Tuesday, 18 November 2014

Introduction to Chlamydomonas reinhardtii

I need to write a 5-page proposal today, so I'm getting myself acclimated by doing some free writing here.

An explanation - I'm switching department and supervisor for the rest of my PhD. A difficult decision to make after spending (almost with futile effort) almost 10 months in BioAnth. It's not that I hate human evolutionary genetics, but it's not my cup of tea. So, upon discussion with various people, especially with my current supervisor and college graduate tutor, I embarked on the search for a new project, new supervisor, new department... Hard to bid goodbye, but it's better for everyone, especially for myself. I've nothing to lose in the first place, except some loss of time, but it's for the better.

If the official approval is granted, then I will be joining Professor Howard Griffiths' lab to work on Chlamydomonas reinhardtii together with an awesome team to eventually contribute to the CAPP (Combining Algal and Plant Photosynthesis) project.

An brief introduction of this species which we work on - the Chlamy:
Source: http://upload.wikimedia.org/wikipedia/commons/1/19/Chlamydomonas_TEM_04.jpg
If you could see the area which is densest in the TEM photo, that's our group's interest. The pyrenoid story. There are various aspects which we are looking into, but for now, it shall be a suspense, as it's time for me to run back to the proposal.

Yes, I'm a happier me after the 10 months of struggles, though I'd have tonnes of work to be completed in lesser time than others. Yet, I am still happy and glad. I am thankful to God for answering my prayers and to St. Jude for interceding for me. Miracles do happen, if we also work in tandem with Him.

Thursday, 16 October 2014

Stupid Fish, Really??

It is hard for me to explain my current situation openly right now, but tonight I shall listen to Einstein. 

Hear ye all my fellow PhD friends out there! Dear Einstein and his wisdom!
Source: http://om.symphonyoflove.net/wp-content/uploads/2014/09/Albert-Einstein-Everybody-is-a-genius.-But-if-you-judge-a-fish-by-its-ability-to-climb-a-tree-it-will-live-its-whole-life-believing-that-it-is-stupid.jpg

Tuesday, 23 September 2014

Ubuntu on VirtualBox

I began to realise the need to eventually get a computer with Linux/Mac OS since many of the softwares developed for genomic analyses are Linux-based softwares. Though I might be an ardent supporter of Android phones and Windows 8 computers, for the sake of work, I probably am going to request for money to buy a computer with Linux or Mac environment.

Right now I'm in the midst of the troubling question if where I am currently is matching to my real interests. I felt ashamed, fearful and disappointed that I am where I am right now, and it didn't help when everything I proposed didn't work and I don't seem to be very enthusiastic about this. I know it is a sign I am not suitable to be in this area of research, as much as I wish to feel belonged here.

Back to what I've learned for the past nine months... More aware of computer language for sure. I might not speak any particular language yet. I am at beginner's level in Spanish and Japanese if I were to compare to "speaking" Python 3 and R.

Right now I'm installing Ubuntu on Virtual Box with the help of wikiHow's instruction. Very precise and convenient indeed. Now I can try to install some of the softwares which I desire to use. Let's see if it works.

My Windows desktop with Ubuntu running on VirtualBox

Monday, 22 September 2014

Wimpy = Small & Weak

At times, I am tempted to change my blog address to something else because the definition of "wimpy" according to Urban Dictionary is small and weak. Right now, I am feeling small and weak, with the recent wave of uncertainties. I had difficulties since the start of my PhD to form research questions and to grasp the bunch of theories formed by evolutionary biologists when it comes to whole genome studies of different populations, both the modern and archaic genomes. It was the first time I heard terms such as coalescence theory, Mal'ta Boy, Denisovan, neanderthals, plink, balancing selection, permutation, imputation, and so many other terms. It was a foreign field to me, which I honestly thought I'd be able to make it through even though I felt stupid the moment I joined the first team meeting. As what everyone in the team, including my supervisor, told me, I would eventually know while reading up. No idea which papers to start with, in fact, I abandoned reading papers for the first three months because I wanted to catch up on the definitions. I couldn't even comprehend a simple term, let alone the big theory behind it.

