project planning(?)

Coming from an industrial background academic life is quite a different culture. There is far more autonomy in the roles, from technicians to PI’s there seems to be a lot more self directed work with a far less formal hierarchy. I find this a refreshing and liberating experience compared to industry which can often be suffocated in bureaucracy and deliberately restrictive pecking order. Recently I have been struggling to make progress in my project, bogged down in a cloning step that is threatening to sink the whole project. I have attempted to create milestone targets and interim reports but all of these have gone in the mists of time and any attempt to produce interim reports or project updates is rejected by my supervisor as unnecessary paper work. I have struggled to install any kind of organisation or direction with my supervisor and have hammered away in the lab watching the calendar pages spin by. I am in the weird inverse position of failing to explain and fully articulate the dire situation this project is finding itself in, which I thought was meant to be the other way around, with the boss chasing the over-relaxed student around the lab.

Although many industry project planning sessions are an excuse to drink coffee and an opportunity for management to exert their authority over their minions it is strange that academia has never adopted any formal planning in research projects. If done properly, effective project planning can attempt to provide structure as the project begins and early warnings of things starting to slide. Gateways can be useful to decide when it’s time to stop, and milestones even if missed or not achieved present formal time points to re-assess progress or the project’s direction. While team members can become bogged down in the details of their own tasks and problems, the landmarks on the project plan are opportunities to step back and re-assess what everybody is doing. Perhaps things will change when funding dries up or the beneficiaries want to keep a closer eye on where their money is going if there’s a greater risk of loss in the global economic melt down.

Until then, I continue to wander on….

Kahn Academy

As a student on a systems biology programme I am forever being subjected to data and theory of subjects I don’t quite understand. As a biologist on a systems biology program this mostly means maths I don’t understand. Fortunately it’s 2010 and as well as online poker the internet provides a tremendous tool to educate yourself in just about any subject. Back when I was doing my B.Sc I was limited to shuffling through journals, often to find the article I was searching for had been ripped out pilfered by some very non-socialist student type. Things have changed a bit. MIT provide all of their lecture content online with video footage and downloadable course material enabling anybody with an internet connection and some free time to cover all of the material in an undergrad course of their choosing. The maths centre provides a range of maths tutorials covering basic algebra up to calculus which was indispensable during my first year training, and the University of Manchester provides the helm maths resource with downloadable material.

I recently stumbled over a slashdot story reporting on the Kahn Academy. I hadn’t found this before today and it would have been a great help when I was starting down the maths road. Salman Khan founded the Khan Academy with the goal of using technology to educate the world. Sal received his MBA from Harvard Business School. He also holds a Masters in electrical engineering and computer science, a BS in electrical engineering and computer science, and a BS in mathematics from the Massachusetts Institute of Technology. Not happy with the way he was taught at school Kahn bought himself a $200 camera, $80 tablet, some free software and youtube and began his mission to educate the world. All the material is published under the creative commons license meaning that it’s freely available for anybody to use. There are many hundreds of short video tutorials covering topics covering maths, chemistry, physics, biology, finance, statistics, and history. Kahn expertly takes the viewer through well structured material which is well presented, well delivered, and easy to follow. There are even follow-up tests available online with his “mental bootcamp”. I am currently working my way through the calculus section after brushing up on my algebra and I hope to get the time to explore the rest of the material.

The website is an amazing resource for anybody with an internet connection and the will to educate themselves, and in our corporate run capitalist society I really hope Salman Kahn achieves his mission to educate the world. If he can educate me, he can educate anybody!!

ronin

My situation continues to worsen with each day. For the past year I have been unable to complete a plasmid construct as, what should be simple cloning steps, continue to fail. After over 100 DNA preps I had a construct that appeared to be correct however it failed to sequence and the insert looks to be ~1kb too small for some unfathomable reason. I have now wasted a year of my project with no progress and go into the final year with 2 plasmids and a mechanistic model of a genetic interaction I have never tested. To compound the problem, my supervisor has announced their resignation which will be effective in weeks, disbanding the lab, and the post docs and technicians re-deployed or finished up. Unless I move with my supervisor to the new labs in another university a few hundred miles away my funding will be cut and I will remain here, alone with no wet lab support. To move means selling a house and forcing my partner to quit her training and move to a more expensive part of the country to live together on my stipend, with no guarantee of a job after I finish in a year. The consequences are that if the project continues to fail and I don’t graduate I end up with no house, no job, and the both of us with no qualifications amidst potentially 5 more years of recession. If I stay here I work alone with the same risk of failure but with somewhere to live and a small income to pay the mortgage from the other half. Gamble nearly everything or everything?

