I really that I seem to start every blog post here with an apology for not posting recently. The last 8 months at work hasn't been the most positive time of my life, and while I have written plenty posts, I haven't felt able to publish them.In short, things fell apart on a personal and professional level in the lab group where I work. That is a whole blog post on its own, but one that has to wait a month or so before I can make it public.
Then, my wife and I changed our living arrangements somewhat to try and stabilise our finances, with me living and working in Dundee through the week then going home to Paisley at the weekends where she was living full time. To go from living with someone for 7 years to sleeping in a single bed and only seeing them at the weekends is, to quote a friend of mine, a "shitty situation".
But, now, it's all over. Three weeks ago I was informed that I had been offered a Research Fellow position at the University of West of Scotland in Paisley. This means: I'm going home. I can live with my wife. I will only need to have one flat to pay for. I can see my close friends more often again. I can be closer to my sister, brother in law and nephew.
And, of relevance to this blog, I can do my own research. While I still have a boss to report to, the brief of the research position is so very wide/vague/general that I can explore things that interest me. Quantitative high frequency ultrasound for biomedical and life sciences applications, but over on the engineering/physics side of that interface. I'm returning to work that I did during my PhD in to teeth and tooth decay detection, but also expanding in to the world of breast cancer. Hell, it looks like I might even be setting up my own dictyostelium lab.
The group I'm moving to work with is the same group I started my ultrasound 'career' in for the first year of my Phd, before my supervisor left to go to Dundee. This means there's lots of friendly faces there for when I start in January.
I am currently equal parts excitement and sheer terror, but all in all, this is a good thing.
Showing posts with label dictyostelium. Show all posts
Showing posts with label dictyostelium. Show all posts
Saturday, 17 November 2012
Saturday, 2 June 2012
What I do for a living (Part Two)
In the last post, I wrote about the biological aspect of my work and now I'm going to get more physic(al?). I trained as a physicist, and see myself more as an engineer (which is really just applied physics). My salary comes from a large EPSRC (that's the government research council for engineering and physical sciences) grant for a project known as Sonotweezers. The grant was worth roughly £2m and split between four universities (Dundee, Glasgow, Southampton and Bristol), but being a lowly post-doc, I don't see much of that £2m - so don't get the wrong idea!
The aim of the Sonotweezers project is to research and develop electronically controlled devices which use ultrasound waves to manipulate particles and objects. Before explaining what I do with them, I'll tell you a bit about how it works. All sound, from the stuff you can hear to the higher frequencies that bother dogs and above (say, for looking at your unborn baby), is just pressure. And, by definition, pressure is just force divided by an area of surface. So, if you have pressure, you have force.
Clear as mud? Ok, consider a deep sea diver. The pressure of the sea down below is much higher than at the surface, and can result in a crushing of the diver, hence James Cameron, while commercialising human tragedy, had a specially created submarine that could withstand large pressure. This pressure on the diver is uniform all around him, pushing him to his core.
So, in our laboratory we create non-uniform pressure fields around objects to move them. We do this with ultrasound because the higher frequencies mean the objects we can move are much smaller than if we did it with audible sounds. People have used lower frequencies to levitate objects in the past, useful research like floating ants and fish.
Ok, this was a bit longer than I thought, so there's going to be a third (and possibly final) part of this where I'll tell you about the computing that I do. There will be some more pretty pictures (perhaps prettier as a computer will have drawn them...)
Hope you're enjoying reading these, and again, happy to answer questions.
\0/ SCIENCE.
The aim of the Sonotweezers project is to research and develop electronically controlled devices which use ultrasound waves to manipulate particles and objects. Before explaining what I do with them, I'll tell you a bit about how it works. All sound, from the stuff you can hear to the higher frequencies that bother dogs and above (say, for looking at your unborn baby), is just pressure. And, by definition, pressure is just force divided by an area of surface. So, if you have pressure, you have force.
Clear as mud? Ok, consider a deep sea diver. The pressure of the sea down below is much higher than at the surface, and can result in a crushing of the diver, hence James Cameron, while commercialising human tragedy, had a specially created submarine that could withstand large pressure. This pressure on the diver is uniform all around him, pushing him to his core.
 |
| Pressures on a deep-sea diver giving rise to forces. |
Now, consider what would happen if on his right hand side the pressure was higher than the left. He'd still be getting crushed, but more so on his right hand side. Provided that he's floating down there, he'd find himself being pushed more on his right hand side. This is an unbalanced force,and by Newton's equation of Force being mass times acceleration, he'd accelerate away from the higher pressure on his right.
