Living Fearlessly in 2016

For 2015 and all that happened, I thank and praise and honour God. He who brings me to this, will bring me through it. So I shall trust in Him and keep going. And thank God for bringing a very special person into my life - my tall, dark and handsome love. Without him, the past seven months would've been worse.

A summary of 2015, academically-speaking:

I lived my life in fear for the best half of 2015 - after the series of traumas in my first attempt to be registered as a full PhD candidate.

First, I was told that I should not travel, or attend any soft skills training programmes or conferences, since I have so little time left to do a PhD after transferring to the department. So every time I took a few days off I was feeling guilty and then was told I took too many days off. I didn't know all PhD students were eligible for a month of holidays per year. I didn't know there was Christmas shut down of the university. So I worked through most of Christmas and New Year holidays...

Then, after conveniently trying to get rid of me partly because I had really bad writing skills and horrible time management plus being unwell most of the time, some non-academic-supervisor individual who somewhat was involved with my work announced during a meeting to resolve all these problems the reasons I was not good enough in his opinion to be a PhD candidate. A stack of papers was passed to me... And so, I found out that my daily attendance in the department was tracked for two months without my prior consent/knowledge, my lab books were scrutinised and was given a spreadsheet of all my experiments with dates, I was threatened that if the supervisor and others let me stay, they'd show me the door the next time I make a slight mistake... I know by keeping silent and taking their rubbish offer wouldn't help me to overcome all these, so I asked for help....

Fast-forwarding to skip all the meetings and the nights spent to construct timelime of events, etc...

Seven months later..

The current trade off package: I get to stay and work on the project, but I'd have forgo my complaint to the university against the individual whom I claimed to be psychologically-bullying me for that past eight months and to apologise to that individual that I had undermined him. I did part 1...

Truth is... I only get to stay if I submit a report. That's the real deal. And I only found out I'd need to submit a very formal report a week before Christmas holidays began. Maybe the communication between my supervisor and I really sucks. The worst is my paralysing fears due to all the traumatic experiences I had with them mess up my brain the moment I start writing - all the bad things that happened in 2015 crashed in and I'd be so fearful that I couldn't think at all.

So, after welcoming 2016 in a very Scottish manner with my boyfriend and his family, I'm resolved to live fearlessly in 2016.

Take breaks every now and then, as I am eligible to do so.

Try to strike some form of communication with my supervisor without fearing he'd kick me out from the lab.

Manage my experiments using online lab book tools to avoid incidents where the individual can be tempted to stalking and bullying and stealing ideas again.

To live life to the fullest (John 10:10).

Thanks for reading.

To a great year of academic writing! #AcWri

PLOS Synthetic Biology Event: Interview with Dr. Fuzhong Zhang

There's an event coming up this afternoon, 4pm UK time - an interview by Dr. Steven Burgess (Department of Plant Sciences, University of Cambridge) with Dr. Fuzhong Zhang (University of Washington, St Louis) on the role of cyanobacteria in space (and more!). Dr. Zhang's research is currently funded by NASA and it'll be cool to join them in the discussion on NASA research.

Click here to join the Google Hangout session

If you guys have watched the Martian, you probably know what this movie is one of the few which featured a botanist as a hero in a film. Dr. Zhang is researching on growing cyanobacteria in space. There are other research going around the world - including growing plants in soil from Mars, etc.

Your job will be to ask questions during the interview!

Just in case you wonder how does cyanobacteria looks like. Here's an image of it!

http://www.waterboards.ca.gov/water_issues/programs/bluegreen_algae/docs/cyanobacteria_microscope_big.jpg

Enjoy yourselves!

#syntheticbiology #PLOSSynbio #livestream #interview #cyanobacteria's role in #space #research #NASA today 4pm BST
https://plus.google.com/u/0/events/c2gnundras37n5c08pvst80cgj8

PhD: A Decision in Life (. or ?)

A last minute plea from a fellow Malaysian to fill in the slot for another PhD student who was supposed to share his/her PhD experience brought me to an eye-opener PhD event by the Cambridge University Biological Society (BioSoc). It was interesting how the event was designed - where types of PhDs available in UK and US were discussed, how to get into a PhD programme, what are the requirements, how PhD is linked to industries (thus no longer confined to academia alone) and finally some form of sharing by a graduate student about the Cambridge graduate experience (that's where I came in).

