Navier-Stalks. Dispatches from the front line in s

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It ain't what you do, it's the way that you do it.
2008-04-23 12:55:00
Sorry to take so long to post this piece. I?ve been spreading myself too thin, lately, and as a result I?ve chipped away at many problems, but demolished none. Nonetheless, after some selective reprioritization, I?ve found the time to tell you about this curiosity of a paper.ReferenceNykter, M., Price, N.D., Aldana, M., Ramsey, S.A., Kauffman, S.A., Hood, L.E., Yli-Harja, O., Shmulevich, I. (2008). Gene expression dynamics in the macrophage exhibit criticality. Proceedings of the National Academy of Sciences, 105(6), 1897-1900. DOI: 10.1073/pnas.0711525105Please don't hate me for covering a paper from the Proceedings of the National Acadamy of Sciences (PNAS). They may have deeply dubious refereeing practices, but they remain a prestigous publisher and somehow their impact factor continues to hover over the heads of most other journals.This paper is a bit of a shark. It looks quite innocuous on the surface, but beneath the surface lurks a neat portent, a harbinger of the shape...

Strictly Bucky-Ballroom
2008-03-11 22:39:00
The crazy professor is a very familiar character: Professor Frink from the Simpsons; Dr Emmett Brown from Back to the Future; Jeff Goldblum in The Fly; Bunsen and Beaker from the Muppets. Scientists have always been portrayed as sightly out of tune with the rest of society. Sometimes this is unfair, but sometimes it is absolutely spot on.The latest affirmation of our nerdiness was the Dance Your PhD contest in Vienna, in which researchers try to convey their research results using the medium of modern dance. Performers were divided between three separate classes: students, postdocs and professors and the performances included a tango representing the amalgamation of galaxies and a tap dance describing post-translational regulation of mRNA.The classification seems oddly unnecessary. You wouldn't think that a long research career would be much of an advantage in the choreography of your performance.As a publicity exercise, the contest has clearly scored highly (covered by Science...

Suicide is painless, it brings on many changes...
2008-02-21 20:09:00
Cell suicide does indeed bring on many changes, but it's far from painless, or at least modelling it is. To get an example of just what's involved, I'd recommend having a look at the wonderfully well written paper by Cho et al. The authors use first order ordinary differential equations (ODEs) to show how the protein TNFa (Tumour Necrosis Factor-alpha) triggers a sequence of protein interactions that lead to the release of NFkb (Nuclear Factor-kappa-beta), a bound group of proteins heavily involved the response of the immune system. NFkb activity is closely associated, for example, with inflammation and cell termination (known as apoptosis).The pathway is written as a series of chemical reactions where each reaction is catalysed by an enzyme. These reactions can be described using the law of mass action, which says that the rate of a reaction is proportional to the product of the concentration of the reactants. In a chain of reactions, the products of each reaction combine wit...
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I am a model, you know what I mean (and I do my little turn on the catwork)
2008-02-11 15:27:00
I recently started a project to model certain signalling pathways in our favourite macrophage cell and it's been an eye-opening experience. Once its complete, we will learn volumes about the role of cholesterol in the immune system. But at this stage, just working out the angles has been fascinating. The challenges don't come from the directions you might think.At first, I thought they'd be computational. People have been modelling pathways for years, so I reasoned that all the straight forward work must have been done. In established fields, the new challenges come from the projects that push computing power to its limit, so I assumed that ours must have been computationally complex. But it turns out that this isn't the case. Few trusted models of signalling pathways exist and those that do are quite simple, so they are pretty straight forward to simulate.If the challenges weren't computational, then I thought they might surround model validity. A living cell is a complex bea...
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Ground control to Major Tom.
2008-02-02 20:07:00
In the last post, I mentioned that I work on exploring the complex network of interactions between genes, proteins and microRNAs that mediate a cells response to its environment. This field is known as cell signalling and the possible routes through the network are signalling pathways.To give you an example of how a typical pathway might work, suppose a cell is attacked by a virus. The virus might emit a protein that the cell, over millions of years of evolution, has learned to recognize as indicative of that threat. In this case, it will have evolved so that the viral protein binds to another protein on the cell surface, triggering a cascade of protein-protein and protein-gene interactions within the cell. The triggering happens because the binding causes a third protein to detach from the interior of the cell surface, which then floats off into the cell interior. Along the way it interacts with many other proteins in a huge variety of ways. For example, it might bind to another pr...
More About: Ground , Control , Major

