Tag Archives: DNA

DNA: You’re Doing It Right

Or: wrapping up salmon semen

When I started out, I justified this blog’s creation by imagining that I would try to make the process of science a bit clearer. This would involve describing what actually happens in that murky void between some clever sod having an idea and the media wildly exaggerating them. In my head, this was inevitably accompanied by self-aggrandising metaphors: imagine beacons lighting the way for lost souls desperate for enlightenment and you’re in the right ball park. All I appear to have produced, however, are a few introspective musings, perhaps better described as sputtering gas flames when it comes to how illuminating and insightful they are. To remedy this, I thought it would be useful to explain what I am doing in Grenoble, as this might just constitute something worth reading.

Ludicrous dreams and badly-thought-out metaphors

My position at the Institute Laue-Langevin (ILL) is a stagiaire – which I am reliably informed is equivalent to an intern, except for the fact that in France they must legally draw a salary. Thus France gains a green tick in my Big Book of Everything and, as my supervisor quipped, “score one for socialism.”

I have a long-suffering  post-graduate on an Erasmus Mundus masters course looking after me and for the past three weeks, her glorious role has consisted of patiently answering my simple questions and coping with my constant lack of understanding. Eventually though, the mists parted and the gist of the experiment slowly permeated into my consciousness.

The institute has a nuclear reactor which produces neutrons, particles that, along with protons, lie at the heart of atoms. These can be focused into beams that are used to investigate certain properties of materials. The principle of this is relatively straightforward: by looking (closely, with a really big lens, if you’d like a nice idea of what isn’t happening) at how the neutrons bounce off the  nuclei of a material, you can infer a lot about its structure and how it behaves. The actual process involves complex quantum-mechanical treatments of the neutron  and target but, thankfully, that’s a story for another day.

A different sort of Neutron

My supervisor, the masters student and myself are looking into DNA (hence the excitement about it in my last post) and its different forms. Although still essentially the same ol’ double helix, it can exist as  A, B, and Z-DNA. The first two are identical aside from the former being slightly more compact, whereas the Z form’s “ladder” twists in a different direction. The plan is to put some samples in front of a beam of neutrons and see whether we can force the molecules to change between the forms by exerting different pressures.

My first reaction was slightly-less-than-perceptive: “This is pretty fucking cool.” We’re investigating the behaviour of the molecule that codes for every single bit of our bodies. This collection of nucleotides is the reason that life is still hanging on here about four billion years after it started out and what allows you to spend about half of your time awake looking at what other people are doing on the internet; it’s pretty fundamental stuff.

Salmon sperm is a very plentiful source of DNA, so large quantities of this are necessary for the experiment (hence the admittedly attention-seeking subtitle) and it all must be aligned in the same way in order for the neutron scattering to reveal anything useful. It is then necessary to catch these DNA threads on a rotating cylinder in order to fix a large amount of it. While being an interesting mechanical process in itself, it literally takes hours to complete and must be meticulously observed in order for the samples to produce results that we can analyse. When sharing my woes with a friend at the ILL, he nodded sagely,  remarking that about 70% of his time was spent cleaning his apparatus. I clearly have a long way to go with understanding the life of a chemist.

Thanks guys!

After a few weeks of this, my enthusiasm has faltered slightly, especially due to my incompetence when it comes to any manual tasks. The noticeable absence of equations from the work also makes me slightly uneasy, as I’ve developed a habit of fleeing to numbers and data whenever I’m uncertain about something. This is tricky when your day’s work involves trying to catch minuscule white threads with a glass rod while swearing as loudly as possible.

However, we have been granted some elusive beam time, which means an end to the production of DNA samples and experimenting with neutron diffraction for up to 48 hours. Expect posts in the coming weeks to contain a hint feverish excitement with tinges of narcolepsy-induced bitterness.

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Tribalism and Blurring Boundaries

As the impending doom of real life draws closer and the prospect of a working week fills myself and my friends’ boots with terror, it’s interesting to watch the way people pigeon-hole themselves, attempting to categorise the type of person they are, or want to become. At university, this results, perfectly naturally, in identifying with people studying the same subject, but tribalism among students is only getting worse. From philosophers arguing that no other subject can bestow the virtues of a critical mind quite like theirs, to business students convinced that market knowledge is all you need in the world, baiting other courses is an enjoyable pass-time. Being no stranger to this myself and all too frequently venting my true feelings on the world’s inadequacies, I thought the phenomenon deserved a few words.

Not an actual tribe, Bruce Parry!

For me, there has been segregation between the sciences for as long as I can remember. Even in the glory days of year seven, when no-one knew precisely what girls were and shocking news consisted of who was Sitting Next to Each Other On the Bus, physics, chemistry and biology were taken separately. This makes a lot of sense at a twelve-year-old’s level; most of the concepts covered tend to be easily defined by one of the three subjects (or, alternatively, the two subjects PHYSICS and STAMP-COLLECTING if you happen to be Ernest Rutherford). As more is understood about the sciences, this simple picture of three discrete disciplines is no longer relevant. DNA is a good place to look at this blurring of boundaries. Due to its role in the evolution of living creatures, it seems to obviously belong in the realm of biology, but describing its molecular nature and properties requires chemistry and its helical structure was discovered by physicists.

Look at a group of science undergraduates though, and you wouldn’t believe there was such a smooth mixing of the subjects. Despite many of my friends being natural scientists (meaning they can drift between different science modules throughout their degree), there is still an overwhelming sense that they belong to one of the major streams and as such, it’s still common to overhear complaints of biologists’ lack of work or the arrogance of physicists when they talk about how important their work is.

While this is usually just harmless chat (or harmless cat, in this case), in the long term, it is detrimental, both to science itself and its audience. In a time where the boundaries of neuroscience are giving us glimpses of an astounding future for the human race and physicists just keep on threatening to come up with grand unifying theories*, cooperation is the only way we’re actually going to progress on, and maybe off, this watery rock. Some of the most exciting advancements in science and technology are appearing at the boundaries and it would be a terrible loss if these were to be neglected due to squabbling and infighting. Additionally, it’s hard to see how scientists wouldn’t lose favour with the public if they were solely seen to bicker amongst themselves. It must be remembered how much research is dependent on the public’s purse and how quickly funding could dry up if pushed.

When I discovered the level of mixing between disciplines at the ILL, and in fact between all the scientific groups at the Polygone Scientifique in Grenoble, I was very happy but not a little intimidated; acorns have grown into huge oak trees, mountains have been worn down to sand (etc., etc.) since I last looked at a  textbook that wasn’t related to physics. Yet I found myself working with a mathematician, in a building with biologists trying to produce samples of DNA using what looks awfully like a chemistry set-up.

This apparatus has been my life for the past seven days.

Got into full scientist mode (w/lab coat + rubber gloves) for this machine

A more in depth explanation of just what the hell I’m doing at the institute will appear in the near future, but for now, suffice to say that I’ve sat and watched a cylinder rotating for far too many hours on a regular basis.

While this integration hasn’t yet led me to flee from the warm embrace of physics, it has given me a much-needed perspective on how science operates en masse as well as an appreciation of those who do this for a living.

*This is often followed by scientists in varying degrees of irritation explaining exactly why said theory will not live up to expectations. An excellent dissection of the last attempt can be found here: http://telescoper.wordpress.com/2013/05/29/the-curious-case-of-weinsteins-theory/