Wednesday 30 January 2013

Redemption by gel

Well I'm delirah!  My molecular biology class had to run some cut DNA down another agarose gel today.  After our disastrous foray in the world of gels two weeks ago, I was apprehensive. The conCSIeit was that some DNA had been found at/on/in a crime scene and DNA had also been obtained from five suspects: the cook, the butler, the husband, the lover and the nephew-who-will-inherit-everything.  Our team had to treat the DNA with a battery of restriction enzymes to break it up into unique small chunks that would 'uniquely' identify one of the suspects as The Perp.  As always where I work, there's never quite enough equipment, so there were several bottlenecks in the process and things got delayed.  The delay was made much worse by the fact that we (that is I - the buck stops with me) had loaded the gel-rig but not switched it on.  So by the time everything should have been running, or indfeed finished, the class was over.  Luckily I had a free hour immediately afterwards, so I was able to finish up for the class AND use another piece of kit to take a UV picture of the results.  And the pictures were fabulous or, more accurately, 3 out of 4 of them could be interpreted in the required way.  So I feel that, after an interval of some 25 years, I can finally add I can add "can run a gel-rig" to my CV. 

Note for sleuths; the left hand track is the Crime Scene, the others are suspects A,B,C,D,E

Sunday 27 January 2013

The Darkside

Years ago I spent the summer in the Netherlands at an international agricultural institute.  One of my co-workers on the course hailed from  Madagascar. His name still rings in my mind – Rakotodramananana: just that, no first name, no last, just the whole chunk.  How wonderful is that?  Of course, from his perspective Aimairaghan Ui’Sulliebhean is quite exotic too.  Which is my point. Diversity is delightful: it adds spice to the daily grind and makes a much more interesting cake of life.  And about 70 years after the foundation of the state (that’s after seven decades of colcannon and Catholicism, hurling and horses) Ireland started to climb exponentially up the diversity scale.  Polish shops appeared in every small town selling kielbasa and frozen piroguies.  Bacon and cabbage families started to have frozen pizza for dinner.  It was great.  Nobody was compelled to eat vindaloo or go fishing for pike but if you wanted to try something different it was increasingly easy.  The downside was that bargains were less easy to come by – you couldn’t buy tiny delicate delicious dabs at 28p a pound at the fishmongers or chicken livers for half nothing as we did in the 70s of the last century when there was no demand for those things.

Ten years ago, I started a new research project funded by the Department of Agriculture.  It was fundamental research that brought lab work and computer-power together to help make Irish food-production safer and more efficient.  The group hired a highly effective molecular biologist trained in the best US colleges and currently working in an Irish university.  He was old enough, smart enough and skilled enough to be running his own research group but was still working as a humble post-doctoral researcher.  These things happen; you keep applying for posts and coming second.  You keep applying despite knowing there is an internal candidate.  It takes ‘bottle’ under such circumstances to keep slogging along in science and applying for jobs because you’re good at it, because you love finding out what makes the world tick, because you can’t stop saying “that’s what I am”.  So we were fortunate to get him.

One teeny problem was that, because he hailed originally (before his stellar career in the US) from the Indian subcontinent, monoglot me could never remember how to spell his name.  His first name that is, because his given name was easy even if it came last.  How cool is that?  A place where you’re called Murphy Paddy.  Rather than asking him, I thought I’d take a guess and google it.  Ooops! The top three hits referred not to his science but to a sorry series of reports from the Dublin Equality Commission. My colleague lived in the outer suburbs and commuted in by bus, so he bought a season ticket and used it every working day for months until one day it was seized by the driver as invalid.  My pal argued that his ticket might be tatty from use but was still valid. It was clear, however, that everyone was being held up.  So he paid full fare to get to work and was told he would have to go to the central Dublin Bus office to get his season ticket back and sort it out.  In the afternoon, he took time off work and trogged across town to O’Connell St where an inspector apologised and gave him his full fare back but advised him to get a (free) replacement season ticket to avoid such problems in the future.  It was clear from the record that my pal snapped at that stage and took a case against the driver to the Equality Commission. He did this not for himself but for his children, and the single mother from Nigeria, and the student from Ethiopia whom he saw getting dissed every day in some, often trivial but cumulatively demoralising, fashion. As a middle-class educated man with a suit and a mortgage, he himself could rise above The Look, The Not-look, The Hesitation, The Unaccountable Difficulty.  The case was, I think quite properly, eventually dismissed, from lack of admissible evidence, but it has the ring of truth doesn’t it? 

If we’re to benefit from the colour, the energy, the opportunities, the availability of scrumptious food that cultural diversity provides, we all have to work at making New Irelanders welcome.

