple of days ago. Both during the conference and after I came back, I would feel like it was coming back for short periods of time (less than 15 min). During those minutes, I would feel something else; cold. My feet, my nose, my hands would get cold. When I put something on, keep myself warmer or start moving it would disappear.

In this house of course there is no keeping myself warm enough. The house temperature is slightly better than outside but certainly not habitable by my standards. I have wool socks, sleepers, wool carpet and a thin layer of laminate over the stupid linoleum but nothing keeps my feet warm. So my theory is that this annoying pulsatile tinnitus is related to my body temperature and circulation/swelling. Look at this beautiful graph:


There is no way that bullshit “Oh it’s your jaw” diagnosis is true. Now to gather real data, I should get several thermometers for indoors and for body, blood pressure monitor. If this tinnitus sound is objective, I could also get recordings. There must be a next generation stethoscope, mustn’t it?

Yes I am going crazy over this. How can I not! As I said, I literally want to stab my ear, only it is not detached from me and I would be stabbing myself. I fear that would be enough of a reason to lock me up.  I will not stab in order to keep my freedom. However I will find a solution. Maybe within a year, maybe a decade or a century. And when I do, I will be wishing every doctor I have seen a nice travel to hell.

Padam… padam…

I wish there was an on/off button in our auditory system to eliminate the internal sounds. It’s really tiresome to hear these sounds all day long.

I kept saying it can’t get worse for sometime after the tinnitus started. Let me correct myself, there is tinnitus and then there is pulsatile version… If you think tinnitus is hell, you have no idea what you are talking about. You get the pulsatile one on top of that and now you have seen hell.

I couldn’t find any remedy yet to the problem other than a temporary relaxation while the ear is sealed but I’m afraid it will make the problem worse. It also doesn’t make sense. If this is my heartbeat/bloodflow why I feel relaxed when I should be hearing the internal noises more loudly?

I guess I should be prescribed the medication called ‘Nature’, find my peace with my nervous system and all should be well. Not much left… July-August… sea (me not swimming), beach, sun or a cabin in the woods with some books (there has to be a fireplace)…

Scripts Toolbox for Protein Art

Look at me, all grown up using git and creating websites with sphinx. Why I started all this? Well to finish a course project. And also I had to obtain better programming practices. If you want to read a fancier, longer answer including why I needed better programming practices here is your answer:

Coding is an activity feared by quite a few biologists yet it is a necessary skill to have at least on beginners level within many fields of biology. Computational biology is on the far end of those fields, as it requires more knowledge on programming than biology.

Why is programming more important than the biology in this field? Well to answer this question I will summarize my own experiences as a biologist in computational biology field before I made the decision to tame my computational skills.

I have used a computer for the very first time in 2004. I have met with terminal in 2009. I have tried to learn programming by myself. However, let’s face it, no purpose means no progress. So I it wasn’t until my master thesis that I wrote a functional script. I learned Python and wrote lines of codes in the worst possible way, perhaps and those lines gave me what I needed. All was well at that point.

I started my PhD, subject is structure & function of ligand-gated ion channels. The name doesn’t strike as something extraterrestrial. It is a protein and I’m a biologist. Besides the title, everything was and is extraterrestrial. I have learned that quite many of the data on articles were generated by in house scripts or programs. Even if there was a tool, the output was not in the format you desired. Porting 5000 data points to excel and manual clicking 100 times to get a simple bar graph was meant suicide and no thesis would be finished within my life time. I had to rely on my scripting knowledge increasingly.

I am a person who learns things on the fly and gets the job done in any possible way. Then finds a way to improve it if needed. Although this motto provided me with three articles and a few more about to be published, it also damaged my sustainability. Spending the same long hours for similar analysis was just ridiculous. And that’s why I needed to obtain better practices: version control and documentation especially.

Enjoy the Scripts Toolbox for Protein Art and watch my baby grow up (sounds creepy). Just enjoy the website.

Yay! I have got the response. I was expecting a score well below the threshold but seems like I have got a good, ambitious idea. I bet many do make it to the the threshold point. Anyways, I just need a CV boost to provide background for it for they have no excuse in giving me a 100 over 100 🙂

That pretty much decides the question for the future. Keyboard or pipette? While I have a good connection with keyboard, I need to obtain a pipette to get funding for the project.

But first things first, I need to write that thesis!!!!

Making a Change

That wasn’t so bad… I actually survived the infectious attack with the minimal possible damage, meaning in about 3 years I’ll be deaf in my right year. If I’m lucky I’ll still have a healthy left ear by that time.

I found myself wondering what I really want to do with my life after PhD. I’m seriously considering something more public. Say go help build a school or shelter… Go be a volunteer in an education park… Just go play with the kids… Take care of elderly… I don’t know if I’ll ever do any of these but it’s nice to know there are people who actually does try to make a change.

Living on One , Born Into Brothels

Just two examples came to my mind, watched recently. I guess I’ll start by not having that PhD party after all. I have these days when I get skeptical about the long chains the donations passes through. How much of that donation actually goes to the very reason of the donation in the first place? I don’t know. I never searched for the answer. Some other days it feels like you make a donation just to feel better about yourself. Well whatever days are left, in those days I think you make a change with the donations. So I’m thinking now… skip that PhD party. Host a small cocktail at SciLifeLab. Ask people to voluntarily make a donation for clean water, education, food or clothes instead of contributing to the party.

I should actually finish writing my thesis for all this to happen, of course. I’m writing just not as fast and not as nice. I hate organising my thoughts. Everything is a big network of neurons for me. Finding a path within that complex interconnected thoughts is just… sad. Not difficult, not impossible no. It’s upsetting. Is it because writing marks a change, marks an ending I wonder. Contrary to the wish of making a change for a better world, I don’t like to make a change for myself for better or worse.


Day 8 or 9

I forgot the count already. Yesterday was a lie, it is all back! The headache, the blocked ears, everything… In case of a real apocalypse, I want to be the first one dead! Surviving viral infections in 21th century with food, clean water and sewage systems is not something I can accomplish. I can’t possibly imagine myself raising from ashes to save the humanity.

Or maybe I could survive… as a zombie tough not human, or vampire. I’m eating the wrong food, maybe I need zombie or vampire food to get better 😛 (as in a joke!)

What’s Happening?

Day 7

I actually feel fine. I spent the day sleeping with high-fever. Oddly enough I didn’t have fever till today. I woke up to eat food only and drink some water. At 5pm today, I woke up again for dinner (only to realise that I have slept too much and my brain forgot how to function) with no ear pain, no blockage. Sure I still have my sinuses full and my usual tinnitus level but my ears…

The long standing problem I had with them… Could this be the end of it?

As I was told, I have bilateral hearing loss, cookie bite shaped. It’s hereditary and I should not worry about it at all. I kept it checking with this awesome program:  Hearing Test . I was convinced that after a year of no change in the level that it was something I always had, even tough it was discovered after a long lasting respiratory infection. Today for the first time my hearing did increase. I only have a dip at 2 kHz. The rest is pretty close or above 20dB.

Have I finally grown up and fighting back with those bacteria? I wonder whether that 2 kHz dip is related to a damage by infection. Let’s see if I can preserve this level.

I have the urge to write to all the doctors I have seen so far and say politely that they were wrong!