Tag Archives: biology

Starting Grad School: You don’t have to wrestle the snake!

Before we start, you need to read this:  Partly because my punch line is going to hang on you being familiar with the metaphor, and partly because if you’re here, then basically you need it in your life.


It would be safe to say that my PhD has not been plain sailing.  I’m not sure that anybody’s doctorate actually goes smoothly and pleasantly at all times, but I genuinely believe that – as the lovely Jenny Rohn from LabLit.com said yesterday – if you can survive this then you can survive anything. So how do you? Survive, I mean. I’ve talked about making your PhD easier by being organised from the start, and finding a support network and by not letting yourself get dragged down. But what about when you’re completely at rock bottom? What about when it’s time to do or die?

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Adventures in protein land part 2: Cytosolic protein extraction

So this is going to be more like a lab book entry than anything else, but I’m finally starting to get my head around some of this protein malarkey and figured I should write it down in multiple places!  Continue reading

Essential response to anti-GM from Mark Lynas

No full length post here, just a suggestion that you all go to read Mark Lynas*’ fantastic deconstruction of various anti-GMO arguments. Obviously none of the arguments mean ‘go grow GM across the world immediately!’ but he gives some lovely detailed responses to the inconsistency in various people’s thinking (e.g. how objecting to Monsanto creating a monopoly on corn should not lead to trashing open source disease tolerant papaya in Africa) and explanations of how environmental groups are doing things that simply aren’t good for the environment.

It’s long, but a very good read.

Following a decade and a half of scientific and field research, I think we can now say with very high confidence that the key tenets of the anti-GMO case were not just wrong in points of fact but in large parts the precise opposite of the truth.

This is why I use the term conspiracy theory. Populist ideas about conspiracies do not arise spontaneously in a political and historic vacuum. They result when powerful ideological narratives collide with major world events, rare occasions where even a tiny number of dedicated activists can create a lasting change in public consciousness.

The anti-GMO campaign has also undoubtedly led to unnecessary deaths. The best documented example, which is laid out in detail by Robert Paarlberg in his book ‘Starved for Science’, is the refusal of the Zambian government to allow its starving population to eat imported GMO corn during a severe famine in 2002.

Full link is here

*Mark Lynas as in the authors of Six Degrees, a pop science book about how the world would change as average global temperature increased by 1 degree, 2 degrees, 3 degrees etc… It’s basically a huge meta study of primary literature and very enjoyable. Apparently he’s good at writing about GM too – who knew?

Rusty Research: Fighting Bread’s Biggest Bad-guy

This has been a bad year for farmers: last year’s wet summer and then the cold winter that just won’t end have scuppered one harvest and probably knocked this year’s right down too. Even when conditions are more ideal than they have been this year, farmers and breeders fight an uphill battle trying to prevent a significant proportion of the crop being lost to various pathogens. When it comes to wheat that means rustblack rust, brown rust and yellow rust. Where it strikes, yield losses are likely to be around 20% in susceptible varieties, and the problem is getting much worse. Most resistance to black rust (Puccinia triticina) is caused by a single gene, which a new resistant kind of rust (Ug99) managed to overcome in much the same way as MRSA became resistant to methicillin in our hospitals.

Close-up of wheat leaf rust (”Puccinia triticinia”) on wheat. Photo by James Kolmer. http://www.ars.usda.gov/is/graphics/photos/jun06/d519-1.htm Image Number D519-1 PD-USGov-USDA-ARS

Now scientists from Norwich, Cambridge and the USA are trying to find out how some kinds of a similar disease, yellow rust, (Puccinia striiformis or PST) are able to overcome the plant’s natural defences and infect.  Continue reading

Salvaging the salty small holdings

When people interested in food security aren’t busy worrying about plateauing crop yields, they tend to be worrying about how much agricultural land we’re losing. We already use so much of the world for growing food crops (around a third) that there’s very little spare land left, and some of the techniques we use for growing crops lead to the land we already have being lost. When crops are grown in an area with insufficient rainfall they must be irrigated (i.e. watered). But all standing water, even if it doesn’t come from the sea, contains small traces of salts: just look at the label on a bottle of Evian. This means that over time, the land becomes saltier or salinised and since plants don’t like salty soil they struggle to grow there.  Continue reading

Molecular Biology 101: Synteny, Conservation and two wheat genomes

Somehow between going to the Netherlands, the Easter break, a week-long lab course and a conference talk to write I managed to miss not just one, but two really interesting, exciting and useful papers in Nature (Incidentally, I try not to write too much on here related to my PhD: I’m always a little scared that I’ll end up saying similar things about papers in my literature review and then being pulled up for plagiarism or something, but these are two interesting to miss.) But I digress.

Sequencing the wheat A and D genomes

Two weeks ago a consortium of Chinese and American scientists published two papers about sequencing both the A and the D genome progenitors for bread wheat. (Quick re-cap for the un-initiated. Wheat is a hexaploid i.e. instead of having one maternal and one paternal copy of each chromosome – that is, 2 in total, it has 3 pairs of each, making its genotype AABBDD). This is pretty big news for a couple of reasons: Continue reading

Adventures in protein land

I’m not a protein biologist.

I wouldn’t usually describe myself as a geneticist either, unless trying to clarify what it is that I spend my time doing, in the same way that for years I would describe myself as playing the violin rather than as a violinist, because that seemed to indicate some level of skill that I didn’t feel I yet had.

But I’m definitely not a protein biologist, because I did no protein work as an undergrad, and I didn’t sign up to do a protein based PhD, and there’s only one post doc in the lab who has the first clue about proteins and – while she is possibly the most helpful post doc ever to cross my academic path – there’s only so much help someone can give you when you don’t know what questions to ask.

Yet in spite of this, I appear to be in a situation where doing protein work is inevitable. A few months ago I learned about PAGE gels and Coomassie blue staining and Western blots. Now, I must actually start extracting protein from real live plants, as opposed to my nice-n-easy-burst-like-a-bubble-E. coli. It turns out that this is rather more complicated than I had hoped.  Continue reading