So what's it all about (Alfie)?
2008-01-27 14:34:00
The area of biology that I've landed in is fairly new and it's known as Systems Biology. As in all new developments it is not without controvesy. No-one's exactly defined what Systems Biology is, so all sorts of work has appeared under the Systems Biology banner. The wikipedia entry for Systems Biology reflects this ambiguity. Naturally, with researchers eager to make the most of their work, the banner has been subject to a little abuse, but such is life.Really, it's about understanding the behaviour that emerges when you put together a network of biological interactions. This can be on almost any scale, from the study of epidemics to the analysis of cellular biochemistry and the work that I do sits at the small end of this spectrum.We try to get to grips with how the cell works in terms of its constituent genes, proteins and RNAs. Actually, this isn't strictly true. We work on one specific cell, the macrophage, part of the immune system, and we study only one part of its funct...
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Carry on Conferencing
2007-11-28 14:25:00
Academic conferences are strange beasts. The basic premise is to bring together a bunch of people working in related areas and to get them to exchange ideas. Hopefully, as the ideas flow between attendees, the resulting swirls and storms will inspire new ideas. Some people contribute to the flow by giving talks, others by presenting posters, but, after the formal sessions are done, everybody gets involved there's plenty of chatter.That's on the face of it. If you look below the surface, you see slightly more. Most attendees combine this exchange with a skillful level of political cunning. People will cosy up to potential reviewers, if they are about to submit a manuscript, or try to establish reputations, if they're thinking of changing their position. In fact, many would say that the need for political manoeuvring is really what drives most conferences. Needless to say, you gain the most insight into this at the bar. In fact, the more conferences I go to, the more ...
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FAQ: Why Navier-Stalks?
2007-11-20 21:54:00
Navier-Stalks is a play on words. In the early 19th Century, Messrs Navier and Stokes devised equations for studying the flow of fluids. Since then, the Navier-Stokes equations have baffled and frustrated many a mathematician because they have non-linear properties which make them very hard to solve.I was in Japan attending a conference, at which an eminent Professor gave a talk outlining his vision of how he saw the field progresing. It was the sort of passionate talk that had a high tally of buzzwords, but that lacked bankable details. Among the many ethereal ideas was one about how introducing maths into biology will position us to calculate quantities describing the human body and its behaviour. But he warned us that the body would be highly non-linear and as he said this, Navier-Stokes appeared in big letters on the screen behind him. Only it didn't say Navier-Stokes; it said Navier-Stalks.This is an understandable mistake if you'd never read about the work, but I can...

FAQ: What's the purpose of this blog?
2007-11-14 19:18:00
Scientists enjoy a strange existance. We spend our time investigating the unknown, learning new ideas and fashioning new tools with which to unpick big knots of problems. Some of it is also spent politicking; finding out who are the movers and shakers, what research is in demand and who is pulling the strings. I'm learning all this afresh, having just moved jobs from theoretical physics to biology, and I thought it would be fun to document the experience.The transition from physics to biology has been fascinating. It has also been bewildering. Biologists and physicists are completely different. They talk a different language and take a completely different approach to scientific discovery. Basically this comes down to the difference in subjects. The human body is a vast, unknown, highly complex machine and it's very difficult to study aspects of it in isolation. Physicists, on the other hand, have done a good job at pairing down matter to its basic building blocks and now...
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Welcome to Navier-Stalks
2007-11-14 12:24:00
Hi there. Allow me to warmly welcome you to this new and shiny blog.I've set this blog up for a bunch of reasons. At the top of the list was my need to describe the weird and wonderful world in which I work. Until recently, I was a theoretical physicist, studying the more mathematical aspects of quantum field theory. But, having completed my PhD and finding myself unemployed (and unemployable), I thought I'd try my hand at biology; specifically bioinformatics.At the boundary between biology, mathematics and computer science, bioinformatics concerns itself with developing algorithms to study the huge volumes of genetic information that exist in the DNA of each specie of organism.Having aimed for Bioinformatics, I managed to miss the mark and was offered a position doing something slightly different. Instead of analysing the genetic information as it is encoded in the DNA, I was offered the chance to try to model how the DNA is used in the cell to allow the cell to respond to ...