Chemistry, ferns and other musings

Music

2012-01-04T17:39:00.002Z

It's been quite a good Christmas for getting new music: here are some thoughts on the CDs I've been given (or purchased - I strongly recommend visting Prelude Records if you are ever in Norwich!).

Words and Music is a 2007 release on the Chandos label with vocals and piano by Richard Rodney Bennett. There's a mixture of standards from the American songbook (I won't dance/ How long has this been going on?) and lesser known songs, as well as the title track, a Bennett composition.

Graduation features Richard Hills playing the Dickinson High School Kimball theatre organ with his usual style and flair. I particularly enjoyed his Songs from the British Isles and Viva Mexico - a Mexican fantasy. If you aren't familiar with Richard Hills or with theatre organ music, then watch this video of Hills playing Tiger Rag - I guarantee you'll like it!

I've also acquired a recording of the Bach tocattas (Angela Hewitt [Hyperion]) and Naxos recordings of Dvorak symphonies 3,4,6, and 8, which I'm getting to know for the first time and enjoying immensly. I've also bought a 2CD set of harpsicord suites by Jean-Henry D'Anglebert. I'd never heard of this composer (a friend of Lully) and have yet to listen to the CDs ... more to follow.

Resolution

2012-01-02T10:31:00.002Z

Each year I make a resolution to write more on this blog. Maybe 1. i. 2012 will be the turning point?

Happy New Year to one and all!

Still no solution yet

2011-07-03T06:14:00.002Z

I'm still thinking about the cone problem. I've now acquired a classic text on co-ordinate geometry that devotes substantial space to the conic sections. Brushing-up on this topic would probably be worthwhile in any case, but I'm hoping it will give me the apparatus to work on this problem.

More updates to follow in due course, I hope!

2011-06-05T09:25:00.003Z

The mathematics problem from my previous post continues to occupy my thoughts. Whilst I have made some progress with a solution, I have come up against a seemingly insuperable barrier. One of the things I need to be able to determine is the ratio into which a section through a frustum of a cone divides the volume, as illustrated above.

I had approached the problem by imagining slicing the cone into discs. The section would then create cicrle segments whose areas could be integrated to obtain the volume. Unfortunately, the expression derived for the area in terms of the height is very hard to integrate. It seems such an obvious question to ask, I can't believe that a solution isn't out there somewhere!

Water in a glass

2011-06-01T09:40:00.005Z

A scientist is someone who sees the world around them and wonders how it is like it is.

Even though I've been a scientist for most of my life, it still surprises me that so many interesting problems can arise from something as simple as a glass of carbonated water. Here are three that have occurred to me during the last week.

An economics problem: why is Sainsbury's own-brand carbonated water cheaper than their own-brand still water (by around 10%)? Surely, the carbonation process requires more input of energy and materials, so it should be more expensive.
A physics problem: when the bubbles rise they clearly accelerate, but is the acceleration constant, or is there a significant change of force with depth, resulting in non-negligible variable acceleration?
A mathematics problem: what is the relationship between the volume of water in the glass and the angle by which the glass can be tipped before the water spills? This would, of course, be the same regardless of the nature of the liquid in the glass, providing surface tension is ignored. I am assuming that the glass is a frustum of a right circular cone.

The economics question doesn't really interest me, although the answer might.

The physics problem could probably be answered with a bit of thought and some back-of-an envelope calculations and might make a useful diversion when stuck invigilating internal examinations next week.

It is the mathematics problem that has really gripped me. Despite appearing fairly straightforward initially, it turns out to be really quite complex, requiring a determination of volume of a conic section. There are 2 cases to consider:

a) a fairly full glass, where the liquid forms an eliptical section of the frustum;

b) a fairly empty glass, where the liquid forms a section of the frustrum in the form of a elipse segment (the base of the glass constituting the chord).

Finding the air/liquid contact area would be straight forward, but extending to the volume seems to be quite tricky. A volumes of revolution approach will not work as the volume section has no cylindrical symmetry. The internet doesn't seem to be very helpful, but then I might not be constructing a suitable search as the sections I'm interested in might have a "proper" name. My next stop will be my Euclid, although I don't hold out much hope.

