Fuzzier Logic

Impact factors, Colossus and the Wakefield retraction.

Tags: MMR, news, posterous

Defining absolute protein abundance

At the heart of Systems Biology is a vast hunger for measurements. mRNA abundance, metabolite concentration, reactions rates, degradation rates, protein abundance. This last measurement has long been problematic for researchers, mass spectrometers get increasingly accurate and powerful, but are still hindered by the simple fact that observed signal intensity does not necessarily correlate directly with the abundance of that peptide in the sample. Factors such as peptide ionisation efficiencies, dominant neighbour effects, and missing observations all give rise to erroneous estimates of peptide quantities. Until recently, the best way to get close to measures of protein abundance was to use a peptide tagging methodology, but these are typically expensive, and provide only relative quantification (useful for expression proteomics studies, less useful if you need to know the absolute levels of a protein for a Systems Biology study).

Recently, a three step method has been proposed for determining the absolute quantities of proteins in the cell, on a proteome scale. Step one is isoelectric focussing of tryptic digests of whole cell extracts. Step two, calculating the absolute abundance of a small group of proteins by Selective Reaction Monitoring (SRM). SRM uses spike in, isotopically labelled peptides of known concentration as references to calculate the actual abundance of peptides of interest. Finally, step three uses these abundances as reference points to calculate the abundance of all proteins in the sample, using the median intensities from the 3 most intense peptides for each protein.

Leptospira interrogans (Wikimedia Commons)

Using this methodology, the abundances of >50% of the proteome of a human parasite (Leptospira interrogans) have been determined to an accuracy of ~2-fold. These abundance measurements were confirmed by almost literally counting the number of flagellar proteins present in a cell by cryo-electron tomography.

Although current hardware probably limits this technique to a few thousand proteins, that is still a big step forward on what was previously possible. If whole proteome scale absolute abundance measurements become an achievable reality, maybe proteomics can finally take on microarrays as the dominant technique in the post genomics world.

Malmström, J., Beck, M., Schmidt, A., Lange, V., Deutsch, E., & Aebersold, R. (2009). Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans Nature, 460 (7256), 762-765 DOI: 10.1038/nature08184

Tags: proteomics, Research Blogging, science

Nature Methods

I love my free Nature Methods subscription. It allows me to get my hands on a paper journal, which I rarely get to do these days, and the content is actually pretty marvellous.

This month there’s a new technique for enzymatic assembly of DNA molecules from the Venter Institute, a standardised methodology for proteomics sample preparation, and a great technology feature from Nathan Blow about new proteomics techniques, including surface plasmon resonance (about which I knew nothing before today). Not to mention cool pictures of mice having light shone on their brains.

You can still apply for a free subscription, and if you are eligible to do so (individuals in North America and Europe involved in research within the life sciences or chemistry), I would urge you to.

Tags: freebie, journal, nature methods, Review, science

Save the Scientist, Save the World?

http://www.youtube.com/watch?v=7iPaiylUYW0

Gordon Brown has already saved the world once, but it didn’t take. So the world needs another solution. i humbly suggest that the way to help save the economy, of Britain at least, is to invest heavily in Science and Technology. In the following I try to justify this as anything other than pure selfishness.

Science is very often one of the first casualties of government spending in a recession. This is because it is seen as a luxury, a good-time frippery that is difficult to justify when times are hard. The reverse should be true, science and technology investment are not disposable because they are the generators of future income, the basis of a future successful economy.

The economy of this country has, for a long time now, been based in the service sector. This keeps people employed, which drives the economy because employed people buy things. But we no longer produce anything of note, we don’t generate significant external input into our economy – except through the financial sector… and I think everyone knows what happened there by now. We reached a point where confidence amongst those employed in the service sector collapsed, so they stopped buying things, this means that the service sector looked to the financial sector for support, but the financial sector, to all intents and purposes, no longer existed, so the service sector began collapsing upon itself. This is self-perpetuating, it leads to job losses, which leads to less buying of things, which leads to further job losses… and so on. (I realise this is a gross simplification of the real situation, and not 100% accurate, but it is pretty close to the real thing, and makes my point).

The government has declared its intention to follow a Keynesian approach and spend its way out of recession, taking upon itself the responsibility of injecting the cash that the economy needs to rebuild itself. This is a well recognised approach, and has merit, the new investment has to come from somewhere, and no institution has the borrowing power of the government. However, we (as a nation) must be able to recover this investment at some future point. This means we have to create wealth that is not already in the system. We have to make something that the rest of the world wants to buy.

So, invest in science, engineering and technology. Reverse the decline in these disciplines, the unpopularity of Maths and Physics in the classroom, the hemorrhage of the talent we do have overseas. Make the product the rest of the world buy into our innovation. Funding research keeps the current generation of innovators employed (the selfish bit), and creates new opportunities for the next generation. And not just for those lucky enough to have the education to pursue this route. Infrastructure is needed to surround research. Newcastle University is one of the largest employers in the North East.

