Week 14: Still in Hostility

Hi,

It’s been two weeks now since my break. It’s such a weird feeling—the thought that I’ve ‘come back’ to Jerusalem. Just another confirmation of the relativity of what is normal. It’s the feeling of trying to explain something to a visitor about your hometown which in actuality makes no sense—and realising that you’ve been taking for granted the universality of what you consider to be mundane. Living in Israel has shown me that sometimes I should just accept things as they are. Looking for explanations only breeds frustration in this country. Anyhow, I realise I’ve belaboured the point. But I hope you will empathize that I’m still in the disillusionment/hostility stage of moving to a foreign country.

The next stage on the cultural adaptation curve is the humour stage. So I hope can laugh about this soon. But at the moment, I guess I’ll just have to push through the growing pains.

Lab Stuff

Things are getting interesting in the lab. I’ve put my foot down and made some executive decisions with regards to ordering materials (e.g. plasmids, primers, etc) for the experiments I’m planning to carry out in the coming weeks. I’ve got a handle on the data I have and what more data I’ll be needing. When the items arrive I’ll begin the temperamental art of cloning. I’ve deliberately chosen methods I have carried out previously as to make this process as painless as possible. I want to see how much I can get done before the next semester starts and I’ll have to take some classes as per my credit requirements.

Spoke with my supervisor this week also. He’s been away for a few weeks so we haven’t had a chance to catch up in a while. I think he is in agreement with my plans at least in the short-term, but we will see about everything when I finally get some preliminary data.

A bit of a short entry this week, I will endeavour to make more notes throughout the week so I’ll have more to talk about in future posts. And again, I need to finish my systems biology post ASAP.

L’heeterot for now.

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Week 13: Back To The Lab Again

Shanah Tovah!

It’s time to end my Christmas hiatus and to get back into writing and posting updates. It’s been around three weeks since my last entry. Over my holiday I visited family and friends—it was a whirlwind of airports and airplanes. I probably spent more time travelling in the last two weeks than I had the whole year. Spent time with my grandparents and cousins I hadn’t seen in years, ate some incredible food—satisfied my cravings for some good Asian food (nigh-impossible to find any in Jerusalem!). To cut a long story short, I definitely appreciated the time off, but the show must go on!

I’ve been writing a piece on Systems Biology and promised to post it before the new year. Unfortunately this didn’t happen, but I’ll get it out ASAP.

Lab Stuff

I arrived late on Saturday night back at Ben Gurion and went back to work the next morning. It was easier than I thought getting back into the swing of things. Continued to process some RNA/cDNA samples and performed some RT-PCR analyses. I wasn’t successful, i.e. there are some unreconcilable anomalies with what I was trying to do (looking at induction of a particular gene). But I did have some good news! Sequencing results from the CHIP-seq I did ages ago finally came through. They seemed to pass initial quality control. However, it may take some time to work with the data and for further downstream analyses as the data files are very large (1.5 gigabytes a piece). I’m hopeful.

Thawed some mESCs for new efforts in tissue culture. I’m kind of trying to do many things in parallel, so that I’m always spinning one or more plates so to speak. When one drops I’ll always have something else to focus on, so as to not lose momentum. I’m going to also start ordering plasmids and planning experiments with dCas9-activators as I mentioned in a previous post. Decided to use HEKs as the cell system for ease of transfection. When this project gets off the ground and running I’ll explain in greater detail what the plan here is exactly.

General Thoughts

I’m growing more and more comfortable with life in Israel. I’ve somewhat come to terms with all of the inconveniences and frustrations that seem to be unavoidable in this country. This has occurred through an adaptive process where I reflexively lower my expectations and plan for the ‘weirdest-case-scenario’. Absurd things happen all the time in Jerusalem, trying to find rational explanations is a futile endeavour. For instance, the intercampus shuttle bus here at the university is very unpredictable. It’s often very early or very late, and the places they stop at change at random for reasons I’m clueless of. There also aren’t any signs on the buses, so you have to ask the driver each time where he’s going. And the thing that probably bothers me the most is that on a particularly busy time, there aren’t enough seats for everyone and so people need to stand in the aisle. This normally wouldn’t bother me, but it also turns out that sometimes they send more than one bus to the same location at the same time— there was even three at one point. As no one gets updated or informed about any of these things, you just never know if you should get on the bus or wait for a potential second one (some of the time there’s only one bus!)… /rant

Overall I’m optimistic about this year—for the challenges and opportunities for growth that I’m sure to encounter. But I feel also like the hardest part of my journey has yet to come. I’ll only get one shot so I’ll try not to miss my chance to blow this opportunity only comes once in a lifetime.