NotSundayMisc IV

The Horseburger Protocol

But let's leave the pastures of the past and - revenons nous a nos moutons - get back to the day job.  I wrote earlier about my molecular biology lab section.  We're spending the next tuthree weeks using the enzymes (restriction endonucleases -REs) which cut DNA at particular sequences of bases pairs [e.g. an enzyme from our homely commensal E.coli, called EcoRI, cuts DNA at GAATTC].  We have a CSI protocol where DNA from 4 suspects and a crime scene sample is treated with a couple of REs, and the fragments run out on a gel. The pattern generated by The Perp will then be compared to that from the butler, the husband, the lover and the nephew-who-will-inherit-everything.  In circulating this proposal, the Course Director put a footnote "and maybe Bob would have some bioinformatics ideas on this".
As I've spent most of the last 25 years doing 'the storage retrieval and analysis of biological sequence data' aka bioinformatics, you'd think I'd have loads to contribute.  Well I didn't, and frankly I was a teeny bit teed off that They would expect me to do anything beyond float-not-drown in the deluge of my new responsibilities. But two days later, I was driving to work through a literal deluge and had the wireless off, so I could concentrate on the traffic, and . . . I had an idea <ching!>.
There has been a scandal recently in Ireland over the revelation that cheap frozen '100% beef' burgers have been packed out with horse-meat.  There is 'no health hazard whatsoever' in this but if the producers finagle the label, what else - that we cannot detect - might they finagle?  Then again, as the rhetoric has it: what do you expect if you spend €1.49 on a dozen burgers??
ANNyway, in my last job as a Comparative Immunologist, I spent a lorra time comparing DNA sequences from different species - a lot of them mammals.  So my <ching!> was for the students to e-go to NCBI in Bethesda MD and fetch out a pair homologous sequences: one from Equus caballus and the other from Bos taurus. They can then search the sequences of the genes for GAATTC and the other RE sites.  A random pair of homologous genes from two species of different mammalian Orders might be 15% different, so there should be differences in the restriction pattern, even if you have to try a couple of different enzymes.  Appropriate-technology-me likes this a lot because you can do the whole analysis with a highlighter.  But you can't expect students to carry out tedious repetitive tasks nowadays - we have software for doing that.  So I'm suggesting that they use Fuzznuc from the EMBOSS suite of binfo software, to do the grunt work for them. The Horseburger Protocol - sounds like a racey Robert Ludlum thriller.
Haven't a clue what gene to choose?  Here's a starter list: ANXA1, BRCA1, CFTR, DRD1, EFNA1, FZD3, GSTK1, HSPA1A, IFNG, JBS, KLHL3, LPAR2, MTNR1A, NECAB2, OPRD1, PELI3, QARS, RNASE1, SOCS3, TSHZ1, UBXN8, VCF, WAS, XDH, YEATS2, ZBP1.  Don't like any of those?  There are 20,000-26 = 19,974 others to choose from. Go to!

Saturday 26 January 2013

Dandelion wine

This morning I've been prepping my Envir Chem class on Radon, whc is due for delivery (breathe, push, pause, repeat) on Tuesday.  Couldn't do Radon without elementary radio-chemistry, and then you have to mention Chernobyl and Fukushima.  And like Proust and his madelaine, just thinking about Chernobyl transported me back to that weekend in April 1986.  We were living in Newcastle-upon-Tyne then. Since returning from Boston 3 years earlier we'd been getting more serious about fermentation.  Not only was I making a lot of bread, we were also making a variety of alcoholic bevvies.  Anything that could be fermented seemed to finish up bubbling in a 1 gallon demi-john in our house: elderflower, elderberry, dandelion, strawberry, plum, parsnip, old tea, old inner-tubes - we'd brewed them all.  You had to brew enough to get ahead of yourself, because they all improved a LOT with keeping, and we were stipping the enamel off our teeth with some of the first taste product.  Dandelion was a favorite: golden in colour, intriguing in flavor, forgiving the day after.  The only down-side was they you had to take the yellow bits (the ray-florets botanists call them because they're not petals but individual mini-flowers) and discard every bit of stalk and green bract.  Failure to do this separation (by hand, each flower head separately) could release fungicides into your brew and kill the yeast. 
In the Spring of 1986 I decided to scale up from the piffling 6 bottles that you could squeeze out of a gallon to a 25 lt batch in a big plastic brew-bucket.  Accordingly we took the bus out to the meadows in Rowland's Gill, SW of Newcastle and spent the whole of Sunday morning picking bushels of brilliant yellow dandelions.  Eeee it were great: like being immersed in that painting by van Gogh.  Back home after lunch, the whole family sat on the stoop of our terraced house in the sun and twisted rayflorets off until our hands went black.  Then we washed our hands, had a cup of tea, and went back to twisting.  It was a huge investment, but eventually we got the brew all-sugared up  and starting to fizz.
So imagine our annoyance and chagrin the following evening when The Man told us that a reactor in the Ukraine had blown it's top and sent a plume of radioactive strontium, iodine and caesium across the meadows in which we'd been frolicking.
Never having dealt with a barrel of ferment before, I was really reluctant to tip the experiment down the drain. So we left it bubbling away in a warm corner.  And when it was finished, the marginal cost of bottling it seemed trivial, so we did that and left 30 golden bottles on a rack in a dark place.  And then it seemed sensible - it was an experiment in the qualities and economies of scale, after all - to open a bottle after a few weeks to taste it.
Maybe it was the added Sieverts of radioactivity, but that first taster was delicious and over the next few months we downed the whole batch, each bottle better than the one before as it matured.