At this point I am clearly in danger of getting carried away, so it’s probably best to wrap up. Since I started writing this particular perma-draft, many things have happened. Gordon Brown spoke in congress, about the need to ‘educate our way out of the downturn, invest and invent our way out of the downturn and re-tool and re-skill our way out of the downturn.‘ The US stimulus package has promised vast investment in science and technology. And just today President Obama unfroze research into Stem Cells in the US. All of these are obviously good things, let’s hope the momentum can be maintained, and the doom merchants don’t win.

Tags: doom, politics, science

Fixing Proteomics

I’ve only just discovered the Fixing Proteomics Campaign, thanks to a post on FriendFeed. It’s an initiative that I probably should have known about before, since it appears to originate, at least partly, from Nonlinear Dynamics, a Newcastle based proteomics informatics company. The campaign is also dedicated to a message I have been trying to spread among the researchers I interact with during my work: experiments must be robustly designed, and an unreproducible experimental result is meaningless.

The website for the campaign contains some useful resources for spreading this message, most effective are the analogies that illustrate the most common experimental design techniques, and the 4-step guide for Fixing Proteomics (the subject of the FF link, above). I have used something akin to the analogies in lectures I have given about experimental design (indeed I have used the apocryphal ‘Fahrenheit and the Cow’ story itself), and I will certainly be using the 4-steps in the future, and referencing the Fixing Proteomics website too.

Just one note: as Frank points out in the FriendFeed thread, the PSI could be highlighted a little more. Proteomics experiments would not be reproducible at all, particularly cross-site, without the efforts made by the standards community. As AnalysisXML enters its public comment phase, it is worth remembering the contribution they have made to opening up data formats and making data and metadata available in a non-proprietry way.

Tags: data standards, proteomics, science

Blog for Darwin

This post forms part of the ‘Blog for Darwin’ blog carnival.

I wasn’t going to write this post. I am very much of the opinion that holding up one man as a figurehead for an entire science is a mistake, and sets up too many straw-man arguments for detractors to propound (of the nature of: x was mistaken, so his theory y must also be wrong). Darwin lived in the 19th century, limited by the 19th century’s knowledge of science. A period where ‘Biology’ as a science didn’t really exist. Of course he was wrong about some stuff, and by equating Evolution with Darwinism, we give the denialists a stick with which to beat us (and this also leads to misleading and pernicious headlines like that in the New Scientist a couple of weeks ago). I ‘believe’ in the theory of gravity (as supported by the weight (ho ho) of evidence), that doesn’t make me a Newtonist.

There is no doubting that evolution is more than just Darwin, and that the Darwinian view of evolution probably doesn’t totally hold water any more, but that is hardly a surprise. It is 150 years old (in its published form). So, much as I admire his achievements, I wasn’t totally behind the idea of ‘Darwin Day’. Grist to the mill of creationists who see Darwin as the sole pedestal for the Theory of Evolution.

But then you see the amount of pseudoscience that persists in the mainstream media, and results of surveys like this one, which suggests that around 10% of Britons believe the earth was created by a supernatural being sometime in the last 10,000 years, and you think: ‘Why should I be churlish about something which is basically pro-science, and is getting a shed-load of high quality, high profile coverage?’. So, yes, if I can increase the positive noise surrounding February 12th 2009, I will. I will shout about Darwin from the rooftops if it gets something close to actual science in the news pages for a change.

For the rest of this year, this is where the battle will be fought. The hearts and minds of the anti-science luddites must be won over by the elegance and wonder of a beautiful theory, arrived at by a brilliant man who spent many years of his life in painstaking examination of the many glorious wonders of the natural world, and slowly formulating a way in which they were all connected. He truly changed our understanding of the world. Let us celebrate that fact.

Just don’t call me a Darwinist.

Tags: blogswarm, Darwin, science

MMR scaremongerer sicks the legal dogs on Ben Goldacre

Let the blogosphere and twittersphere spring to his defence!

See here for full details, but a London broadcaster had a half hour long rant on her show about the ‘dangers’ of the MMR jab on 7th January. Ben Goldacre subsequently posted the entire, repulsive, segment on his blog, to show this woman up for the scaremongerer she is. The radio station she works for has now set the lawyers on him, insisting he cease and disist.

So I am reposting his plea for help, and posting links to the relevant content (original post here, complain about the broadcast here). If you have the know-how to help him out, please do so.

EDIT – You can get the audio of the original broacast from YouTube or WikiLeaks… if you want your head to explode with frustration… Also note this graph, which illustrates the very real effect of irresponsible woo like this.

Tags: badscience, doom, MMR, weirdos