Peace out

(featured pic is my grandma in ramen)

Week 12: Homeward Bound

The months have flown by. On Monday I’ll be flying off to Malaysia for the Christmas holidays. Christmas isn’t really celebrated in Israel so it’ll be just me and two others from the lab who’ll be taking time off from work for family and festivities. This post will be my final status-updatey entry of the year so I’ll do my best to summarise and reflect on my experiences over the past 3 months. Also, I plan to finish up the article I’ve been writing on and off for two weeks now and get it out before the years end.

Frankly, it’s been a whirlwind of a time in the best and weirdest possible sense. New people, new places, a new language, and new perspectives. I think I’ve grown tremendously and I think a big part of that growth was realising that I still have a whole lot of growing up to do. This country is a place where you have to speak up if you want to be heard, no one will assume you want something if you don’t make it explicitly clear. Beating around the bush will get you nothing but frustration. Being direct and verging on crass is not only acceptable, but expected when interacting with Israelis. I’m not completely comfortable with this yet, my British sensibilities are not conducive to this mindset. Although I’m getting better at it as time goes on, and I think it’ll be better still when I get some more Hebrew under my belt.

It’s been a steep learning curve and I’ve definitely developed a thicker skin as a result of living here. You know, every cloud has a silver lining. I don’t regret my decision to come here—I doubt there is anywhere else in the world that would give me the experiences and challenges that I’ve faced here and still be a hub for world-class research. I still can’t get over the absurdity of my being here, but everyday life gets a little bit more normal and less exotic—and honestly I can’t wait until the honeymoon period wears off and I can start really living my life and connecting with people without feeling like an alien observer.

Lab Stuff

Not much to report this week. I’ve been pivoting out of tissue culture back to my lab bench/readings. Had some anomalies in some of my results that I’ll have to unknot, but all indications suggest that the problem is benign (I hope).

Featured pic is of Bethlehem from the North

Week 11: Hills and Valleys

Been feeling a little burned out this week. I am not entirely motivated to write this week’s post, but since I’m committed to this project it must be done. I’m exhausted. It’s not even that I’ve been particularly busy, but the stress of acclimatising to both Israel and PhD-life has accumulated without much of a reprieve. I think I’m still going through growing pains. I need to be patient. I’m sure eventually I’ll be able to direct more mental energy towards improvement and thriving rather than simply surviving.

One thing that struck me in the last few days is how my perspective on life in and of Jerusalem has changed since I got here. Namely, I understand a lot more about many things I found strange and unusual. Religiosity is something that’s difficult to wrap your head around if you don’t interact with very conservative types all that often. I’ve gotten a much better sense of what makes people tick around here. The sectarian nature of Jerusalem and Israel in general makes it very beneficial to belong to some form of tribe. In-group solidarity is amplified when you have greater discord between factions. I think this concept is best exemplified by the prices of general goods/services you get depending on whether or not you’re seen as a part of the community. I’m pretty sure I’m paying twice as much for groceries at Yehuda Market than a local, and although I’ve never visited, I wouldn’t be surprised if this is the case in the more tightly-nit districts and religious suburbs around the city. I’m quite fortunate that my lab-mates and fellow PhD students resemble a cross-section of Israel’s demographic reasonably well. I’ve had some pretty fun chats so far. And seeing as I’m completely ignorant of a lot of things people here take for granted, I think it’s been fun for the other side as well.

Lab Stuff

Getting pretty comfortable now in tissue culture. Harvested cells after doing an experiment activating a dox-inducible gene. Extracted RNA, but still need to think about what to do with it. Went to a few interesting talks as well this week. I’m continuing to transcribe onto my Zotero with the notes I take during the presentations according to a system I wrote about in a previous post. One thing I’m concerned about is that I’m slacking a little with regards to reading papers. Tomorrow I’ll think about compiling a list of papers I want to read in detail at the start of each week, and set a goal to make my way through them by the week’s end. This is something that would probably suit a sticky note at my desk. For me, physical reminders seem to work better than digital ones. Generally, I’m sensing a decline in my productivity. I think I’m due for a hiatus to recover my energies. Christmas can’t come sooner!