Wednesday 23 January 2013

Ladies and gentlemen: commit!

Last week, my 1st Year Chemistry lab was tasked to carry out a redox titration.  What we used to call ferrous ammonium sulphate when I last did such an experiment, is now called Iron II ammonium sulphate.  The first step was to make a 0.1M solution of (NH4)2.Fe.(SO4)2.6H20.  This is a solution that contains 6.02 x 10^22 (1/10th of Avogadro's number) molecules of the salt in every litre.  To achieve this you have to calculate what the molecular weight of the compound is, then weigh out  1/10th (0.1M) that number of grams, add it all to 1 litre of water and stir.  You can find the mol.wt. of each of the relevant atoms (H=1, N=14, O=16, S=32, Fe=56) from a periodic table and the molecular formula tells you how many of each species there are. So the computation should be completely straight forward – why a child of six could do it!  But the night before class, it took me three goes to get it right.  You never really learn unless you try and get it wrong a tuthree times, so I was happy enough.
One problem is that nobody adds (can add?) in their head anymore - because we have calculators on our phones.  In my first science-qualified job in 1983, I was in charge of massive 1st Year Genetics classes which generated large amounts of individual data.  These had to be aggregated to get a class total.  One of my graduate teaching assistants used to stand in front of the blackboard where the results were tallied, adopt a fixed expression, make a faint whirring sound and after a couple of minutes announce the answer.  Where are you now when we need you, Rob?
So in class last week, I wrote up the formula asked the class to calculate the molecular weight and write it down in top right hand corner of their manuals in ink and put a box round it.  5/15 got it right, which was about as good as I did.  And nobody was allowed to pretend that they knew how to do it really, and would have got the right answer if they’d had time to check it.  So I think that was a valuable lesson.  But how do you know what the right answer is, if there is no neighbour to copy from or teacher doesn’t tell you? One method is to add the numbers up in two different ways:
By groups (the natural way). (NH4)2. = 36 + Fe = 56 + (SO4)2 = 192 + 6H20 = 108
By atoms (20xH=20; 2xN=28, 14xO=224, 2xS=64, 1xFe=56)
If they tally, you just might have the right answer.  Being confident enough to stand over your calculations/results/data is an essential part of the training to become a scientist.

Flood frost

For Ireland, it's been really cold these last few days and especially nights.  I've been anxious about snow and being either stuck on our mountainside and unable to eaqrn my salt or unable to get home after work.  40km is hefty enough of a commute in a car and I have done it, there and back, by bicycle, but I can't walk home if the roads are unsuitable for cars.  I was delighted this morning to go out to the car in the dark to find it frost-free.  The cold snap is over, I thought.  So imagine my surprise when I drove the 300m along and 30m down our rough bohereen to find the surface all icy at the bottom on the county road; and all the way into work.  If we discount the idea that our yard has sent up a bollupe of ionising radon gas that warmed the very air, it must have been an example of flood frost.  I can do no better than clip wikipedia "A related effect is flood frost which occurs when air cooled by ground-level radiation losses travels downhill to form pockets of very cold air in depressions, valleys, and hollows."  I've never seen this phenomenon so clearly present.

Monday 21 January 2013

A is for etymology

In my massively parallel teaching life at The Institute, I spent much of last weekend prepping the Nitrogen Cycle which investigates the wonders of the fact that the major component of the earth's atmosphere Nitrogen is almost inert chemically and so unavailable for most living things.  Several quite distantly related microbes can make a living from reducing N=N to ammonia by using an amazing enzyme called (surprise!) nitrogenase.  But why do we call it Ammonia?  Ammonium salts are highly soluble, so they are only found as crystals in the natural world in places where there's no water - like deserts.  The Romans' richest source for these useful chemicals was near the Temple of Amun in the African province of Libya, so they named sal ammoniacus what we now know as ammonium chloride.
Another part of my brain was simultaneously ploughing through the autonomic nervous system, in which the hormone adrenalin plays a substantive part.  It's called adrenalin because it's produced by the adrenal medulla (the bit on the inside of the adrenal gland).  Where is the adrenal gland?  It's where it says on the tin - ad-renal - on top of the kidney.  And I should know where they are because I spent six months of 1984 dissecting dozens of mouse adrenals out of their fatty matrix to weigh them, but that another day's story.

Sunday 20 January 2013

The Ringstone

Like characters from one of those fantasy novels, whose cover features a busty woman wearing armour and riding a flying horse, we have become Guardians of the Ringstone.

In the beginning it was just a stone; a boulder of granite, hard but fine-grained, spat out by some volcanic surge long before people walked the earth.  Millions of years passed and then came the ice, which scoured one face of the stone flat and left it exposed on the side of an Irish hill.  Perhaps 5,000 years ago, there came a neolithic mason, a craftsman who knew the stone’s qualities at a glance; it could be worked: on the flat face a story, a map, a gateway to another world could be carved with precise blows of an obsidian hammer.  And he made it so.