So, in our laboratory we create non-uniform pressure fields around objects to move them. We do this with ultrasound because the higher frequencies mean the objects we can move are much smaller than if we did it with audible sounds. People have used lower frequencies to levitate objects in the past, useful research like floating ants and fish.
 |
| Ultrasound standing waves giving rises to forces on cells |
I use ultrasound quite like that picture there, to push cells around when they want to move somewhere else. This allows us to get a measurement of how much force the cell is able to produce, and that helps us better understand the motions that I spoke about last time. It's mainly an engineering job, since the physics are understood, but getting them to work with biology is the main problem.
Ok, this was a bit longer than I thought, so there's going to be a third (and possibly final) part of this where I'll tell you about the computing that I do. There will be some more pretty pictures (perhaps prettier as a computer will have drawn them...)
Hope you're enjoying reading these, and again, happy to answer questions.
\0/ SCIENCE.
Friday, 25 May 2012
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.
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/
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/
Tuesday, 3 November 2009
Sales pitch
Today was pretty exciting at work. Well, as I'll explain in a minute, the morning wasn't, but the afternoon was pretty cool. Without going in to much detail, but the device that I've been employed to work on at the university showed its first signs of working today. I recorded lots of videos of the cells doing cool stuff under the influence of the device. Not bad for only two months in the new job.
Why was the morning not exciting? Well, I had to go to a course about a piece of software called LabView. Anyone who has worked closely with me over the last, oh, I don't know, perhaps 8 years now will know that when I want a computer to do something, LabView is second from the bottom (only to a fucking hammer and nails) in my choice to achieve my goal.
For those who haven't had to experience Labview in all it's glory, it's a graphical programming language. You create programs, namely scientific data capture and analysis programs by dragging and dropping Virtual Instruments from a tool box on to your canvas so as to build up a picture of your house with your pet cat outside that you can show to your supervisor so they can see what a clever five year old you really are.
The people who were hosting the class were very much sales persons, with the main 'tutor' getting right on my nerves for a couple of reason. Reason number one, he introduced himself as an engineer who had never really been a fan of computer programming and so Labview was perfect for him since he had no experience of using "C-basic or whatever". Direct Quote. Heya, I've only ever drank coca-cola so I'm going to tell you exactly why it's the best drink out there.
The second reason he irritated me was that he continuously made reference to the fact that in "C-basic" if you were to miss out a semi-colon, you would have to spend hours looking through your code to find the error. Where as with Labview, this doesn't happen since Labview shows you exactly where your mistakes are. Erm, sorry, but anyone who's using a programming language as part of their job would more than likely be using an editor with syntax highlighting, that after compilation would, going by the compiler errors, highlight the offending line of code. Perhaps even give a line number.
Labview on the other hand doesn't even have a zoom out feature so that when your pretty picture, I mean code, gets so large you can't trace what the hell it's actually doing. I asked the presenter why the new version still doesn't have a zoom out feature, to which the answer was "we usually just recommend people buy a bigger monitor".
I could go on all night about this, but I won't. I haven't even mentioned the boasting of "multithreading", which was just a rebranding of the "multi-tasking" introduced in every operating system with the POSIX standard. You did not invent it, you merely made use of the fork functions available on your target platform. I could do that in C, and the program wouldn't need to be restarted every time I want to open a word processor on the same fucking computer.
Thank you, and good night.
Why was the morning not exciting? Well, I had to go to a course about a piece of software called LabView. Anyone who has worked closely with me over the last, oh, I don't know, perhaps 8 years now will know that when I want a computer to do something, LabView is second from the bottom (only to a fucking hammer and nails) in my choice to achieve my goal.
For those who haven't had to experience Labview in all it's glory, it's a graphical programming language. You create programs, namely scientific data capture and analysis programs by dragging and dropping Virtual Instruments from a tool box on to your canvas so as to build up a picture of your house with your pet cat outside that you can show to your supervisor so they can see what a clever five year old you really are.
The people who were hosting the class were very much sales persons, with the main 'tutor' getting right on my nerves for a couple of reason. Reason number one, he introduced himself as an engineer who had never really been a fan of computer programming and so Labview was perfect for him since he had no experience of using "C-basic or whatever". Direct Quote. Heya, I've only ever drank coca-cola so I'm going to tell you exactly why it's the best drink out there.