And I ended up feeling stupid and helpless as each day went by silently. I used to describe myself as the kindergarten kid working with a bunch of highly intelligent graduate student when I started, and some of you might know from one of my first few posts that I was ecstatic when I saw myself creating a plot using R when I did some tutorial. It didn't stay for long, because I was still so behind.
Source: http://mentalfaculties.files.wordpress.com/2013/05/student-depressed.jpg
By April, I was being asked to give a format of how I envision my PhD thesis to look like, and what research topic I want to scrutinise for the next three years and to form a set of specific research questions which I want to ask for the research topic I want to do. It didn't help to be constantly reminded I only have three years of funding but almost nobody in the department could finish their PhDs in three years, and that I couldn't expect the department is able to fund me in case I couldn't complete it within three years.

I proposed the first topic to look into the ancestry information markers using SNPs since there's still a gap to have a standard set of SNPs for world wide populations, just as how STR markers had evolved to be. It was rejected right after I said the final word of what I thought because the lack of expertise of supervising me and the group is doing EVOLUTIONARY studies, hence I should focus on something along selection, etc. Let's just say, I'm not fond nor knowledgeable of this, but if required, I can try. Provided I get enough support from the group. As if there was any to begin with.

Then the malaria topic came into discussion and I became quite fond of it, despite the fact that all I could do with it was the selection studies of the affiliated genes using population dataset without any phenotypic information, nor epidemiological information. Assumptions would have to be made. ALL THE TIME. However, when I started presenting research questions, everything I proposed was either too generic, not specific, someone had done it so it is of no interest to study it again, impossible, or insignificant. I was at loss after being in the condition for more than a month.

Source: http://drhurd.com/wp-content/uploads/2014/06/Depression.jpg
The typical question when one meets another is "How are you?" without expecting anyone to reply anything other than "I'm fine" to them. This is probably the most hypocritical question in the whole world. It sounds better to exclaim "Today's weather is ..........." to initiate conversation than to use that question. After months of telling people "I'm fine" when the truth wasn't at all fine, my barrier caved in. I sought help first from my supervisor and the college graduate tutor. To my supervisor, I was honest that I might not carry on with a 95% bioinformatics PhD for my lack of skills, and I'm uncertain if I'm suitable for this field. Same goes to my graduate tutor. Initial suggestion of the tutor at college is to talk to my supervisor. When I spoke to my supervisor about my fears, he suggested a change from the 95% bioinformatics to a lab-based project with basic bioinformatics. No more looking into malaria though. My two months worth of effort turned into ash in a single hour. I wasn't fully convinced, for there's the ethical commission approval to apply both in the university and locally, travel research grant (I don't possess wings to fly nor rich parents), and that very set "research questions". The assumption made about me was simple: "I must have had read a lot so I would possess ability to form research question by now". I could only smile feebly, because the truth is I might have been reading the wrong stuffs all together, since there's no basic guideline for PhD students on what kind of papers I should read to get an idea of what's happening. Especially someone without any basic knowledge of evolutionary biology of any kind.

After speaking to a few people, I felt more encouraged to tackle the challenge to collecting new samples, so I contacted a few people to see if they could help and some email addresses were passed to me for initial contact. Guess what? All the suggested populations were told to me as "not interesting if you still insist on doing malaria" and "it would take a long time to apply for ethical approval so in the end it would be impossible".

I am disappointed and hurt and lost. I have no project, no research ideas, no research questions... When I wrote to graduate adviser of the department informing my struggles with this PhD situation and the uncertainty if I am in the right research area, as he is dealing with family crisis at the moment, I was told that the department is shorthanded so there wouldn't be anyone who can supervise me. I am free to look outside the department for other projects or supervisors. Every time I recalled this email which I received, I cried. So this is what departmental support is like. Great.

My college graduate tutor recommended me to see the college counselor to have a chat about all these. I saw her this afternoon, and would be seeing her for a few more weeks to work out some of these things. Thank God for all the listening ears I have for the past two weeks. I am glad to have some people who still see me as someone who is capable to be here, when I no longer see myself that way. Dealing with this current issue in my PhD has caused me to lose confidence in myself. I know God is with me in this, despite the fact that some people think that religion is silly. I would have long committed suicide if not because God has been journeying with me all these whiles as I dealt with various issues in my life.