No featured pic this week due to the aforementioned lack of spirit. How about a quote instead?  I remember Dr. Dre saying this one time in the Netflix Quincy Jones documentary—’learn to take care of the valleys, the hills will take care of themselves’. Not entirely convinced I know what that means, but I think it’s what I need to do right now.

Week 10: Philosophy of Tissue Culture

Today marks the 7th day of Hanukkah. If you don’t know, Hanukkah is an annual Jewish celebration that lasts for 8 days and begins around late November to late December—the exact date differs depending on the Hebrew calendar. I had the good fortune to attend a lighting of the menorah for almost each day of the past week. I also ate a lot of sufganiyah, which is basically a jam donut with an extra dollop of jam on the top, and sang along (badly) to the songs that are sung during the candle lighting. This year, the holiday started a little early on the 2nd of December, which thankfully reserves the rest of the month for the season to be jolly. Sorry my Jewish friends, but Christmas still holds a dear place in my heart.

Science Stuff

Lab work proceeded as usual, albeit slower due a few absences caused by the festivities. I’ve had to postpone sequencing of my ChIP-seq libraries again after an already lengthy process of troubleshooting and quality control. However, this gave me a some leeway to try my hand at a little tissue culture, after procrastinating for far too long since I arrived. Managed to get somewhat of a feel for the mouse cell lines that our lab works with and the rhythm of my own workflow. I’m quite fond of the work, despite my occasional complaints of the mindlessness and tedium of it all. There is something hypnotic about working under the lab hood to the drone of the automatic airflow system. It’s conducive to reflection. At a couple instances this week while staring at my 6-well plates, I had a series of philosophical meanderings about the nature of work and of academic or intellectual pursuits. More specifically, I was thinking about how wet work is mostly just following protocols and making sure you’re keeping everything sterile and are pipetting correctly. It’s for sure a kind of craftsmanship. The work that goes into planning and designing experiments is reminiscent to an engineer or an architect coming up with prototypes or drafts. And the execution of a plan feels like the busy work of a construction site rather than the idealised image of a scientist. Yes, the aesthetics of it—beakers, test tubes, gloves and lab coats— fulfil the stereotype, but the work itself stripped of these decorations is quite repetitive and may go the same way as what some have predicted for computer programming . The creative part—the actual science that is—seems almost over-shadowed by what makes up the rest of the ‘science’ that goes on in laboratories*.

In any case, I was more than aware of all of this before I committed to the scientific path. I do appreciate the meditative aspects of the work, and am glad I don’t need to problem solve 24/7. It’s nice to be able to chill out and know that the science will get done in its own due course, regardless of any excess ‘scientific thinking’ I’m actually doing. It takes a lot of pressure off needing to be ‘brilliant’ or ‘talented’ that perhaps plagues other more theoretical fields. Actually, I wouldn’t mind discussing this idea with scientists whose progress solely depends on intellectual pursuits. How does the type of experiments you are expected to conduct change the way you perceive productiveness? Are more hands-on fields inherently less conceptual in terms of the questions they attempt to answer? Intuitively, more mathematical-oriented subjects are more abstract, but are mathematicians expected to be productive to the same degree as biologists (e.g, number of hours spent working/thinking about a problem)? Science is a such a broad umbrella, considering all the different disciplines and ways that science is carried out. Perhaps I need up update my answer to ‘what does it mean to be a scientist’? I think being a scientist is something one becomes after learning the tools and tricks of the trade, and when you begin to understand a field deeply enough to apply your knowledge and skills to novel questions and hypotheses.

To live a life of the mind is something I’ve told myself I want to aspire towards. However, I realise now that to do that most effectively it is also necessary to live a life outside the mind. To have practical knowledge of how the outside world responds to changes in the environment is an important part of what it means to understand. That is, creating and recording inputs and outputs with your senses provides a qualitatively different experience to simply reading about it. I’m not sure how to explain this disconnect philosophically or epistemically, but it makes intuitive sense to me.

Featured pic is a photo from French Hill overlooking East Jerusalem.

*at least in the life sciences

Week 9: December Already?

Another Shabbat has come to a close. Nine weeks now in Jerusalem and December is already here! I’ve remarked to multiple people how I miss the Christmas spirit that all but envelopes the UK around about this time. Although people here are gearing up for Hanukkah, there isn’t really the same kind of tangible festivity in the air. I can imagine  a few reasons for this that are perhaps obvious, but in any case, it’s suffice to say I’m feeling a little homesick.

