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

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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.

Week 7: To Europe and Back

Spent the past 4 days or so in Turkey. The graduate network I am associated with organised a bioinformatics workshop in collaboration with a local university in Istanbul. The workshop covered many different techniques like ChIP-seq and functional enhancement analysis using GO-terms. Unfortunately, due to technical issues the sessions didn’t always run as smoothly as I believe was planned. Out internet connections were limited, and the programs we were meant to be using weren’t always compatible with each other and our own machines. In any case, I was glad to get to visit Istanbul and learn about Turkey—a country which I am embarrassed to say I know very little about.

One thing that surprised me about Istanbul was simply the magnitude and size of the city itself. Around 15-17 million people live in Istanbul—it’s Europe’s largest city (Moscow and London are 2nd and 3rd, respectively). I got a sense of this just from the taxi ride from the airport. Another interesting fact about Istanbul is that it straddles both geographical entities, Europe and Asia. The continental boundary lies on the Bosphorus strait—thus, the three suspension bridges that span this body of water are effectively transcontinental, pretty cool! I had the pleasure of crossing these bridges on multiple occasions—I’m sure there is a metaphor in there somewhere concerning my own Eurasian identity, but I will forgo the trouble.

Anyhow I have to get back to work, I have a presentation to prepare for tomorrow. It’s already my turn to present the POTW (paper of the week). I’ve chosen this paper. It’s a neat adaptation of dCas9 technology for manipulating chromosomal loops. The paper used two dCas9 constructs from different species (S. aureus and S. pyogenes) fused to an inducible dimerizable plant hormone system to regulate the expression of β-globin. The Stanford authors have since commercialised their system. So I’ll definitely be watching out for other creative uses of this technique in the chromatin organisation space (not sure if that was a pun, but either way it wasn’t intended).

Feature pic is the Blue Mosque in Istanbul.

 

Week 6: Sudoku

Got my hands dirty in the lab this week. Tried to follow a pretty involved ChIP-Seq protocol and got stuck on a few steps, i.e., what should have taken me around 30 minutes ended up taking the entire afternoon. In any case, I’m slowly learning how to navigate my way around the lab, where things are kept, who to ask for help, the logic of how things work generally. I’m not really feeling like I’m making any progress, but I think it’s normal at this stage. Been thinking that I need to read more, but not entirely sure what I should be reading. I’ve kept up with making notes and highlighting every paper I’ve tagged as ‘To Read’ on Zotero, so there’s that. I’ve also been listing the presentations I’ve attended and taken notes on. There’s no harm in cultivating this habit so I’ll check back in about 6 months to see whether there’s been any tangible benefit to this practice. Intuition tells me that it’s one of those things that you make small but measurable progress on day by day.

This week I didn’t learn anything particularly interesting about Israel I feel like sharing. Although I’d like mention one thing that happened a few days ago at a marketplace. I am East-Asian and look it so I get a lot of ‘ni haos’ and ‘China’ directed at me by various vendors and people on the street. They seem rather uninhibited here at doing that sort of thing. When I first arrived it was a little uncomfortable, but I’ve gotten used to it and treat it as an expression of curiosity rather than malice. Although the other day, a youngish Arab guy shouted something at me as I walked past his stall, I ignored him and kept walking. He didn’t give up and I noticed him staring at me, he tried one more time, but this time shouting ‘sudoku’. It amused me so much I forgot to get offended.

 

Week 5 – Are Giraffes Kosher?

The giraffe belongs to the family of grazing animals that have cloven hooves and chew the cud…

…and therefore yes, giraffes are kosher for eating—this week’s fun fact.

In the lab I’ve been reading about note taking and organisational/time management techniques for streamlining my efforts at research. I’ve definitely got this idea drilled in my head that I have to be efficient and effective in everything I do and that any lapses in this efficiency must be avoided at all costs. Admittedly, this obsession has ironically been taking up a lot of the time that could be spent actually being productive. It’s a trap I’m often guilty of falling into—a form of procrastination disguised as ‘optimisation’ you could say.