About 200 years ago, as the press of population pushed families into the marginal uplands, our valley was settled by hardy farmers – Hickeys, Crowes, Shannons, Wards – intending to scrabble a living from the peaty soil between the rocks.  By the time of the first Ordnance Survey in the 1840s, the map of the landscape had become gridded with lines to show the boundaries of  2 and 3 acre fields.  The material for these demarcating dry-stone  walls had been cleared, by quite super-human exertion, from the meagre fields to expose more top-soil and make cattle-proof barriers to manage stock and crop rotation.  These men knew the qualities of stone quite as well as their Neolithic forebears: this fine-grained granite with a flattish face could, with a stone-pick, lump hammer and steel wedges, be cleaved into manageable right-angled chunks to make a gateway in the wall with neat verticals. And this they did.

Five winters ago we decided to widen the gap between two fields, so that an opening previously suitable for an ass-and-cart could be made accessible to  modern industrial-sized machinery.  Not being super-human, I asked my neighbour Liam and his valiant mechanical digger to break down one side of the gateway, which consisted of three roughly squared off steamer-trunk-sized granite boulders back-filled with rubble, and rebuild it 2 meters wider.  When the middle stone tumbled out into the field my jaw went slack on seeing the  mason’s ancient design, intricate with the decoration known as cup-and-ring marks, exposed to light for the first time in 6 or 7 generations.  These characteristically Neolithic carvings consist of a central circular indentation – the cup - surrounded by concentric circles – the rings – and can be seen at Newgrange and  thousands of prehistoric sites across Western Europe. This message from the distant past was too evocative to be returned to the gloom so, when Liam reassembled the widened gateway, I asked him to put the carved stone back so that the interesting side was vertical and faced outwards. Two weeks later, my neighbour Martin, who as a geologist also knows the qualities of stone, came to marvel at what we were already calling ‘The Ringstone’.  From the regular indentations on one edge, he realised it had been split from a larger rock.  Taking the measure of one cloven surface with his fore-arm, he hunted up along the wall until he found its complement. 
In the Summer of 2010, we assembled a team of enthusiasts, experts, and another resolute digger. We dismantled the other side of the 19th century gateway and found the rest of the four (and only four! which was a relief) pieces of the jigsaw. It reveals a complex design of cup & rings, gutters, chevrons and lines. Following a lot of discussion and a little hard-work, the team reassembled the mystic, wonderful symbols of the Neolithic mason  to their cosmic whole.  At pains also to respect the imperatives of the 19th century farmers, the decorated face of the stone now doubles as a vertical sheep-proof gateway.  My neighbour Brian, artist and fell-runner, pointed out that the original design, perhaps a homage to the Earthmother, has been broken by that quintessentially male symbol of the cross. Layers of function, layers of meaning, all jostling for attention.

As the current Guardians, we’ve done what we think is right;  respecting the several traditions which have worked the stone, it now works for us as it worked for them. Who knows but that, in these mythic and turbulent times, one day soon a winged horse might deposit its rider in the field beside the Ringstone of Knockroe.  

Update Fall 2013: more recent (1850!) Ringstone News

NotSundayMIsc III

Saturday 19 January 2013

Research early, research often

My 'easiest' class is probably "introductory ICT for 1st Years".  The manual starts with 'how to send an e-mail' and I'm reliably informed that some of our (older?) students have never done this before.  The first point I wanted to get across was that mouse-work requires a lot of static muscle activity from wrist to shoulder, which leads to lactic acid build up (it's hard for this by-product of activity to flush out if the muscles aren't pulsed), which increases fatigue, muscle mass, deep-vein thrombosis and death.  So keyboard short-cuts are the source of a longer and happier life.  Surprisingly, not a lot of people know this: ctrl+c for copy; ctrl+v for paste; ctrl+z for back-track commands; ctrl+b for bold.  Less surprisingly, and this electrified my 4th Yr class to take notes, too few people know how to do sub- and superscripts in Word or Powerpoint: ctrl+"=" and ctrl+"+" (ctrl+shift+F;b;<return> and ctrl+shift+F;p;<return> works also).

After e-mail; forwarding e-mail; e-mailing a list; deleting an e-mail and a brief foray into Boolean operators (AND OR NOT) in Google we were ready to do some research.  It's never too early to learn how to find stuff out and how to present your findings coherently - which I find is a rather neat summary of science.  So I wrote out a list of possible topics and asked them to choose one that interested them enough to find out more.  As always I exhorted them to pick a topic the really interested them rather than slavishly agreeing with my definition of interesting.  Half the class are doing Sport Science or Sport Rehab, so there is a certain bias in the following list: Cruciate ligament; Lance Armstrong’s drugs; The human genome; World population growth; Greenhouse gases quantified; Helmets in American football; Evolution of Rugby scores; Distribution of ABO blood groups; Chimpanzees; Athletic records over time; Detection of horse in burgers.
Woot!  I'm going to learn a lot when it comes to their presentations - and I won't have to work.  Like Kipling, I'm fascinated and deeply respectful by expertise outside my own - be that match-box collecting, eppendorf 101, team sports or backing a tractor and trailer round a corner through a narrow gate.