Indeed I am weak, I am a wimpy scientist, and I am stopping the pretense that I am fine, because the truth is I am not and I need help and support. Yet I know, there must be a way out. Even if it means I would have to change department, change project, spend an additional year to get things done, more extra hours and all, if this is the way out, I will walk it through... God is there. He brought me here, He will definitely see me through it.

Source: http://www.word-picture.org/wp-content/uploads/2013/07/b.2Corinthians12.10.jpg

Thursday, 4 September 2014

Night Owl or Early Riser?

These days I'm finding it tough to stay awake in the day time and to fall asleep at night. A bit of a mess but I guess it's normal for any graduate student to go through such phase. For a while I identified myself as a night owl, working better after sunset. Then I found joy in rising early and sleeping early. What came next was I screwed up my own biological clock by not being disciplined. I can't be both an early riser and a night owl but the greed of wanting to buy more waking time to get something done tend to mess up the circadian time of this poor body. Outcome would always be the phase where I have to deal with my weird and unproductive sleeping pattern. Ha ha ha!

It takes a while to sync back to norm. I do recognise the importance of sleeping at night. Working from home these days doesn't help with regulating sleeping pattern or discipline on when to work and when to rest, since my life is entwined in the research which I want to do, which is a series of things done while sitting in front of this laptop. Reading papers, or working on my R skills, or figuring some stuffs out, or feeding my enthusiasm of picking up Korean language while watching yet another an episode of Korean drama, or having a meal. Leaning towards a very unhealthy lifestyle, but that's life of many graduate students. It's an amazing cycle of sleep, eat, research, eat, sleep. I sometimes wish I have lab work which would force me to walk out of this comfortable and warm nest fully equipped with the right lighting to work. Yet, I probably have my whole lifetime ahead to work in the lab in future.

Probably lots of coffee would help with staying awake in the day? Or maybe I should just quit coffee? Nah... Life without the coffee aroma... is a loss.

Source: http://my.englishclub.com/profiles/blogs/early-bird-or-a-night-owl
I guess right now it's more important to get myself on my feet with some regularity of work hours. It is getting back at me, this weird schedule and sleeping pattern.

I should blog about something technical which I sort of picked up last month. Interesting personal achievement which I forgot to pat myself and reward myself for doing it right.

Time for lunch!

Wednesday, 27 August 2014

Budget, Scholarship and Happy Graduate Student

Yes, I know I need to do my work, but I can't help but to write this post.

In my previous post, I mentioned I am just a poor scholar here at Cambridge. I compared my currently scholarship with the Erasmus Mundus masters scholarship which I received for the past two years, which was a very handsome amount of money. I know this can't be compared. The payment system is different. I used to receive monthly scholarship allowance, plus mobility fund every start of 6-month term. I was pretty much able to spend when I needed to.

Source: http://i.telegraph.co.uk/multimedia/archive/01811/cash_1811300c.jpg
As for now, my scholarship installment comes thrice a year. It means I get 4 months worth of scholarship allowance in one-go. It gets dangerous when the mind is switched to "I have tonnes of cash to spend" thought. It took me about 6 months to psycho myself back to the mindset that I am not as poor as I think I am. If I budget properly, I can stretch every penny I have for food, entertainment, transport, travels, and SAVINGS.

I find this article on "Student MoneySaving Checklist" highly useful for those who need some ideas on how to stretch every penny we have. What I do is within the checklist of 50+ items of how to save as a student.

Source: http://www.studentuniverse.com/student-blog/wp-content/uploads/2012/10/budgetingpiggy.jpg
Yes, I do monthly compulsory savings. And no, I don't touch the money at all. That's my emergency cash in case I need to fly back to Malaysia at any point of my graduate studies. It is still not enough to fly back, but if I start touching it habitually it, it'll never be enough. I am using Llyods Bank, and the best thing is I could have three different accounts under the same name, so I started a compulsory savings account which the money from current account is auto-debited monthly. I also have a savings account for all the accommodation money I need to pay per term. My current account is almost always out of cash, with the lowest I got to was about £10 in it (end of the month kind of situation).

