A different kind of stupid

This article was originally published for Cambio Ltd. on 20-09-2012. Access it here.

Take one reasonably intelligent person. Persuade them to do an undergraduate degree in a subject they declared as a child to be boring. On completion let them out into the real world to realise that a job isn’t much cop, and that their intellect is rotting in an office environment. Guide them to decide to return to university and spend £6K on a master’s degree rather than accept a manager’s job paying £30K. Three months into this course, get them to apply for a PhD in a subject area loosely connected to their university training. Conspire with fate for this person to be accepted for both the course, and the funding grant before they know what’s happened. Stand back.

Whoever decided this little scenario for me, I don’t know if I want to hurt or hug them. True, I was going stir-crazy working in an office, but I felt stupid because I was bored rather than because I had to regularly confess I didn’t understand basic biochemical concepts/ anyone else’s research project/ my own research project/ what possessed me to undertake a PhD. Also, my day-to-day tasks generally gave me the outcome I anticipated rather than a completely different one. When I went to a meeting I generally spoke to other people about a pre-arranged topic rather than, for example, turning up to discover that I was actually due to give a talk to members of the Royal Society on string theory (I know nothing about string theory). This latter scenario is how scientific research feels to me.

This week has not gone well. After spending the best part of 6 months getting my PCRs working reliably, they have now stopped doing what they should. I put in my standard mixture, and out comes something new and surprising. Unlike what I read at A-level, my experiments do not generally work, and they do not give me results that I can easily interpret. My gels go wobbly. Bands disappear inexplicably. I have to re-run my samples changing one of my 6 ingredients each time, then alter the PCR programme, the gel concentration, the voltage I run the gel at. This easily eats up a week. Then I discover that the PCR machine is running strangely, that the lids of my tubes are inexplicably popping open (despite my cramming them on with force not that short of hitting them with a hammer) – resulting in my samples evaporating. Then I find that someone used the last of my PCR strips and didn’t re-order any. With my lack of a biochemical background, I am generally forced to bug my lab mates for help and advice, or face the disparaging gaze of my supervisor. I feel stupid about 90% of the time.

Why did nobody warn me about this?!

I recently read a very good article entitled “The importance of stupidity in scientific research” (accessible here – or Google it) which was published in The Journal of Cell Science. At the start, the author describes meeting up with a PhD friend many years later, only to discover that she didn’t complete her course. Why? Because she was fed up with feeling stupid all the time. I feel her pain. But this is what scientific research is all about –after all, the reason you’re doing it is because no-one knows the answer. I’ve found this especially hard as I’m a super trendy inter-disciplinary student. So not only do I have the fun of diving into the unknown, I also have my arms and legs being pulled in 3 different directions. Deal with that Tom Daley!

But for all of this, there is no way you could drag me back to that office. My PhD winds me up, it makes me cry, it makes me question my sanity – and it makes me feel very, very stupid. But there’s a strange kind of freedom in the challenge, in knowing that realistically there are very few people who could do what I’m doing. In the end, no-one else will understand my subject as thoroughly as I do.

It beats working in an office any day.

Goodbye granny

 On the 2^nd September 2012 my granny passed away following a long battle with dementia. The trickle of brain cells that were switching off finally resulted in her losing the reflex to swallow, and she eventually died peacefully in her sleep.

I wanted to write something about this wonderful lady and the impact she’s had on my life. Now that she’s gone I finally feel I’m allowed to remember her as she was, rather than the shadow of herself residing in a nursing home who I would always feel guilty for not wanting to visit when I went home. 

My granny was the most wonderful grandmother anyone could ever hope for. As a child my brother and I would go to their house after school until my mum would collect us after work. Dinner (always at 5pm) would invariably be alphabites, turkey drummers and peas followed by one of those 10 for £1 ice creams in a plastic tub – or a variant on this formula. She would help us spell things out with the alphabites, and if the right letters weren’t available she’d get a knife and turn E’s into C’s, L’s into I’s or X’s into V’s. Her attention to and interest in people was phenomenal, and I only realise it now. If she was busy she'd tell me I'd have to wait for her attention, but it was always worth it when I got it as it would be undivided, and full of praise for my mediocre achievements. As kids we must have been a right handful but I don’t ever remember being seriously told off by her – she managed us so well. 

