Mental Indigestion

by Jim Caryl

Month: July, 2009

10 year anniversary…

Graduation, University of WalesTHIS week has seen many graduation ceremonies at the university, all imbibed with veritable Hogwartian pomp. It makes me reflect on my own graduation, which curiously enough was exactly 10 years ago this week.

I was full of excitement in the event of getting my BSc. It meant a lot to me, I’d worked ‘fairly’ hard for it, I’d gotten a good grade and was ready to go off and try to be ‘a scientist’. I hadn’t yet figured out how I was going to do that; it would turn out that I would use do a Master’s degree whilst I decided what I wanted to do (which was in fact to go and do a PhD; how inventive of me).

The degree ceremony, held in both Welsh and English (it was the University of Wales after all), was excellent; they actually took the route less travelled and entertained us. There were musical recitals, an award winning Harpist, some meaningful words of wisdom and the usual traditional grandeur. No pulling of fingers or such silliness.

It is in stark contract to the format of the ceremony at my current university, at least five years ago when I graduated with my PhD, where they decided that the appropriate means to celebrate the achievement was to talk about how much research funding the university had received, and what a good job so-and-so vice chancellor was doing. No one cared, everyone just wanted to get their few seconds on stage and be off.

I was of course, like all newly minted graduates, full of cock and bull, ideological and desperately wet behind the ears. I’ve yet to meet a graduate who doesn’t think they know it all, but as is ever the case, within a year, most graduates realise they know nothing. As the brighter ones will admit, ‘the first step on the road to wisdom is admitting that you don’t know anything’; a derivation, I guess, from Socrates’, ‘The only thing I know, is that I don’t know anything’.

Ten years on and I’m still in contact with some of those with whom I graduated, all of whom seem to be doing well in their lives and careers. I remember being reticent to refer to myself as ‘a scientist’ at that time, being worried of being a fraud (an uncharacteristic display of graduate humility); yet I’m glad to say that I can now refer to myself as a scientist in the truest sense, which I think I would have been happy about back then.

Once again I am faced with a summer during which I will have to make some difficult decisions. Either I step up to the next rung of the ladder and become a lectureship somewhere, or I step to the side and find another way to ply my trade, all be it away from the bench.

Still, at least I feel confident saying that the only thing I know, is that I don’t know anything.

The creation of matter…


NanodropAT SCHOOL we learn that energy cannot be created or destroyed, it can only be converted. As matter is basically energy (revise E=mc2), then it follows that you cannot ‘create’ matter, it can only be converted.

Fortunately for us, we are lucky as a lab, for we have a Nanodrop that is able to achieve the impossible. The Nanodrop is a device used for measuring the concentration of biomolecules such as DNA, RNA and proteins, based upon the degree to which they absorb different wavelengths of light. All labs have such a device, but not all labs have the much lauded Nanodrop.

So when you’ve been labouring in the lab to purify DNA or protein, you then skip down to the Nanodrop in order to determine just how successful your preps have been. However, joy turns to dismay when upon clicking the special ‘Measure’ button on the computer software that powers the Nanodrop, the small value you see tells you that you have very little material; that in fact, you’ve wasted your time.

No longer though, because on our Nanodrop, if you press the magic ‘Measure’ button again, the value increases. In fact, each time you press the ‘Measure’ button, the value continues to grow. Keep doing this enough and you arrive at the kind of value that you were hoping for. With a few mere clicks of a keyboard we can quadruple the amount of DNA or RNA in our sample; an amazing feat given that there is no source of the raw materials needed to create the extra matter.

It really is the most impressive machine in the world ;-p

[update: following this post I was contacted by a representative of Thermo Fisher Scientific (formerly NanoDrop Technologies), to describe why we see the problem. The problem, it seems, is in the Chinese whispers by which one is taught to use the machine. It appears that one is only supposed to take one reading of any sample; repeated measures of the same sample show an an increase in absorbance over time as the 1-2 ul sample, being so small, evaporates – yielding a more concentrated sample. So there you go folks, quite logical really – you still can’t create matter; the search goes on.]

Artistic breaks…

Final_smallI’VE had a long weekend away, re-kindling my artistic proclivities by staying in a yurt on the edge of a moor in the Preseli Hills of Pembrokeshire; also the source of the blue stone used to build Stonehenge. It is an ancient landscape of winding roads, erratic stones strewn across the landscape, burial barrows, stone circles and various other random dolmens. Overwhelmingly Pembrokeshire is defined by its patchwork of green fields that hug the coastline right up to the lips of the characteristic Pembrokeshire cliffs.

On the way down to Pembrokeshire was Aberystwyth, home to the sister of my alma mater university, and also home to a fine promenade (see pictures below), great cafes, and delicatessens. Also not far from Aber is Machynlleth and the Centre for Alternative Technology (CAT). When I first visited the CAT 12 years ago, on a university field trip, green technologies were bulky, poorly commercialised and required a significant commitment to implement. However, times have changed, and it’s never been easier, or cheaper, to make the change to green energy, water and waste recycling, and sustainable lifestyles. The CAT is looking a little dated in some areas (most notably the rickety old water-powered funicular, which isn’t exactly a technology that should be rickety), but in other areas it has continued to grow, develop and implement newer green technologies.

One thought-provoking CAT display is a pictoral time-lapse of landscape (mis-)development between 1953 and 1975, with obvious connotations of the negative impact of urban development. I photographed them and reassembled them here, which is the image on the left of this post.

Also at the CAT I discovered the Small House Society, something I’m sure has been rather more successfully promoted in the USA, but alas has received little notice over here. Spending time in a yurt, with a small adjoining shed containing a mini kitchen and shower, a hay bail to piss on and another small shed containing a sawdust toilet pit, it makes you wonder just how much space we really need. I guess the point it, if you live in a beautiful place, then sacrificing your living space isn’t too much of a chore; if you’re trying to ‘get back to the garden’ in a Joni Mitchell sense, then surely it’s better to have more garden than house? It’d be nice to see more communities of small (<300 sq yd) houses, rather than sprawling urban ribbon development.

Speaking of the yurt, on the same grounds was a pottery studio where I learnt to ‘throw a pot’, which is apparently pottery parlance for the making of a pot using a wheel. I have subsequently returned home with several new dishes, some random small pots, a coffee mug, a milk jug and a strong desire to add ‘Potter’ to my long list of alternative creative career options.

Four days isn’t really a lot of time to see everything, and rather than bore readers with a long account of a destination that you are better off visiting, rather than reading about, here are a few taster photos:

Traditional barn roof, mid-Wales Polytunnel at the Centre for Alternative Technology, Machynlleth, Powys Potting table, CAT, Machynlleth, Powys

Garden waste stove put to multiple uses, CAT, Machynlleth, Powys Aberystwyth promenade, Aberystwyth, Ceredigion. Aberystwyth pier

Aberystwyth beach jetty Book shop next to the Old Merchant House, Tenby, Pembrokeshire Brooding sky above an otherwise sunny Tenby beach

Lifeguard flag, Tenby beach One of my first thrown dishes Pentre Ifan burial chamber, erected 3,500 BCE!

I will add to these as and when I make headway through the seveal hundred captures I made!