Friday 18 January 2013

Help from abroad

Every Weds at 0900hrs, I'm running molecular biology practical classes.  Last week we were doing 'agarose gel electrophoresis' of 'lambda DNA' that had been cut with three different 'restriction endonucleases'.  See: it's hard to describe science without using technical terms or drifting off into metaphor.
'lambda DNA' is the genome of lambda, a virus that infects E. coli.  It consists of 48,000 base pairs (bp - the As Ts Cs Gs that comprise the universal genetic code) of DNA.
'restriction endonucleases' are enzymes that cut DNA at specific sequences of bases - GAATTC for example.  They are produced by bacteria like E.coli to protect them against viruses like lambda.  If the E.coli genome can be arranged by natural selection to have no GAATTC sub-sequences, then an enzyme that will cut at that sequence will do (fatal?) damage to any incommming DNA that does have such a sub-sequence.
'agarose gel electrophoresis' hinges on the fact that DNA is negatively charged (it's an acid: DNA) and can be driven through a thin slab of jelly made from seaweed extract by an electric current.  The distance a DNA fragment travels is proportional to it's size - large fragments get slowed down by the agarose matrix while smaller ones zip through it.
What should happen is that the students cut the lambda DNA with a tuthree different RE enzymes, so that the 48,000bp are divided up into lengths characteristic of each enzyme.  After running these fragments on the gel, you should see a ladder of DNA bands.  Each track with a different pattern because it's been cut with a different RE.
Last time I was running agarose gels in anger (and frustration) was in 1989, in my disastrous foray into 'real science' molecular biology.  So the students were much more competent than me - they'd used the technique before Christmas.  Nevertheless we made a pretty complete bags of the experiment but I didn't have this confirmed until I got to see pictures of the experimental run the night before the next session.  (I'm co-teaching the course with two other competent molecular biologists and my Oppo who had the pictures went sick this week).
The task this Weds was to measure, in cm, the distance each band had travelled last week; plot distance travelled for the fragments generated by the known RE (X-axis cm) against the length of each fragment (Y-axis bp); then calculate the fragment lengths of the unknown REs by interpolation.  Neat.
So I went to bed uneasy about what we were going to measure the next day at 0900hrs with the wretched blobs, spatters and dark-matter that we'd generated the previous week . . . and woke up screaming at 4 AM.  I'd figured that, as this was bog-standard molbiol class material, there would be crisp, clean interpretable pictures of the same experiment on The Internet.  Which as we all know is infinite in extent.  It took about 20 minutes for Google'n'Me to track down such a picture, and I e-mailed it to myself-at-work and my colleagues, before dropping back to bed
Four hours later, I get to t'office to be told that the college network is down, so I can't retrieve my solution.  But I meet the students on time; harangue us all for making a hames of the experiment; try some Socratic with them to work out what went wrong; ask them to talk amongst themselves; hare along the corridor to my office to find the network lurching back to life; download the picture; print 18 copies; hare along the corridor and . . . science is back on track.
So I'd like to thank students Nguyen and Painter in Skip Lovelady's class in Redwood High School, Larkspur, California for being the cavalry for our problem by making available their quality material.

Sunday 13 January 2013

Right and wrong

Here's an odd bit of  deja presque vu: in an earlier post I noted how Wm McBride got it right on Thalidomide but wrong on Debendox.  Paul Crutzen was one of the three 1995 Nobel Prize-winners for his work 20+ years earlier on ozone depletion.  He showed that nitrous oxide generated by soil bacteria was stable and long enough lasting to reach the stratosphere where it could be converted to nitric oxide by UV photolysis. Nitric oxide (as any fule kno) then goes on to strip one of the Os from ozone.  Crutzen suggested in 1970 that piling nitrogenous fertilizers onto the corn-fields of the Midwest would substantively increase the stratospheric nitric oxide burden.  That's all copacetic.  The following year he pointed the finger of shame at supersonic airliners as another significant destroyer of ozone. This turned out to be wrong on two counts: a) supersonic airliners never became economic enough or popular enough to replace subsonic planes: only a dozen Tupolev Tu-144s and a few more Concordes were ever built and b) as NOAA boffin David Fahey calculated in 1995, even 500 such supersonic planes would only drop the ozone concentration by 1-2%.

Multitasking Me

The first week in the new job was, as always there, a bit chaotic, so I had to cancel/postpone a few lab classes and I lost one class entirely as we were looking at different editions of the timetable. But the students so far are all engaged, or well-mannered or happy or all three .  So I been teaching Lovelock and CFCs; epidemiology; the human nervous system; introductory e-mail; confidence intervals a la ExCel; density, dextro-rotation, viscosity to determine [conc] of sugar solutions.  I've got a desk, a telephone, a parkplatz, an _excellent_ colour laser printer, unlimited pens/post-its. I borrowed my first two library books, found the staff canteen and the t'ilets.  I haven't worked so hard for 20 years and I've spent the whole weekend prepping 2 hours on the ozone layer.  I know I'm going to learn a LOT in the next few months.