I won’t list all the memories I have, as the list of things I did with her is so long: painting, sewing, gardening, cooking, icing the Christmas cake… thinking about it now she gave so much time to me. It gave me confidence I didn’t get from anywhere else. And it gave me green fingers, for which I can only thank her profusely.

Yesterday I helped clear out her wardrobe and drawers. In some ways it was very sad because so many of her possessions had been lost or damaged as a result of her decline with the disease (clothes and books ‘altered’, items discarded for reasons I imagine she neither processed at the time nor remembered afterwards). Some of the things I most closely associated with her, and really wanted (her pot of face powder with its ‘grown up’ smell – bewitching as a child) were nowhere to be found. 

It was however massively rewarding though, as the main item I have salvaged was a badge I made her when I was about 7: it is 1 inch in diameter with a yellow background, and the word SUNDAY and some stars across the middle in those black transfer letters I struggled so hard to use when I was small. Whilst I don’t remember giving it to her, I do distinctly remember her wearing it the next Sunday at church and me being really, really proud. On being reunited with it I was struck by not only how it had survived, but also how utterly DREADFUL it is. At the time I obviously thought I’d done a good job at transferring the letters (I hadn’t – there are corners missing everywhere) and decorating it with the stars (I hadn’t – there’s about 3 randomly flung around the place). It is naff. It really looks like a child made it. But because I was so proud of it she wore it with pride, and that only bolstered my confidence. 

Dementia is a vile disease, and I really hope that by the time I get to that age developments have been made that will make it an easier journey for me and my family around me, assuming I get the genetic short straw. I spent a lot of time with my grandparents around the time my granny was first diagnosed, and in recent years I have occasionally wondered where my career would be had I decided to go for a job in London after graduation rather than stay in my home town working in a less than ideal job so I could visit my grandparents several times each week. Maybe I’d have completed a PhD and be doing work ‘proper’ by now… who knows? But I wouldn’t change it for anything. 

My mum worried years ago that by having such a close relationship with my granny it would be harder for me when she did finally die, but she’s so completely wrong. Yes, it aches like hell, but I have absolutely no regrets now she has gone – just lots of wonderful memories. Everyone has to go sometime, and I’m just glad I got so much out of the relationship when I had the chance.

When I was 6 she obligingly wrote in my autograph book (from when I was meeting just SO many celebrities!), and what she wrote will stay with me forever:

The kiss of the sun for pardon,

The song of the birth for mirth,

One is nearer to God in the garden,

Than anywhere else on earth.

…So get weeding!

I promise I will. I miss you granny.

The limits of bacterial hitchhiking

This article was originally published on the Society for General Microbiology blog on 22-08-2012. Read the original here.

Bacteria are able to move across oceans, deserts and mountain ranges with relative ease, by hitching a ride in clouds of dust or water vapour. The rules that govern the dispersal, or ‘biogeography’, of larger organisms simply don’t apply to bacteria because they’re so small. So how do we know where they came from? And how do we know if a bacterial strain found in Alaska is the same as one found in Costa Rica?

A study published in the August issue of Microbiology has shed light on the dispersal of nitrogen-fixing rhizobia bacteria in North and Central America. By sequencing portions of six common genes from Bradyrhizobium strains, researchers at the State University of New York, Binghamton were able to compile phylogenetic trees which show how different strains are related to each other. Those that group together are likely to have evolved from a common ancestor.

The team found no evidence that any Bradyrhizobium strains had evolved from a common ancestor in any one region, but that the same strains were found simultaneously across North America. However, they also found that each location had its own distinctive population composition, suggesting some adaptation of each rhizobium to its environment and its legume host.


There was a trend towards higher diversity in genes from rhizobia in tropical regions: strains isolated from Panama had a significantly higher diversity than those from Washington State. This was not due to the number of legume hosts sampled in the study, or the considerably higher annual rainfall in lower latitudes. Of the genes analysed, nifD, which codes for an enzyme involved in nitrogen fixation, tended to have the greatest nucleotide diversity – double that of the other five genes.