It's not easy to start budgeting, but once we get the feel of it, we'll be living a happier graduate student life!

P/S: I still do get to travel a bit with the limited budget I have...

I saw Giant's Causeway in Northern Ireland end of June 2014, thanks to the budgeting I made from the start of the year.

Coffee and Graduate Students

As I venture deeper into the journey of a graduate student, I find that coffee becomes a part of my life, as much as I don't want to be "addicted" to it. I'm trying to deny the fact that I might be a coffee addict at heart, refraining myself from overdosing since the forensics background I've accumulated reminds me anything too much isn't good for me. So far, I'm fully aware that any caffeinated drinks from Nescafe would cause me drowsiness. I suspected the case when I tried staying awake to study using Nescafe Gold (yes, I only go for the best stuffs) but I ended up sleeping for hours after that cuppa. It didn't help me to study more, but my body was indeed well-rested due to the blood-pumping caffeine.

When I speak to my graduate friends, I noted that almost everybody (shy those who are allergic to caffeine, and those who drink tea like water) would have at least a cuppa a day. Some would be at the extreme of consuming more than 6 cups daily. On average, about 2 to 3 cups. As for myself, it is once a day, in the morning when I have my breakfast, usually around 9ish. Today I woke up late so I got my brunch by 11am. According to this website, the best time to drink a cuppa coffee is between 9.30 am to 11.30 am.

The initial realisation came when I stopped by Costa in Grand Arcade daily to grab a cuppa on my way to the department. I tried to be more environment-friendly, so I bought its travelling mug. Uh-huh... it stuck with me for two weeks, and I noticed how my purse bled to death. I am but a poor scholar, honestly. Money should be spent on real, filling food. So I had to think of alternative... While Costa can be my choice when I hang out with friends. Always - the hazelnut flavour!!!!

Source: http://upload.wikimedia.org/wikipedia/en/thumb/4/42/CostaLogo.svg/1024px-CostaLogo.svg.png
I was deciding between a coffee maker and a cafetiere. I chose the latter, not because I couldn't afford it but due to the fact I don't have much table top space to keep it. A stainless steel Grunwerg 3-cup cafetiere quenched my thirst of brewed coffee. Adorably shiny little thing that my heart fell in love with. Got it from Amazon using the prize money I got for being the kid with best performance of my MSc. degree. Wheeeee!!! Now I can have non-instant coffee at home. Whenever I want to.

Source: http://ecx.images-amazon.com/images/I/21ovJ5WYYcL.jpg
Initially I stick to ground coffee from Costa, as much as I like it fresh, it's not the same as what I get in the shop. Of course, no frothy milk to accompany with it does make a difference. That's when I re-discovered my love for OldTown White Coffee (hazelnut flavour) from my home country, Malaysia. Yet, a pack only consists of 15 sachets, and I died when I found I was left with one sachet the first time my ex-student brought my "supply" from home. Thank God for my kind-hearted best friend who came back for his graduation, I received two packets. And from a friend who finished her Mphil, I inherited her leftovers. Yippee!! That will keep me going for a while. But I need to look for alternatives...

Source: http://i01.i.aliimg.com/wsphoto/v0/669333435/Malaysia-import-old-town-Old-Town-White-Coffee-Hazelnut-flavor-instant-3-in-1-600g-horse.jpg
One random shopping day at Tesco Extra in Bar Hill, I saw this lovely red packet of ground coffee with the label "Hazelnut". I don't know much about this Edinburgh Tea and Coffee Co. but I supposed the price reflects on its quality. It was priced at £3.70. Not expensive, but higher priced than others. I finally made the first cup today. Completely took my heart away. I've found the non-sugary alternative to my OldTown White Coffee.

Source: http://coffee4.me/wp-content/uploads/2014/04/Edinburgh-Tea-and-Coffee-Company-Hazelnut-Ground-Coffee-227-g-Pack-of-3-0.jpg
So, I shall continue my work now. Till then... Have a cuppa!


P/S: Many would agree with me, right??

Source: http://phdcomics.com/comics/archive/phd070513s.gif