Adventures in the bread trade

(It's Sunday again. NotMiscellany time:)

Nearly thirty years ago, we came back from seeking our fortune in Boston to a job with career prospects in Britain – the Irish economy was then battened down in the last recession.  In America, we’d been spoiled by choice in the miles of aisles in the supermarket two blocks away, so it took me a while to track down a decent wholemeal loaf in Newcastle Upon Tyne.  The bakery was across the street from work and I was able to pick up a loaf during my lunch break or on the way home.  The rhythm of this convenient arrangement was shattered when that bakery was taken over by a chain with pretensions towards world domination and my preferred loaf was no longer available – “there’s no demand” they said.  So I got on my bike and cycled a mile in the wrong direction to track down another Mom and Pop bakery whose idea of what constituted bread coincided with mine.  Only a few months later these venerable artisans retired and I was snookered again. But not for long. “How difficult can it be?” I asked myself, “like German beer, bread has only four ingredients – flour, water, yeast and salt – and only the first two (think chapatti) are essential”.  After some trial and very little tribulation, my next bread-driven bike run was out along the coast road to an industrial park where I purchased 500 grams of dried yeast and a 10 kilo sack of strong white flour.

Apart from the occasional baguette, a very occasional sliced pan, I’ve baked all the bread for our family since – and he’s never had a lesson in his life. The thing is that it’s not difficult and bread is remarkably forgiving.  Much easier than mixing cement.  If you slop in too much water and there’s no flour left in the bin, then add oats.  Add oats anyway; or wheat-flakes or rye flour; poppy or sesame seeds; onions, tomatoes or olive oil; raisins or chocolate chips. But you’ll find that there’s nothing better than a long-kneaded, well fermented, slightly over-proved plain wheat-meal loaf. You’re meant to bake most standard sized loaves at 200oC for 40 minutes but if you get caught up with something else and the bread bakes for an hour and 40 minutes it’s still edible – robust, crusty – but still edible. If the gas runs out after 25 minutes, it’s edible too; although you may need to finish the centre slices off in the toaster.

A few of years ago my second daughter read the packet of the standard 2 kilos of strong white flour that I now buy in the supermarket. “Suitable for bread-makers” she quoted.  “What else would it be suitable for?” I asked, indignantly waving my floury hands in the air, “whitewash?”.  Then I realised that they meant bread machines and my shoulders sagged. The message was that bread-making was so technically difficult and/or time-consuming that it required a machine to carry out the task. Well honestly! Even I can do it.  Don’t get me wrong, I can understand wanting  a bread-machine if you’re a not-a-morning person: you can load it up at night and set it on a timer so that you wake up to the smell of fresh bread but the loaf is a weird shape and the machine doesn’t bake baps.

But it is plain wrong to say that making yeast bread takes a lot of your time.  My grandmother, along with many true-born Irish women, was able to throw together a loaf of soda bread in ten minutes from setting down her shopping basket, taking off her coat and getting an apron on – less if the apron was in the wash.  Sure, yeast bread is not instant gratification: it takes more elapsed time than soda bread but each step in the process is separated by long chunks of intervention-free time when the vitamins are slowly released and the carbon-dioxide develops a perfect crumb. Waiting makes the finished product taste so much better and disappear so much quicker.

Every loaf is different, every loaf is good – baking it is a piece of cake.

NotSundayMisc 2

Saturday 12 January 2013

Rashers . . . gone

As well as working harder at the new job than I have worked for the last 20 years, we've suffered another huge change.  Rachel aka Rashers the Dog arrived into our lives as a puppy ten years ago one dark wet November night.  We'd put it about that younger-daughter (then aged 7) wanted a dog.  Indeed she wanted a dog so badly that she spend lots of time as a dog - gruffling, fawning, crawling about on all fours and eating weetabix off the kitchen floor.  So when our farrrming neighbour appeared with a dirty, smelly, black and white scrap that he'd taken from the local (unlicenced, seepy/grim) pound, he said he'd take her back the next morning if it didn't suit.  I think she went to the top of our local mountain (5km horizontal; 600m vertical) for the first time the following Easter: boing-etti-boinging up through heather higher than her ears so she looked like a terrestrial dolphin.  She was biddable, smart and mostly well-behaved although it must be said she and the postman seemed to have taken ag'in each other early on.  Anyway, 2012 saw her getting less fit - perhaps because elder-daughter had left home, so there was one less body to go for walkies - and more fat - perhaps because the Bean an Tí was giving her 'treats'.  She made her last couple of trips up the mountain in the late summer 2012 and was plainly hurtin' at the effort - although still game.  And as winter came in we put her on a diet.  Things went downhill rapidly after Christmas - she seemed to stop eating entirely - and early this last week she was admitted to the Vet Hospital for tests.  The tests came back showing kidney failure and other problems and the Vet suspected poison because the kidney failure had been so abrupt.  So Rashers came home on Thusday at lunchtime and the Vet came out at 8pm to finished her off with intra-muscular ketamine/lidocaine (veins too depleted by dehydration) followed by intracardiac phenobarb.  Younger-daughter had dug the grave that afternoon - up the top of the garden under some honey-suckle near the gate to the lane - and we buried her there at about 10pm,10th Jan 2013.  Bereft.