Nevertheless, I’ve made a note of a few tips and tricks that I’d like to integrate into my daily workflow and general approach to research. The two most actionable of these are as follows:

  1. For watching talks or presentations: make a list of three things as you watch a speaker present their work. These don’t necessarily have to be things you liked or learned about the talk, but have to be thoughts or insights you can take home and could be applied to other situations. For instance, the way a speaker explained a particular topic, an analogy or way at looking at a concept that didn’t seem intuitive or could have been more elegant. Next, try and think of one more ‘thing’. After the talk look at your list of the 4 things about the talk that were noteworthy and cross one out. Try and commit the remaining three to heart. It’s an quirk of human memory that we will tend to actually remember the item that was discarded and even strengthen the connection to the remaining three.
  2. Time management: batch ‘low-effort’ tasks together. This advice draws on the phenomenon that it takes a while for most people (myself included) to enter into a ‘flow state’ that is important for ‘deep-work’ or high-intensity tasks which demand full attention and focus. By setting aside time to do the little things and errands—like email for instance—you can chunk all of these activities together which saves you getting distracted by them when the time comes to do some high-effort work.

Truthfully, it made me feel slightly neurotic when I realised how concerned I am about these little things, and I often question exactly how much my overall effectiveness is improved from small tweaks in the name of ‘optimisation’. However, I believe in the value of compound interest and I want to start off on a sound footing.

On another self-indulgent note, I’m pleased that I’ve kept up these blog posts for well over a month now. Although I’m sure when real work begins and responsibilities pile up I won’t be able to be so smugly impressed with myself.  Will shortly be performing some ChIP-seq experiments. I’ll also need to start culturing some human embryonic stem cells if my idea for furthering some previous work gets the stamp of approval from my advisor. Been thinking about ways to determine how epigenetic features can be manipulated to systematically compare different populations, e.g. neurons of twins where one has developed schizophrenia and the other has not. The new dCas9 epigenome modifiers seem to have a whole lot of potential in this regard, particularly if their multiplexibility proves to be user-friendly.

 

 

Week 4 – The Good Samaritan (With Marital Issues)

I spent yesterday in small city called Holon which is about a twenty minute drive from the centre of Tel Aviv. Holon is home to a small community who claim they are descendants of the Samaritans. The Samaritans were an ancient Israelite tribe who split from the Jewish kingdom during the time of the priest Eli and King Solomon. I visited this community via a tour arranged by the university and was shown around by a local guide who also gave us a short presentation about his culture and traditions. The Samaritans are a small, but tightly knit ethnoreligious group whose population in Israel consists of around 800 people. Their core beliefs are similar to those of Judaism (Samaritans also follow the 5 books of the Torah) but differ somewhat in customs and practices. Our guide walked us through a week in the life of a Samaritan. He stressed that Samaritans did normal things during the week, but on the Shabbat, strict observance of ritual must take place along with refraining from all forms of work. Samaritans are not even allowed to plug in their refrigerators during this time, nor operate any electronic device, including elevators— not too different from ultra-Orthodox Jews who are similarly inflexible in this regard. Interfaith marriages are not prohibited, although according to our guide, ‘marriage is a big big mistake’ and ‘don’t tell my wife I said that’. But, as he continued, if you still want to go through with it, your partner must convert and become a Samaritan or you yourself must apostatize, which must be affirmed by the high priest in a process that takes about 7 years. So basically, mixed marriages are frowned upon it seems.

All in all, I was privileged to receive a fascinating glimpse into a small religious community on the fringes of Judaism. The featured image of this post is of the colourful fruit ceiling that decorates the Samiritan version of the Sukkah (huts constructed during the Jewish festival of Sukkot).

This week in the lab I’ve just been doing some reading, both light and heavy. Made a few breakthroughs with the project I’m working on and am on the whole, quite inspired to continue brainstorming. Still haven’t started wet work proper, but I can feel the tides turning and will try not to take this relatively calm period for granted.