One of the most surprising findings was the lack of community structure overlap in regions with similar characteristics, e.g. Washington State and the north-eastern US, yet overlap existed between dissimilar regions, e.g. north-eastern US and Chihuahua, Mexico. The two latter sites have distinct biotic communities (lowland temperate forest vs. mountainous evergreen oak-pine forest) with no common legume host species. However, previous studies have shown that these regions shared the same flora in the late Miocene era, which suggests the similarity may be a legacy of previous interactions.

The biogeography of legumes is affected by soil type, rainfall and temperature, meaning their distribution is not random. The dispersal of rhizobia, as symbionts of legumes, will be limited by these same factors, though perhaps not for the same reasons. The presence of rhizobia and legumes may also be limiting factors for each other.

This study provides some important insights into the biogeography of rhizobia, and emphasises a frustrating question in legume-rhizobia research: is legume distribution limited by rhizobia presence, or vice versa?

Peat free compost

Considering the attention the destruction of peat bogs has received in recent years (e.g. this from the BBC gardening pages and this in the Independent from 1992!), and how devastating the impact of their destruction can be, I was recently surprised to find how much of the compost available to me contains peat.

On a recent trip to our local garden centre they had actually put the peat content of various composts on their signs...

First up, standard garden centre compost:

So standard compost is 60% peat. This is a no-go for me.

What about John Innes? That's good stuff right?

Good stuff it may be, but it's still 44% peat.

How about organic compost?

Nope, that's still 50% peat!

So it seems the only way to be sure is to buy stuff that EXPLICITLY says it is PEAT FREE!

The problem I find is that while the organic peat free stuff may actually work out quite cheap, it is also pretty rubbish. It seems that it is mostly just bark chippings that have been composted. And I'm pretty sure that if I did a pH test it would come up pretty acidic (it has a rather pine-y scent to it)

We've had a few fungus-related issues too...

Not to mention a couple of sudden-death incidents...

So if I'm honest, I just don't think peat-free compost is up to scratch just yet. It needs to compete with the peat-full stuff if it's to stand any hope of replacing it (before we run out of peat, that is!).

If you want to make a few bob I reckon there's a market opening up here!

Tomato harvest

Today we had our first, long-awaited tomatoes. They were delicious.

We raised some from seed, but they just didn't put on the growth early in the season, and are miles behind the two plants we ended up buying from a local nursery (where these beauties came from). I suspect these latter plants have also had an advantage in being in pots near the house, where it's much warmer than on the allotment (and less swamp-like...). Next year I think we will buy in tomato plants rather than endure the emotional turmoil of massive seedling failure, as we just don't have the facilities to get them going well - and  early enough - just yet.

I'll let you guess which one we found hilarious...

Down in the allotment doldrums

This year has been rubbish for the allotment. Lots of rain has meant our potato patch turned into a paddy field, the slugs have set up a regional HQ in our brassica patch, the alliums have all got a bad case of rust, and the corn is sitting there complaining about the general cold, as it's originally from Central America, doncha know.

Added to this, the rain has meant we have been rather less inclined to venture across town to our mud bath, so the weeds have come back with a vengeance, and I have become increasingly grumpy at the lack of sunshine (I blame my Mediterranean genetics - I'm not meant to be this far north!).

Operation grow-all-our-own-lettuce has been going quite well, but morale is definitely low. On such occasions Jon usually suggests a trip to the garden centre, and I generally resist, citing peat-based compost and excessive use of insecticides as a reason not to buy garden centre plants. However, we went, and I am OH so glad we did!

It would seem that as we're nearing the end of the main growing season, all the unwanted veggie plants are headed to the great compost heap in the sky, unless frugal chaps (and chapesses) like us snap them up.

I love trips like that because a) I love a good bargain and b) I love plants. Most of what we bought were (perennial) herbs and winter veg (though Jon currently has a bit of a pepper obsession, maybe it's a man thing). I will have to do a separate post on winter veg as it's currently my favourite thing, but I will mention that amongst our purchases were beets, kale, endives and chard. If anything it's a little early for some of these guys, but they'll do us well when we move to our new allotment. I also discovered once we'd bought it, that Italian radiccio lettuce also goes under the guise of chicory - an excellent winter veg.