Thursday 10 January 2013


The other class I started teaching this week is teeny.  Four students registered, 3 at the first class and only two for the second class today.  But they are in their Final Year and seem to be bright and engaged.  I'm tasked to teach them Environmental Chemistry which is even further from my comfort zone than human physiology.  At least in the Human Physiology class we can be sure that each of us has in their possession a human body.  I thought that the EnvChem class was more 'under control' over Christmas but it's turning out to be a bit steeper to get copy together.  ANNyway, the day before the first class, I came across a list of elements essential to the human body and thought it would be interesting to see how many of them these young biologists could brainstorm.  They were surprisingly good and were prepared to try  the task, even to the extent of not peaking at the periodic table in the front of their hard-back lab-notebooks.  C H O N Fe Na K F Mn Zn Mg Ca P came out in a few minutes. They were delighted when I added Se Co (which I know about because we live on igneous upland soil and we're encouraged to dose our sheep with them) and when I mentioned Iodine one of the girls slapped her forehead.  Se Co Mo and I are very interesting from an EnvChem point of view.
Lots of folk know about Derbyshire Neck (aka goitre) from the prevalence of thyroid problems in the English Peak District.  Iodine is an essential ingredient in the growth hormone thyroxine.  If there is no Iodine then no thyroxine is produced so that a signal goes out to the thyroid saying "make more thyroxine" which is interpreted as "start thyroid cell division", and lickedy-spit our neck is as thick as our head.
I have flagged the idea we should see if there is a correlation between the adundance of the 25 or so human-normal elements in the human body and their abudance in the geosphere.  We expect some outliers because life is about disturbing entropy, but I wonder if there is a significant trend. Watch this space!
I also tasked us all to pick one of the minor elements (minor in abundance, not importance or atomic weight) and write a mini-report outlining its abundance, physical properties, physiological properties, commercial uses and value.  I was going to take Iodine because I'd already started on that, but one of the students has a mother with some sort of thyroid imbalance (no, not Grave's Disease).  So I took Molybdenum and I recommend you to Wikipedia it up: it's spread on cauliflower fields because it's an essential enzyme co-factor and there is enormously long band of prevalence towards esophageal cancer in central Asia because the rocks are Mo deficient . . . I could go on (and on and on and . . .zzzzzzzzz)

Wednesday 9 January 2013

Certainty: win one - lose one

I had a great day yesterday meeting my two lecture classes.  First classes was Human Physiology for 1st Year Diploma for Pharamacy Technician N=30.   Pharmacy Tech is sometimes what you do if you don't get enough points on leaving school to train to be a pharmacist.  Sometimes it's years since you left school but this might be a way of securing employment.  Drugs (both illegal and legal) is a growth industry in our country but formal quals are often required to sell the latter. 
I thought I'd pep up the pharmacists with some stories about alert medicos seeing connexions and improving the human condition.  Pharmacists get to see a substantive chunk of their community, some sick, some buying sun-screen or condoms. The explicit lesson in the stories was that while dispensing drugs and cosmetics they might notice that the people who bought iron supplements also seemed disproportionately to need anti-biotics (or Lem-sip or Beecham's Powder). 
The best story was about William McBride who noticed that the mothers of children with dysmelia (wrong limbs) seemed to have consumed more Thalidomide than the mothers of normally-developed kids.  Widukind Lenz in Germany was similarly alert but us Anglophones haven't heard of him.  So McBride was hailed as a saviour.  You need a rather well-developed sense of inner certainty - and good statistics - to push a project through from anecdote to data, to analysis, to publication.  20 years later, in 1981, he turned this certainty on another anti-nausea drug Debendox claiming that it too caused birth defects.  Unfortunately, he fabricated part of his data to support the inner certainty and was struck off the Register - although re-instated in 1998.

Day Three Down

Three days into the rest of my life and things are getting a little more settled.  Seems that the first week (or two) of each term are kind of chaotic.  The timetable-guy tries to optimise location-hours for student groups, teaching staff and available rooms.  But it often goes awry somewhere:  room A, which is ideal for the 3 primary criteria has no sink; students have two classes separated by one hour and 200m and petition to have the classes back-to-back (and leave an hour earlier); teacher is sent to the right room but two hours earlier than the students.  Nobody seems to mind much, but it can make me anxious if on top of this, the manuals haven't been printed, or the equipment breaks down.  Actually the manuals HAD been printed, but left in a cupboard and the equipment hadn't broken down but it hadn't been switched on either.  No time to sack out between classes either: the next lecture to prep, attendance registers to be updated, material to xerox or indeed read.  Famous story told about Sydney Brenner meeting earnest graduate student slaving over a hot photocopier and asking him "Have you tried neuroxing all those papers, my boy?"

Sunday 6 January 2013

Duncannon 1961

A couple of months after my father died, my sister and I went down to Dorset to sort out his shed.  This was where he stored all his art works and the matériel for their construction.  Impossible that this was the place where the oeuvre was executed because it was only by gingerly stepping on the few visible bits of carpet that we could reach the desk at the far end and make a start on the drawers.  There were paintings everywhere – later art-class oils of still lives and slabby nudes hugger-mugger with early water colours of well-executed cloudscapes and rolling hills; craggy castles and colourful streets: from Ireland, Britain, Brittany, the Med; a dramatic view from shore of the Straits of Magellan next to a more placid panorama of boats bobbing in Dun Laoghaire harbour.