What I thought was interesting in my talk, of which my boyfriend found it amusing as well is this:
"PhD is not a bed of roses; it is more like walking through the rose bushes where the thorns are poking at us but we'll end up looking at the roses one we get through the bushes".

Other than that, a work-life balance is crucial to stay sane and keep going with our PhD battle. We're all warriors, but remember, we're already first a champion in our lives, when the strongest sperm met the ovum and created us.

I wanted to discuss a bit about the "full stop" and the "question mark" in the opening slide but somehow I didn't. Some people are questioning if they should do a PhD, and some have already decided to do a PhD no matter what happened. Life is full of twists and turns. Ten years down the road, I may not be doing what I'm doing now. But, it is still something I won't regret doing..

So, hang in there, people!



I've attached my slides here (with some info on the deadlines of application for Cambridge).

Guest Blogger

I've invited someone to write a couple of entries for my blog. I read something he wrote recently and thought it'd be nice if he could join me to make my blog more interesting.

First a scientist, a scholar, and a sincere individual. The sunshine in my life too! I look forward to host his writings!

Re: http://bloggingtips.moneyreigninc.netdna-cdn.com/wp-content/uploads/2012/06/how-to-attract-guest-bloggers-297x300.jpg

Never Leave Experiments Alone...

It's norm in research life that we leave something over the weekend to grow, incubate, etc. so that we could have a good start for the week ahead. Likewise, I also did the same most of the time.

The last weekend of August happened to be the last bank holiday of the year in the UK so my boyfriend invited me to visit his family up north. It was a good weekend, and a long one too. We went to the Peak District which is relatively close to his hometown. I wished I brought my proper walking boots so that I could try walking up to Mam Tor. Unfortunately, a pair of simple sneakers was my companion for the weekend. Let's just say, I still savoured the beauty of Peak District from afar where heather bloomed.

View from Mam Tor

Why did I mention such a nice weekend? Oh well, in order for me to not freak myself out after a good weekend, I did set up some cells to grow over the weekend. I ensured the cultures were bubbling with carbon dioxide before I left the lab on Friday. Little did I know what awaited me on Tuesday was a huge shock that some kind individual had turned off my CO2 supply over the weekend! Yes, the conditions of my cell growth was compromised, so I had to subculture them and waited for another day or so before I continued my experiment. I did cry like a sad kitten abandoned by its mother in my boyfriend's lab out of shock, surprise and anger. I couldn't understand why it happened, to the point of questioning my memory if I did turn it on. Thinking back, I was and am very certain I did turn it on and the cultures were bubbling before I left.

Something took me by surprise again on Saturday evening. As you know, recently I am running some experiments which involved electron microscopy. Usually, I do fixing and embedding myself. I started the process of fixation and embedding on Thursday, which meant I had to return during the weekend to refresh the epoxy resin twice a day. I had prepared fresh resin for the day on Saturday morning and then left for a short visit to Burwell to meet up a German friend of mine. An overzealous individual roaming in the imaging center over the weekend had decided to clean up anything that had my name written, so when we returned to the imaging center for the final refresh of resin, I was totally appalled that my resin had gone missing from the stirrer. More upsetting was to find my pot sitting in the oven with so much of waste in it. I felt so sick when I saw the covers which I labeled with my name sitting in the oven covering pots filled with so much of waste. I didn't have my phone with me, else I would have taken a photos of it. I am helping my boyfriend to fix some of his samples which he needs for his publication. So he was with me when I performed the fixation/ embedding process. I'm glad he was with me to witness all these. We had to prepare fresh resin for the evening. I'm saddened by the fact someone is so inconsiderate, especially we sort of knew who was the other person roaming in the imaging center that weekend. I'm not pointing anyone because I can't be sure, but this raises my alarm once again that someone is out to get rid of me.

A threat had been delivered to me verbally on the evening when the outcome of my first year report was out:
"You can either exit gracefully with an MPhil, or if they let you stay, you will lose all your freedom and they'll observe you like a hawk and the slight mistake that you make, they'll show you the door".

