Six months on.

Last post here was when I wrote about getting my new job. I'm now 6 months in to the position and things are going really well. I've been given a lot of independence on my research, responsibility for a laboratory area, students and confidence to apply for funding and seek out collaborations.

In general, my field is high frequency ultrasound. I find myself doing a lot of imaging  with the probes we're developing and fabricating, mainly of dental samples with a view to detecting and measuring acid erosion at high frequency. I still do a little bit of manipulation of cells, but not as much as I would like to.

Career changes

A couple of weeks ago I visited my PhD supervisor, and informal mentor during my last Post-doc position, to have a chat about work and how things have panned out for me since leaving Dundee. We both agree that leaving was the best thing I could have done for my career (and mental well being, but more about that at a later date).

The research group I now work in is a very small group, with two PhD students, myself as a Post-doc RF, a deputy Group leader/lecturer and my line manager who is also the group leader. The recession hasn't been kind to non-red-brick universities in the UK, and as such there has been a lull over the last few years for research funding at UWS. Ultimately, my position was created to re-start biomedical ultrasound imaging at UWS with a view to bring in funding to increase the group. No pressure then.

Suffice to say, the last year at Dundee University was the worst period of my adult life, and one that I'm in no rush to repeat. However, I did meet a few new friends who got me through it and kept me sane/alive. I owe them more than I could possibly say.

NYC

The major event in my work calendar, and one that has been looming since April, is a two and a half month visit to New York to do research with a leading Ultrasound group. In the first month of this new job, my boss recommended that I apply through SUPA for a travel grant to collaborate. In my last position, these opportunities were never brought forward. While I was allowed to travel a bit, my boss was of the opinion that he would deal with grants and funding, we do the work. His work. Looking back, this is not a healthy way to train young scientists who want a career in Research.

Writing a grant application for the first time is a daunting experience. Project costs, times, aims, goals, outcomes, targets have to be designed and, most importantly, sold to the judging committee. I'm not that good at 'blowing my own trumpet', something that comes from my Scottish genetics, and also from three years of having my confidence in my academic abilities pummelled in to the ground as an RA at Dundee.

Anyway's, it turns out that my application was better than I thought it was and I leave in a couple of weeks. I will be staying in Brooklyn and working in Mid-town Manhattan. I'm equal part excited and terrified.

Excitement versus terror

Excitement comes from working in a highly regarded laboratory, in one of the busiest cities in the world, meeting new people, and living in a different country for the first time in my life. Terror comes from much the same places, and the added fear that comes with being separated from my family and support network for a prolonged period of time. My wife is able to visit for 3 weeks in September, but for the other 8 weeks, I'll be flying solo in to the unknown.

I promise to post regular updates here during my visit, hopefully using it as an academic travelogue.

What I do for a living... (part one)

I have decided that this blog has been under utilised, and have therefore set a weekly alarm on my phone to write a post. I'm going to try and keep them strictly non-my-music related and hopefully more science, tech and life related.

To get started, I thought I'd answer a question that I get asked a lot when I'm on tour: "what is it that you do for a living?".  In short, I am a post doctoral Research assistant at the University of Dundee. I have a degree in Physics, and am a Doctor of Engineering in Medical Devices (that's just a fancy PhD).

The long version, and I'm going to do this in two parts, is that I am investigating the motility forces that arise during early embryo development. We use the chicken as our model system, which is cool as you can remove it from the egg when it's only 10,000 cells or so and actually watch it develop up until the heart starts beating.

Before I started this job, I didn't really think about embryology. I mean, I knew the mechanics of mummy and daddy having special hugs because they are very much in love etc, but hadn't thought of it in smaller terms. When the egg (talking cells now, not calcium chicken containers) is fertilized it subsequently divides in to two identical cells, then four, then eight etc. After a while you have many thousands of identical cells in a small blob and something strange happens. The cells start to, for some unknown reason, differentiate in to different cell types and some even move in to specific locations. Very soon a body axis (giving a left and right hand side) is formed and the Embryo develops in to a living thing.

Dave's handy guide to embryogenesis

It is this transition from randomly placed cells to ordered body morphology that I am interested in. There are many questions that we want to answer, and many more to be asked. How do the cells generate forces to move? How do they know/learn where to move to? How and why does it go wrong?

An embryo is a very complex system, and therefore to research these questions we use a simpler model system called Dictyostelium discoideum, dicty for short. Dicty is what is known as a slime mould. Under normal conditions, they exist as single cell amoebas in the soil feeding off bacteria and going about their day.

However, under starvation something completely different happens. The cells secrete a chemical signal through their environment which tells them all to "Assemble!", and they come together to form a multicellular organism called a slug. This is made up of around 10,000 cells, and moves around like a real slug (hence its name). The slug moves towards light in the hunt for food, and when it can go no further, it transforms in to a plant like structure. Some of the cells die to produce the stalk, while others go in to a vegetative state in the fruiting body to wait for food. When conditions become favorable, the fruiting body bursts and the cells start their single celled lives again.

This life cycle and its transitions from single cells to multicellular organisms is just one of the reasons that dicty are interesting from a developmental biology point of view. Other reasons include the ease of genetically modifying the cells for learning about the internal workings, the biological machinery the cell uses to move is very well conserved from an evolution point of view. This means that the method in which dicty cells move is the same as many, including mammals, cells. Therefore, learn about dicty movement, learn and infer about many many more. Which brings us nicely back to why I use dicty. Oh, and it naturally lives in the soil so it's happy at room temperature making it easy for a non-biologist such as myself to use.

That's the biology side of what I do, I part two I'll tell you about the physics and engineering that I do with these squishy things.

I'm happy to answer any questions and actively encourage it.

SCIENCE! \0/

A challenge!

My wife just said that the problem with my blog is that I called it Itchy and Irritated, and thus can't write about happy things. I see this as a challenge.

Work has been pretty damn good recently, I've been working on a cell tracking algorithm for tracing the movements of cells under stimulus. It seems to be working pretty well, which is strange since the code below it is very simple. My boss says we may even get a paper out of it, which would be ace as I've only been in the job three months.

Outside of work, life has been enjoyable. This weekend was spent traveling around the UK being paid to play music, to people who were actually listening and singing along. An upshot of the mini-tour is that I may have a split record (on a cassette format) coming out early next year on a proper record label. That would be pretty sweet, but I can't say much more at the moment.

This weekend has a busy schedule ahead. My mother is visiting tomorrow, which is the first family member we'll have had visit us in Dundee. Then, on Saturday I'm playing with the band at The Vale in Glasgow, which we're also recording for a live CD. Sunday will contain a flying visit to Greenock for lunch with the parentals, and then home to Dundee.

Although, do you know what's been irritating me this week? The fact that I've noticed how much FUCKING LOUDER the adverts on E4 are compared to the program I'm watching. That is fucking annoying.

Damn, almost made it. Now, a new episode of Scrubs is on, and that in itself is fucking irritating.