We finished the drawers, gathered all the brushes into a vase, the paints into a shoebox and started on the paintings, classifying them by theme and geography into the bins of a rack along one wall.  We had a cup of tea and a scone (thanks Mum), and waded back into task.  After some time, I turned over yet another grey-backed Rowney art-board to reveal “Duncannon Strand 1961”.  There we were, my sister and I with our older brother and the red-white-&-blue Lilo air-mattress that we had brought from England that year for the annual visit to Ireland.  There also was the red-white-&-blue beach-ball which never existed but which he had inserted “for balance” or, as we asserted indignantly at the time, because he had the paint there and didn’t want to waste it.

Apart from us and our partly mythical beach-gear, the beach in the painting was empty as far as the Fort on the headland and the sky was full of scudding cloud.  So it must have been the Easter holidays.  We came almost every year, often at Easter, to visit an ever diminishing store of elderly female relatives in Wexford and near Lough Derg in County Tipp.  In Wexford, we would invariably stay in The Hotel, Duncannon.  We spent every dry moment on the beach or in the dunes: damming the stream, making bastions against the incoming tide, daring each other to touch the raw-liver-coloured sea-anenomes or just turning white and wrinkly in the sea.  With such small shoes, we tracked unbelievable quantities of sand back into the bed-rooms.  Wet days were spent in the front-room of The Hotel wrangling and playing cards; watching, through the rain-slattered windows, the showers coming in one after the other across the sea from beyond the Waterford shore. The clock ticked loudly in the hallway and the day inched forward.  If we could blag three-pence each from our parents, we went up the village to buy, and be delighted by, Lucky Bags but otherwise we were sustained by the enormous meals cooked by Nan Doyle.  She laboured away in a fug of bacon-and-cabbage in the kitchen far down the dark corridor beyond the yeasty clatter of the bar.

The pinnacle of my day as a young gannet was the appropriately named high tea: the chairs in the dining room made no concession to little legs and my chin barely cleared my plate.  But the appetite was  undiminished: we ate like arctic explorers to replace the calories whipped away by wind-chill and “bracing” sea-water.  After laying a foundation with slabs of white and brown soda-bread cemented with butter-&-jam, washed down by tea the colour of tomato soup, the fry arrived: rashers and sausage and fried egg sprinkled with the acrid black smuts which flaked off from Nan’s enormous black crusted skillet.  After that, a selection of Nan-made sponge cakes was presented.  We never ate like that at home and I’ve never eaten cakes with such loft, such subtle sweetness and such variety since that time.
Nan Doyle has long since gone to her rest, The Hotel burned down decades ago and was replaced in the boom-time by some handsome apartments.  The crumb of Madeline which sent Proust tumbling back in time to a childhood tea with his Tante Léonie was gone in a minute.  My father’s painting, which wrought a similar miracle of time travel for me, has lasted better. I must remember to tell the grand-children the truth about the beach-ball lest they think we had an extravagantly flaithiúlach childhood.

NotSundayMisc 1

Non-science matters also

About 18 months ago, I was listening to Sunday Miscellany, a magazine (essays/poems intercalated with music) programme on RTE Radio 1 and thought "I could do one of those".  In the 90s of the last century, I used to write book reviews for an on-line newsletter called EMBnet News and eventually was appointed Book Review Editor for new journal called Briefings in Bioinformatics.  I tried to summarise each book in 500-1000 words, point out the more outrageous typos and give an opinion about whether it was worth buying, borrowing or stealing.  I also tried to add 'a little bit more': a comment, a digression or synthesis that gave the review some substance in itself rather than just being a wart (visible, annoying but not usually metastatic) on the face of the book itself.  You can google up those early efforts to see if they have anything to say 15-20 years later.  So the preferred length for SundayMisc (700 words = 5ish minutes of talking time on air) was comfortable.  It's hardly long-form journalism - a genre for which I have a grá - but it's more than a soundbyte.  Longer than most articles in the Irish Times aNNyway.  I promised myself that I would write a SundayMisc essay each month for a year and I kept going for slightly longer than that, despite the fact that not one was accepted for broadcast.  They were all politely acknowledged by what I took to be a robot until one time I forgot to attach the essay and "The Robot", a nice woman with a very Irish superfluity of consonants called Cliodhna, pointed out the error.  So that's the background for the next posting.

Saturday 5 January 2013

New job, nearer home

On Monday, after three decades of teaching and research in the University sector, I'm moving sideways to teach in an Institute of Technology.  This is an alternative tier of Third Level (and indeed Fourth Level) teaching and research, where the student contact hours are much longer and hence the diversity of topics to be covered by one person quite broad.  Insanely broad, I thought, when my new HoD read out the list ofclasses for which I'd be responsible.  So, whatever happens to the students in the next year, I am going to learn a lot.