The same individual who delivered such statement also told someone in the department that my cakes tasted horrible and he wished a previous PhD student was still there because her cakes were great. Apparently my cakes tasted alright and people do love it. It was vicious and mean to say things like that to a mutual co-worker, especially when this person ate the cakes I made. Unless, of course, he pretended to ingest it but secretly had been throwing them away. That, I wouldn't know.

I am worried. I am appalled. I am helpless. I am in the dark. I am getting depressed and paranoid.

Yet I know, I am not wrong to fight for something I know I can do and to fight against those who had been messing with my potential of doing a PhD for the past one year. And I am receiving help from the University Counselling Services to ensure I remain sane. I am still producing results despite all my health issues and weird things which are going on around me.

Here's an article published on Nature 467, 516-518 (2010) about Research Integrity. Have fun reading!

Living with Depression While Doing a PhD

I stumbled into this blog post on PhD(isabled) accidentally, and found it very relevant to PhD students nowadays. I feel deeply for the PhD student who wrote the article... This part of the article hit me harder because I am going through similar hurdle, though it didn't start off with having depression.

Any form of health problem could slow us down in PhD progression. But it shouldn't be a reason why we are being told we are not capable of doing a PhD just because our health isn't great or that we take longer time than average to complete a task. If one has dyslexia, one will be given special aid so that they can do a PhD. But if one has hormonal problem or depression which slows us down, one is told by those normal, healthy people that we're incapable of doing a PhD. Academia has become such a sorry state at the moment. Equality? What's that? Until I see justice in my case, I don't believe there isn't discrimination...

An excerpt from the blog post I found interesting:
My own experience is that it takes time for medications to kick in, and only with the right medication can I start to do any kind of working through the issues causing the depression. My last severe episode was mostly spent sitting around waiting for things to get slightly better. That sounds a hell of a lot more fun than it was. I don’t know if people who haven’t been there can know how it feels. It really is a fight to get through one day at a time. Depression impairs your thinking. It is harder to reason like usual, or be creative, or whatever it is you’re normally good at. My memory goes completely to pot. I get times and dates muddled up, miss appointments and stand up friends, which is mortifying. So if you start trying to create a new model of some important theory or other when you’re under par, its going to be even tougher than normal.

Is there a problem with people (supervisors and students) seeing that as a sign they’re not actually capable of doing the PhD work when in fact its just a sign your health isn’t great just now? Can it magnify the anxiety if you think if you can’t think yourself well then you’re also not capable of doing the PhD? I wonder if blogs like this one have an important role in getting this crucial, fundamental message across to supervisors, departments and funding bodies.

I’ve tried to get involved with causes like this before. I found I didn’t have the resources to keep up.

I’ve seen friends take on enormous responsibility for campaigns and causes at the cost of their health.

I had serious doubts about writing anything about this. I can only claim to speak from my own experience. I worry enormously about anyone reading this and feeling misrepresented, but at the same time it feels right to say something.

In the end my constant mantra is to put my health first because everything else depends on that.

I can only be politically active within the limits of my health.

I can only be a researcher within the limits of my health, and not even the PhD comes before it.

Excerpt taken from https://phdisabled.wordpress.com/2013/11/15/living-with-depression-while-doing-a-phd/comment-page-1/#comment-1159

Electron Microscopy

Just some brief updates of my latest muse - electron microscopy and immunogold labelling (of which I started last Thursday). Perhaps the antibody I probed was abundantly available, so it's pretty awesome to see that the results was as expected for the wild type. As much as I was disappointed that none of the mutants I'm currently looking at has different phenotype when compared to wild type, the data is definitely useful to form future questions for my work. Exciting times ahead!

IgL of my protein of interest - yay!

TEM image of my Chlamybaby - pweeety!!

Here's the paper which I mentioned about the techniques used for IgL. Jeremy is an excellent adviser to me when it comes to imaging techniques. I do my own fixing and cell embedding, so it's always great to have Jeremy around in CAIC whenever I go over. Thanks a lot, Jeremy! :)


Hope you guys find this post helpful :) Cheers!