Visited Tel Aviv for the first time yesterday. It was like night and day if I am to compare the city with Jerusalem. Don’t think I saw a single Haredi (Orthodox-Jew) while walking around the city-centre, nor on the bus on the way there, as opposed to Jerusalem where Haredim seemingly outnumber non-Haredim. To be completely honest, I didn’t much care for the city, it reminded me a whole lot of Canada—and Toronto in particular. Not that I dislike Toronto, but I didn’t get much of a sense of a particular ‘uniqueness’ in Tel Aviv, which is something that I value a whole lot when traveling to a new place. But I’ll definitely give the city another chance at some point down the line.

LAB STUFF (thinking I’ll start using sub-headings to separate general remarks about my life in Israel and what I’m getting up to in the lab, just to make things a little neater)

It’s getting to that point where I’m reaching limiting returns on my efforts researching and planning. I’ve got to get stuck into actually doing the experiments rather than thinking about them and optimising. A little bit of a hiccup with the ChIP-seq analysis I mentioned last week, but I think I’m on track to keep moving forwards. Dealing with error inherent in measurements and knowing when to cut your losses with regards to uncertainties in the output of an analysis. I’ve got to learn about how sequencing gets down in my department and what are the options and rough timescales for getting samples processed.

The week I’ve also tried my hand at learning a little bit of programming (R). Been also toying with different functions on the online bioinformatics platform, Galaxy. It appears to be a very powerful tool that I’ll most likely be using a great deal in the future. I’ve been feeling increasingly grateful that I’m doing research at a time where many computational tools for biology are tried and tested and are becoming more and more user-friendly. I think I’m also appreciative as to how this allows for a less monotonous working environment, ie, research progress need not solely be determined by work at the bench. I’m also planning some experiments using dCas9 methylation constructs. Hopefully I can finish up cloning towards this end before Christmas—I’ll be taking a well-needed fortnight off visiting friends and relatives and will be back just after the new year.

I think my first ‘long-form’ blog post will be about systems biology. I want to finish it before next year so I can say I produced at least one high-effort piece on this blog in 2018. It’s a topic I’ve been vaguely aware of for quite some time, but never really stopped to consider what the term entails on a practical level, or otherwise what immediate applications a ‘systems’ perspective may have for research in general—if any.

Featured pic is Tel Aviv beach, dullness aside, the esplanade is worth visiting.

Week 8: Feeling ChIPper

Got some sequencing results back from a trial library preparation I’ve been working on using some ChIP dna. I managed to get a positive result for enrichment of my barcoded fragments. Pretty pleased and I think I got lucky as this was my first time using this pretty involved protocol. Plus, half of the reagents I used were expired—protip: DNA ligase has a much longer shelf life than is advertised, and this is probably true for a lot of things. But you know, it’s always better safe than sorry, although if something still works, it still works.  I’ll process the rest of the samples this week and hopefully I’ll have the same good fortune with these as well.

I don’t think I’ve mentioned this so far in these blog posts, but I’ve been taking Hebrew lessons twice a week for the past month or so. They are provided free of charge by the university and the class is relatively small. There are around ten of us and the teacher (morah :D) is very attentive and encouraging. I feel like I have a good grasp of the alphabet now and the basics of writing and reading, albeit only phonetically—learning vocab and the grammar is another story. All in all I feel like I have enough motivation to really make a decent attempt at learning the language. It’s a satisfying feeling when I make progress and learn new words as most things here are written in Hebrew, it’s nice at least being able to read a few of the things around me. It definitely helps living in Jerusalem as I think I’ll learn a lot faster—as opposed to Tel Aviv, where there are more English speakers and I’d perhaps have less of a chance to practice.

I’d like to start brainstorming some topics that I can make an extended blog post about. I’ve started getting better at these weekly progress updates, in the sense that they don’t take all that long to write, editing is minimal if non-existent so I’m basically just free-flowing off the top of my head. Stream-of-consciousness style entries have their place, but I want to be a little more ambitious with this project. Maybe I’ll make a point to write one long-form post in December about something I’ve been thinking about recently. Although what this entails is planning, research, and editing, all of which take a considerable amount of time, but are essential to good (more readable) writing. And also, I think it would be more rewarding in the long run and to any potential readers I might gain for the exercise.

The featured pic is a bar/club street by the Jerusalem city centre—I finally found some time to experience a bit of the local nightlife. Although the music at the places I went to was nothing special, the people seemed friendly for the most part. Probably won’t go out much while I’m here.