The second reason he irritated me was that he continuously made reference to the fact that in "C-basic" if you were to miss out a semi-colon, you would have to spend hours looking through your code to find the error. Where as with Labview, this doesn't happen since Labview shows you exactly where your mistakes are. Erm, sorry, but anyone who's using a programming language as part of their job would more than likely be using an editor with syntax highlighting, that after compilation would, going by the compiler errors, highlight the offending line of code. Perhaps even give a line number.
Labview on the other hand doesn't even have a zoom out feature so that when your pretty picture, I mean code, gets so large you can't trace what the hell it's actually doing. I asked the presenter why the new version still doesn't have a zoom out feature, to which the answer was "we usually just recommend people buy a bigger monitor".
I could go on all night about this, but I won't. I haven't even mentioned the boasting of "multithreading", which was just a rebranding of the "multi-tasking" introduced in every operating system with the POSIX standard. You did not invent it, you merely made use of the fork functions available on your target platform. I could do that in C, and the program wouldn't need to be restarted every time I want to open a word processor on the same fucking computer.
Thank you, and good night.
Monday, 2 November 2009
I'm not needy, I'm determined
Today was rather uneventful, woke up early, dropped the wife off at the bus station and then went to work. Played around with some dictyostelium cells and electricity, then came home. The makings of a great day.
I sorted out my drummer conundrum in that we have a new drummer now, and the old one is happy to stand in any time the new can't make it. If that makes sense? I think it will work out for the best for everyone involved, and we've got our first full band practice in a couple weeks.
The new drummer, Woody, fell in my lap which was nice. For some reason I seem to have garnered a reputation for asking anyone I find who plays an instrument in to playing in the band, to the point in which people I would consider friends warn others about speaking about their musical abilities in front of me.
This couldn't really be further from the truth. The band I am playing with came together after I placed a post up on a popular internet forum looking for a bassist, which was replied to by one person (this person became the bassist). I had a mate who was learning mandolin and expressed and interest in playing some folk music with me, I said we'd give it a go and before I knew it he was my mandolin player.
The singers came about in much the same way, an interest was expressed in my stuff and I thought I've got nothing to lose. My original drummer has played with me for over 6 years, starting after my first band lost a drummer. And finally, my guitarist is someone I've known for around 3 years now through playing music and this is the first time we've actually done stuff together.
Hardly me poaching people at the first mention of their musical capabilities. In fact, even when I had the instrument I am most desperate to have (violin), that came about after the violinist and I met at a few punk rock gigs, and then through some very coy statements about her playing violin did I get the hint. Well, in fact, I didn't get the hint, she had to explicitly tell me she was intentionally being coy so as to not look desperate.
This isn't to mention my sister who plays euphonium, the friend of my wife who played cello at my wedding (her present to us), and many more wonderful people I know who play music but have never been approached to play in my band.
And anyways, at seven members, band practices are difficult enough to organise!
I sorted out my drummer conundrum in that we have a new drummer now, and the old one is happy to stand in any time the new can't make it. If that makes sense? I think it will work out for the best for everyone involved, and we've got our first full band practice in a couple weeks.
The new drummer, Woody, fell in my lap which was nice. For some reason I seem to have garnered a reputation for asking anyone I find who plays an instrument in to playing in the band, to the point in which people I would consider friends warn others about speaking about their musical abilities in front of me.
This couldn't really be further from the truth. The band I am playing with came together after I placed a post up on a popular internet forum looking for a bassist, which was replied to by one person (this person became the bassist). I had a mate who was learning mandolin and expressed and interest in playing some folk music with me, I said we'd give it a go and before I knew it he was my mandolin player.
The singers came about in much the same way, an interest was expressed in my stuff and I thought I've got nothing to lose. My original drummer has played with me for over 6 years, starting after my first band lost a drummer. And finally, my guitarist is someone I've known for around 3 years now through playing music and this is the first time we've actually done stuff together.
Hardly me poaching people at the first mention of their musical capabilities. In fact, even when I had the instrument I am most desperate to have (violin), that came about after the violinist and I met at a few punk rock gigs, and then through some very coy statements about her playing violin did I get the hint. Well, in fact, I didn't get the hint, she had to explicitly tell me she was intentionally being coy so as to not look desperate.
This isn't to mention my sister who plays euphonium, the friend of my wife who played cello at my wedding (her present to us), and many more wonderful people I know who play music but have never been approached to play in my band.
And anyways, at seven members, band practices are difficult enough to organise!
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