Lab morale was bad following the announcement and in the days following it turned into a full scale rout with PI’s prospecting our lab space and the entire group actively seeking alternative employment and the prospect of a period on benefits. I have meetings with the university to attempt to form some plan but things look bleak. It is hard to imagine how, after surviving a gruelling 1st year training period and a year and half of 12 hours days, 6 days a week, travelling 4 hours a day that it has come to this. I am re-activating my job search profiles but can’t face the prospect of returning to a science technician role where every day will be a reminder of how close I was to a career and a future.

Even if I was, by some miracle, to graduate I don’t know if I could face a lifetime career in a field as volatile as this. I have experienced redundancy rounds in industry, and numerous changes in senior management, but to be in a situation where an entire department can be liquidated by an individual with no warning has been horrendous. I just don’t think I can live day-to-day by the grace of a single individual who can end my research when the wind direction changes.

Over the past year and a half I have had the privilege to be allowed to work with loyal and hard working individuals who routinely work >12 hours a day, 7 days a week, 365 days a year with no holidays, breaks, or even sleep some of the time. Tireless machines that produce endless data at the highest quality they are capable of, who are suddenly cast to the four winds to fend for themselves with no prior warning or explanation.

As Newscientist publishes articles discussing the future of scientific research for the UK and Universities demanding the highest possible calibre of researcher and students to forge a new generation of cutting edge science, I cannot see how anybody of such calibre could tolerate, or survive a life of thankless servitude and uncertainty. Not while individuals with 1/10th the capability are paid more in a week than a scientist earns in a lifetime kicking a ball around a field. I think Universities need a reality check if they hope to build such a future, as the days of serfdom and medieval guilds have ended.

what colour is your parachute?

Not posted for a while after an exceptionally busy period in the lab. Recently my supervisor announced that they were leaving. This will be a new challenge for the project, to secure the required funding and locate new post docs to assist with training and guidance. This was an unexpected turn of events and has once again shown me that when you are most comfortable you are most vulnerable and you must always be ready for change. We are all now faced with the immediate challenge of finding new jobs, or new labs and funding streams. I hope to continue my project, even if the prospect of graduating took a step or two further away. I am challenging myself to identify the opportunities and potential escape routes rather than the immediate crisis, and turn this event into something positive.

Nobody every claimed a Ph.D was easy!

nothing is certain but death and taxes.

model making

A recent paper by Dalal et al: Rapid digital game creation for broadening participation in computing and fostering crucial thinking skills. International Journal of Social and Humanistic Computing, 2009; 1 (2): 123 investigated how the process of creating video games can boost students’ critical and creative thinking skills as well as broaden their participation in computing. The paper indicates that using rapid prototyping with visual representations and event driven behaviors develop creative thinking as well as computing skills.

Recently I have been going through the process of building a computer model of the gene circuitry I am building in the lab. I have found this activity to be quite beneficial, not only in the simulation tool I am creating but the process of creating it. I have found that simply thinking about the interactions of the various components and drawing out visual representations on paper, even without any sophisticated computer software helps to build on the strategy being undertaken in the lab. The approach highlights missing pieces of data and potentially important experiments to characterize the circuits behavior.

For the programming/modeling work (after a long time hammering away at Mathematica and Matlab) I decided to use the Copasi simulation and analysis software package as this gives me the fastest route to prototyping the gene circuit and provides the option to output as sbml which could later be implemented in Matlab if required. Copasi has enabled me to jump straight into the modeling from the point of view of the reactions and at the moment mass action kinetics seems to be sufficient to represent the genetic interactions. Copasi also enables optimization of the model. Signal to noise ratio is key to the circuitry I am building so I am able to optimize the model parameters with the input and output as objective functions. Copasi can then implement a number of deterministic and stochastic optimization algorithms to evolve the system towards the favored output.

The results of this approach have provided some hypothesis about the properties of the gene circuit components in order to achieve the desired output. This has provided a sort of first round iterative design/development cycle and once the lab data has been obtained should provide some interesting validation of the modeling/wet lab approach to the project.

More information on optimization algorithms can be found in Mendes & Kell (1998) Bioinformatics, Vol 14, 869-883.

Evolution and Design of Biomolecular Systems A workshop exploring the relationship between systems biology and synthetic biology

We’re on pre-flight checks for Evolution and Design of Biomolecular Systems conference in Mallorca, Spain.

I’m looking forward to meeting other synthetic biology researchers.  A few of the conferences I’ve attended so far as part of the systems biology program have been heavy on dry scientists and there has been little interest in wet lab experimentation, leaving me somewhat disjointed from the systems biology community.  I am hopeful that the workshops will enable me to gain advice and incite into the work I am doing, as well as the future aims for the field of synthetic biology.  I’ll try and write something while I’m there if I can get internet access.