Immunogold Labelling

Today I've got some peace by chilling at the imaging centre to run some immunogold labelling (IgL). My samples had been fixed in epoxy resin (I'll show you guys some pics in action when I'm running it next week). For now, I'm using older ones, mounted on nickel grids. I'm using a modified protocol from Skepper (2000), J. Microscopy 199, 1-36. (I'll link it later)

I'm having research fun and I think research should be fun. Science is mind blowing and fun. Unfortunately some people have very distorted and disillusioned vision of what "fun" and professionalism in science means.

Right now I'm battling a birdman who wants to kick me out because he's totally disapproving my idea of fun in science. Calling me unprofessional, unproductive and unknowledgeable is low if not bitchy. Telling untruths and causing me this much of troubles at this point only caused me to find him disgusting, and crazy. Stalking me under the disguise of taking my attendance without me knowing is mental harassment.

Maybe some would think that I'm wasting my time battling against a silent but dangerous birdman but if I don't fight until the last drop of my blood runs dry, I'd do myself the biggest harm. As much as I'd like to live in peace to do a PhD, the evil birdman thinks he can show me the door easily. Making my research life difficult is only making the birdman's life worse. I'm a resilient wild grass. Have always been that way.

The birdman said he'd not help with carrying of gas cylinders for me from now on. I'm perfectly happy that he refuses to help me, though I'm totally pissed with his unprofessional and childish behaviour. Thanks to this behaviour I have more conviction that I should fight till the end.

St. Paul mentioned about him running his race till the end. I need to put up a good fight too. If not, I'll be disappointing myself in the end.

Quantitative Western Blotting

I've been recently introduced to infrared fluorescence Western blotting and the video embedded is helpful to understand the differences between IR fluorescence Western blotting and the conventional chemiluminescence method. I'd have to work more on this method before I can be conclusive on its potential and usage but so far, it seems amazing and more cost-, labour- and time-effective. I discovered more from the video of its other functions which I would like to explore further, if given the opportunity to do so.

Two of my samples from the LICOR Odyssey system for the infrared fluorescence Western blot I did this afternoon. 

Does anyone know why there's a red band below the green band when I only use one IRdye?

Festival of Plants 2015

Yet another of my free writing :)

I went to the Festival of Plants in Cambridge University Botanic Garden last Saturday. A nice sunny day to be out there among the beautiful spring plants. Our first stop was the canopy where there were stalls with interactive games and explanations provided by volunteers of Festival of Plants. One thing which attracted me was the booth on algae and biofuel. I work with Chlamydomonas reinhardtii, one of the few algae studied widely on its ability to produce biofuel, and I do like the idea of this animal-like single-cell lower plant being such a useful tool to study various aspects. We created a furry cartoonish ChlamyBaby (look below). There are some other activities which I didn't stay long enough to gather info. However, it seemed to me that people were enjoying themselves. We passed by the glasshouse and there was an interactive concert going on. Nice vocal for sure!

There were tours around the gardens, according to my friend, it was very beneficial as the guide told the stories of many of the trees around the garden. There was a talk tent where various talks were conducted. Apparently they were good too.

ChlamyBaby wading on the grass

I managed to capture a few nice shots - thanks to the lovely afternoon sun!

Moor hen feeding her chick

Colourful tulips

Peony?

Iris

I had a great time that afternoon. Discovered it was my friend's birthday, which was nice. Since the weather was great! :)

Scientific Walk in Romantic Sintra

I went away last weekend to refocus and refresh before this hectic season. I'm in the process of writing my first year report, but at this moment, I am kinda frozen in time and space. So, as what the trainer of the Graduate School of Life Sciences (GSLS) suggested, I begin a short piece of free writing on some random topic.

Finally, I was in Sintra. After pondering for a few nights on which part of Sintra I should do and how much I was willing to spend, I've decided on Castelo dos Mouros (Moorish Castle) and Parque e Palacio Nacional da Pena (Pena National Palace and Park).

View of Palacio Nacional da Pena from Castelo Dos Mouros at the spot where King Ferdinand II loved as he found it an inspiration for his romantic ideals.

My favourite picture of the Castelo

It was an amazing journey and I did take many excellent shots of the breathtaking views, and plants! I never thought I'd end up in the Dept of Plant Sciences, but since I'm already in it, I should make the best out of it. I may be a ChlamyScientist working on molecular biology/physiology of Chlamydomonas reinhardtii, but my colleagues are great physiologists/ecologists. I'm beginning to see beyond the green and to see each plant as a different species. It will take time, but I hope I can make my way closer to them greenies.

