Monthly Archives: September 2012

Molecular Biology is like baking because … Part II

Over the years I seem to have acquired a reputation as a competent baker. My second set of Bristol housemates decided that I was really quite awesome in the kitchen because of my ability to – 30 minutes after someone said I really want some chocolate… (We lived a 20 minute walk over a rainy, windy, barren field from the nearest supermarket) – produce a plate of hot-from-the-oven damned-good-if-I-say-so-myself brownies. This is slightly hilarious given the clear link between lab and kitchen and my ineptitude at the bench, but is really down to one simple secret.

I’m good at baking because I have a small selection of recipes that work and I never ever deviate from them. Last weekend I tried a different brownie recipe for the first time in about 4 years (two recipes in fact). Utter disaster. Continue reading

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Molecular Biology is like baking because…

If you are a sufficiently regular reader that you have ever googled me directly to get here, you will know that I am not the only baking biologist on the internet. In my haste and excitement to found my blog I neglected to realise that there is another baking biologist over on blogspot. Luckily, she mainly bakes, and I mainly biologise, so there isn’t too much cross over. Then there’s Sugar Scientist  and Domestic Diva MD and of course Dr Isis, Domestic Goddess.  It seems that baking is quite the past time for scientists in general and biologists in particular.

We have a running joke in the lab that there should be a list of questions that we ask to interview candidates before accepting them as members. It’s really a long list of things my PI dislikes about us (in a Grumpy Old Man way, rather than a genuinely-frustrated by way). The current list stipulates that new members of the lab:

– Must not have coloured hair (in the past 12 months alone mine has been purple, scarlet, royal blue and turquoise).
– Must not own cats
– Must not knit
– Must not have or use a mobile phone, especially in the lab
– Must be strongly opposed to the construction of pylons
– Must not read fiction
– Must attend the lab day out (my PI’s favourite day of the year is when none of us come in and he can have the lab completely to himself)

And the most recent addition to the list (thankfully, added after numerous successes not failures) is that new members of the lab must demonstrate their accomplishments as a baker. Because, ultimately, molecular biology and baking are very similar to one another in pretty much every respect other than scale.

Don’t believe me? Well let me explain…

Writing a reference

Whether you’re applying for a job or renting a house, it seems that just about everyone nowadays asks for references. Employer references, landlord references, character references… In normal jobs you ask your employer or your line manager for a reference, and he writes one: or maybe if he’s very busy and important the company writes one. Not so in academia.

Over here (and I admit that I have nothing to compare this to outside of this department, but my PI seems to think this is completely normal) if you want a reference, you write it yourself and then ask for a signature.

I’m sorry, what? Continue reading

Starting Grad School: Stress management

Given that it’s that time of year when both my new undergrads and the new crop of postgrads appear like magic in the department, I thought I might scribble some thoughts about life at the start of Grad School. Call it egotistical, but given some of the rubbish I’ve been through in the last 3 years I feel like I might have a thing or two to share that newbie postgrads could find useful. Continue reading

When science gives you lemons… find out if lemonade exists

Some days, life throws you curve balls. The lights are all red; Sainsbury sell out of orange milk; the weather forecast is clear and then it heaves down. (Seriously though, this is Britain. Who am I kidding? If I leave the house without a raincoat, it’s my own stupid fault).

More frequently – in my case at least – science throws me curve balls. In fact, what am I saying? I can’t even remember the last time science threw me a straight ball.

For the last two days I have been sat sadly staring at this data. There’s a special kind of paralysis that comes upon a PhD student when an experiment might be failing and they’re just not sure: it’s the ‘I won’t know until I’ve finished it… but I don’t want to waste my precious precious samples if I could fix it instead’ sort of feeling. This isn’t really a data set yet, just two qPCR plates. The first one looked a bit funny, but the standard curve just plain didn’t run, so I was planning to discard the plate and run a new replicate. Then the second plate came out looking exactly the same. (The green line is the same samples against a different housekeeping gene).

I am looking at the expression of a gene in the wild type plant, three single deletion lines and a double deletion. (I work with a polyploid, so by crossing and then selfing the deletion lines, multiple deletions can be stacked). I expected that either the plants would show reduced expression (because they are missing a copy of the gene), or that they would be the same as the wild type: because the plant was compensating for the loss.

These are the differences in Ct values between the gene of interest and the housekeeping genes: i.e. how many more cycles did it take for the sample to fluoresce. A value of 3 is more or less equivalent to a ten times difference in expression, so really I guess I was expecting to see a difference between lines of 1 cycle (or about a third). High values mean low expression. Low values mean high expression.

Deletion line 3 is doing what I expect it to: the delta Ct value is higher, because expression of my gene is lower. So far, so good. Expression of Deletion line 2 is static. Okay, so this one is compensating. Also good. The two deletion lines are different: that’s interesting.

Uh… hold on a second. What is deletion line ONE doing? And more to the point, what is the DOUBLE deletion line doing?

*cue freak out*

How on earth can a plant that is missing a copy of a gene then be producing MORE of the transcript associated with that gene?!

For the last day I have sat and pondered. And by pondered I mean I have tried to write an application, I have marked some A-level work, and I have tried to write a chapter for FastBleep Biology that I may never finish at this rate. Today, I cracked. I told my labmates – in a slightly hysterical voice – what my data looked like.

And without batting an eyelid, one of them said “You’ve deleted a regulator.” … I’ve pardon me? “You’ve deleted a regulatory element. Gene expression is no longer being suppressed. In fact if the double deletion is doing the same thing then that sounds even more like the answer.

There’s an answer. Not only is my science not failing dramatically, but there may even be something interesting going on.

Hello science. We meet again.