The herbs are definitely my main success though. Next year I plan on having a lot more of them on the allotment, hopefully to deter some pesky pests, but also as we never seem to be able to grow enough herbs for the amount we get through! Fifty pence for 3 pots of thyme = a bargain in my books.

Hooray for the 'dead and dying' section of the garden centre!

Boring vegetarian food

I often get annoyed when people say vegetarian food is boring: that taking meat out makes the meal less interesting, or that it 'just isn't the same' without some animal protein in the dish. I've known a number of friends struggle with structuring a meal that doesn't have meat as the centre (them: "what's a lamb casserole without the lamb?" me: "why try to make a lamb casserole without the lamb?").

Now Jon and I aren't vegetarian. We do eat meat from time to time. But only if it's local, and only if it's good quality. I'd say 95% of our meals do not contain any meat. Quite frankly, around Christmas time, with the roast beef, pork pie, gammon, pigs in blankets and sausage rolls (no turkey in our house!), I generally feel sick - and tired. My body really struggles with breaking down meat. It makes me feel sluggish and slow, and I feel a million times better (and much less bloated) when I eat less meat.

I get really, really annoyed when people say tofu is bland. Yes, it's bland, but so is chicken if you boil it and eat it. If it tastes bland, you're not cooking it right! Fry it in some oil and soy sauce then eat it with sweet chilli sauce, and then say it's bland. It's like chicken, except it isn't tough and doesn't get stuck in my teeth.

To back my point up, here a some pictures of recent meals of ours. I seem to have developed a habit of going "hang on, I need to take a picture of my dinner!" before we tuck in.

Favourite meal #1 Salad! On this occasion made with home grown lettuce, pepper and herbs, cashews, eggs, artichoke hearts and cous cous. Salads vary completely depending on what's available at the market/ in the garden/ on the allotment. My personal favourites for this year include violet leaves, columbine leaves, watercress and rose petals.

Favourite meal #2 affectionally referred to as 'Japanese noodle soupy thing' as I'm not really sure what it is. I cook udon noodles in water with some soy sauce, chilli and other interesting cupboard ingredients. Fresh veg is chopped up and added for the final minute of noodle cooking time, then miso is stirred in at the end. I LOVE fried tofu, so this always goes in too, along with some home made kimchi, cashews and sesame seeds.

Lunch time! Cheese and coleslaw roll with marigold petals. Jon makes the most amazing coleslaw from cabbage, carrot, apple, walnut and yoghurt, alongside some magical seasoning that I can never replicate.

 Pasta and pesto, our style. This one was actually vegan, as we made the pesto ourselves from wild garlic and hazelnuts (a completely free product if you ignore the gallons of olive oil required). All mixed up with homegrown heritage mange tout, broad beans and spinach - and a bit of red cabbage too. This looked so much better than the picture gives it credit for!

Stir fry with udon noodles. A bit like the soup, only without the soupy bit. Loads of fresh veg and tasty seasoning. Granted this isn't actually vegetarian owing to the pork balls on top which we had because we had a bunch of sausages to use up after a BBQ - but while they were nice, I really didn't think they added much to the meal. I much prefer the kimchi dumplings we get from the Korean shop occasionally, but to be honest it didn't need anything added. When you have that many fresh vegetables, and the right balance of seasoning, meat just seems crude and stodgy in comparison!

So, that's my compulsive obsession with photographing my dinner sated, I thank you for indulging me. As a final point I will add one more picture - of an amazing meal Jon and I had when we visited his mum last weekend.

Yes, just look at that steak! It was delicious, don't get me wrong: it was all local and fresh. Unfortunately for me, it just didn't stay down - I was up half the night as my body tried to rid itself of whatever had offended it. My best guess is that my body just couldn't handle the richness of the food. And the salad would have been delicious even without all that meat...

I am wondering if I should become a full-time veggie and part-time vegan for my own wellbeing. Whenever I eat too much meat - or cheese - or processed food - I can feel my energy levels slump, and my waistband expand. The joy of the moment is always replaced by sluggishness, tiredness and general lardiness. Could I give it up though? I'll keep you posted...