Navelwort I think... also in Parque Nacional da Pena

Sedum sp. in Parque Nacional da Pena

Fascicularia bicolor, a Bromeliad in Castelo Dos Mouros

Failed Experiments are Norms!

I guess I can't help it. For two weeks I've been struggling with the no-results syndrome. It's TOTALLY NORMAL! Yes, I know, and all I need to do is to exhaust all possibilities before I will bow down to the word "defeated". I know many of my fellow scientist readers would feel me, and mentally support me through this "darkness". At least, I'm still doing work. That's something to rejoice for. It's JUST PCR. What wrong can it go, right? Well, it's just probably 101 things which can go wrong in a simple tiny tube with 20 microlitre of PCR reagents. *Laugh ironically*

When I'm in despair, I am automatically brought to reminder of this particular bible verse (2 Corinthians 4:8-9).

Nope, I shan't be crushed, I shan't be in despair, I shan't be abandoned, I shan't be destroyed.

I will come out stronger than ever, because every single moment of failure helps to bulk up the "what not to be done" Pandora box. I was to the point of giving up by telling myself that if it were not meant to be, then it would be okay to give up, but God didn't give up on my intention of completing this PhD. Second chance is received. And so, this is not the time to mope for too long. I'll just whine for another few more seconds and then continue the second part of my day.

Exciting times ahead in June: First year report which will enable my upgrade to proper PhD candidate is due in about two weeks' time (Sorry, not even there yet when it comes to first year report! *sad face*). Then it's the season of viva voce to defend my research and to prove my worth (as much as I don't like to use this as a benchmark of who I am and the potential that I have). And yes, Erasmus+ Students and Alumni Association (ESAA) Kickoff Event in Brussels.

Fingers crossed I'll be ready for the adrenaline-pumping June. I just want to live my life to the fullest, because I only live once, and this God-gifted life I have is not exactly mine but His, given to me freely so that I may live a life of grace and joy.

Now, who says great scientists can't be great believers? I am not a great scientist, nor a great believer. I'm just a trying scientist and a trying believer. If Albert Einstein and Gregory Mendel were great scientists and great lovers of God's own heart, then I can.

Me no want to live a life with excuses, justifying things I did wrong and in regrets all the time.

New Toy: Lenovo Miix 10

This is the first time I used a Windows 8 tablet. Though it was an Amazon Warehouse deal, but to me it is still a new toy nevertheless. In fact, this time round, as much as it is a toy gadget, but I'm justifying its usage as an option to have a "work holiday" when I want to travel, yet still be able to work intermittently. It does help when I draw strength from seeing new stuffs outside Cambridge and then form some new ideas for my experiments.

Enough with the justifications, now back to the toy itself. I spent about £150 on this warehouse deal for a "Used-Very Good" Miix 10 Windows 8 tablet. It comes with original Windows 8, and Microsoft Office 2013 Student package, which helps a lot since I am using a Windows 8.1 laptop with Office 2007. I wanted to install Office 2013, but the product key only allowed ONE single installation *sad face* but I already have Office 2007 so it's pretty much the same.

Let's talk about the operating system (OS). When I purchased my laptop, it was on Windows 8. I wonder how many times I complained about how unfriendly it was. The signature Start button of all previous Windows (95, NT, XP, 7, Vista...) was removed, and I couldn't find my way around for the first few weeks. I sorta got used to it but I didn't like it at all. When Microsoft introduced its update to Windows 8.1, I freely embraced it. The signature Start was back!!! My days from that point forward were great, and are still happy with it. Now, Miix 10 is the first generation to Lenovo's 10.1" Windows tablet, and yes, it is no longer selling on Lenovo's website. Hence, I know it would come with Windows 8. Oh my horror! Then again, I could update it to Windows 8.1 so I didn't worry too much about it.

Though it was mentioned that the hard disk of Miix 10 is 64 GB, the space available was only about 45GB. I got over-excited when I received the tablet, so I started installing my usual need - Mendeley reference manager. Programs eat up disk space like a hungry PacMan. So when I finished with the necessary updates of Windows 8 to enable the upgrade to 8.1, the HDD didn't have enough. Well, finally after numerous uninstallation of unwanted apps,  I finally managed to upgrade to Windows 8.1.  It was as though life returns to the tablet finally.

Other pros and cons of a brand new Miix 10 which I found on the usual tablet review websites - I do agree. So I won't comment much on those aspects, since they'd know better than I do. I would comment on the basis of my current profession as a PhD student in the process of writing up the first year report to be upgraded to a PhD candidate. Since I am writing a lot, so Office 2013 (as I mentioned previously) is an additional bonus so one point for Miix 10. However, the annoying part that the virtual keyboard still pops up though it is docked to the external keyboard will be something I need to address and consider in future.

I'll share the part II of my encounter with this tablet and a possible decision of whether I will be keeping it in the next two weeks or so. My short trip to Lisbon will be an ultimate test for Miix 10 if it is suitable for my use.

Time to return to reality and work on my project. Till then....

Keep Calm and Start Writing!

How apt is this "keep calm" phrase!

Some of my friends have begun writing their theses, some had completed and submitted. As for me, I am just starting my PhD journey (finally!) when I joined this lab (Physiological Ecological Group). Looking at how four months flew off like lightning, I should begin writing the first year report soon since the deadline is on 1st June.

The reluctant mind and body says, "There is still time. Chillax!" But both know better that it is only a lie. One thing would lead to another, and there are thousands, if not millions of papers I need to wade through in order to seek for the knowledge. I have yet to start writing the ONE word needed for me to begin.

It's time to think. It's time to start writing. I shall.. Within this week. Now, I shall give my pair of fatigues eyes a rest. Ciao!

Mating Chlamydomonas reinhardtii

I find this paper by Jiang, X. and Stern, D (2009) published in Journal of Visualized Experiments super cool. It's about mating and separation of Chlamy's tetrad. It's laborious, obviously, but it seems to be something fun to pick up for my PhD. Let's see if it's possible... *chuckles*

Briefly, Chlamydomonas usually exist in haploid single cells, formed by the "mating" of two strains of opposite mating type (plus and minus). An explanation of the diagrammatic representation of the Chlamydomonas life cycle shown below is taken from Zhao H et al., Genes Dev. 2001;15:2767-2777 (click on the link for the full paper). Gametes are formed when vegetative mt+ and mt− cells undergo gametogenesis induced by nitrogen deprivation (middle left). When gametes of opposite mating type (or sex) are mixed together, they adhere to each other via mating type specific adhesion molecules (agglutinins) on their flagella to form large collections of agglutinating cells (upper center). Flagellar adhesion induces gamete activation that leads to release of cell walls, erection of mating structures at the apical ends of the gamete cell bodies (upper right), and several other cellular and biochemical changes that prepare the gametes for cell fusion. All of the events associated with gamete activation can be induced in gametes of a single mating type by incubating them in dibutyryl cAMP (Pan and Snell 2000b). The tips of the mating structures fuse to establish cytoplasmic continuity, and soon thereafter the two gametes merge completely to become a zygote (lower right). Zygote formation can be extremely rapid, and within 5–10 min after gametes are mixed together, 70%–90% of the cells fuse. Immediately after cell fusion, the zygote developmental pathway is initiated and at 2–4 h after fusion, the zygotes form large aggregates of tightly adherent cells (lower center) as a consequence of synthesis of zygote-specific extracellular matrix molecules and cell body adhesion molecules. At about the same time, the mt− chloroplast DNA is degraded. After an obligatory several days in the dark and upon return to nutrient-rich medium, meiosis and germination occur, and each zygote forms four progeny, two mt+ and two mt− vegetative cells (lower right). Vegetative cells undergo mitotic divisions until the nitrogen is depleted from their medium and the cycle begins again. Diagram modified and adapted from Figure 1 of Pan and Snell 2000b.

Source: http://genesdev.cshlp.org/content/15/20/2767/F1.large.jpg

Sounds fun. Enjoy watching the almost 10-minute long video. I found it rather exciting! *Thinking cap ON*

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.

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

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

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

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!