Any suggestions would be most gratefully received.

Of course, being a scientist I could just be a bit empirical about this: I could go and get some data and then see if I can find a relationship. Maybe that should be my next stop ...

Halcyon days ...

2011-05-14T09:48:00.002Z

... are here again.

There is a short period in a teacher's year when examination classes have departed for study leave and internal examinations and reports are not yet threatening, so that workload eases for just a couple of weeks. This calm is perhaps the best time of year - time to relax, reflect and generally reorganise one's life.

"Oh, come on," I hear you exclaim, "what about those long summer holidays?". Somehow, they never seem to be the treat that you think they'll be. There's always something to be doing, either domestic chores or the planning that you hope will ease the burden of the new academic year; somehow several weeks of "free" time are never so greatly enjoyed as a rare work-free weekend.

I'm hoping to finish The Daffodil Affair (Michael Innes) and Nature's Chemicals (Richard Firn) and there's a fern to plant out (once I've dug up an the remains of old ornamental current tree) - photos to follow.

A day out in London

2010-10-29T10:14:00.004Z

On Wednesday, I had a day out in London. Such excursions are always a somewhat mixed experience because whilst I enjoy the things I visit, I find London a fairly miserable palce to travel around and the people less than friendly. This was actually my second London visit in two weeks, having attended my sister's graduation in the Albert Hall last week.

My aims for the day were two-fold. Firstly, I needed a minor repair to my Howarth oboe (I play an S20), which meant leaving it at their shop in Chiltern Street and then collecting it in the afternoon. Secondly, I wanted to research the medicinal/cosmetic uses of a particular fern species. I was pleased to gain access to two important libraries - the Lindley library (Royal Horticultural Society) in Vincent Square and the Botany Library at the Natural History Museum. This was time well spent and I returned with 7 A4 sides of notes. Both libraries were welcoming and friendly (not a universal experience, as visitors to some of Oxford's libraries will know only too well) and I was pleased to be given access to material that otherwise would be difficult for me to read. One of the things I most miss about Oxford is not having ready access to good library facilities; to adapt Kenneth Graham - there's simply nothing half so much worth doing as simply reading around in libraries.

Getting around proved easy in the morning, but difficult in the afternoon, mainly because the police had elected to shut park lane (N) for no obvious reason. I ended up walking from Hyde Park corner to Howarth (near Marylbone) and then back to Waterloo. Fortunately this did take me down Charing Cross Road and I was able to buy some sheet music from Foyles.

I really don't know how people can stand to commute into London every day.

Giant molecules

2010-04-16T08:55:00.001Z

I recently reviewed Walter Gratzer's book Giant Molecules - from Nylon to nanotubes (OUP, 2009) for Education in Chemistry.

You can read the review here.

The Secret Agent

2009-12-31T12:06:00.001Z

I finished Conrad's The Secret Agent during my time away over Christmas, which included two quite long train journeys.

Currently reading (start of Christmas holidays)

2009-12-20T15:43:00.002Z

Hugo: Les Miserables (in English translation!)
Conrad: The Secret Agent
Lewycka: A Short History of Tractors in Ukranian

Barke et al.: Misconceptions in Chemistry
Rhiordan and Hoddeson: Crystal Fire

... and also a book that I'm reviewing.

Campion update: I've read the two war-time novels
Traitor's Purse (see previous post)
Coroner's Pidgin

I don't think I'll finish all of the series in 2009!

2009-12-20T15:23:00.010Z

Following a few days of cold weather I found some interested ice crystals outside my front door this morning. Unfortunately we were in a hurry to get to church, but I managed to get the following photographs later in the day. The ruler is 20 cm for comparison.

I think they have formed by vapour deposition from the cold damp air. This is essentially a process of diffusion-limited aggregation, similar to the growth of zinc or silver crystals under electrodeposition, which is the usual chemical fractal demonstration. The delicate fingers would be called "dendrites".

I thought they were pretty cool - such intricate and elegant beauty produced, quite literally, out of the air.

Graduate student life ... summed up in a comic strip

2009-07-30T15:07:00.002Z

http://www.phdcomics.com/comics/archive.php?comicid=1204

It's true that Tajel is a social sciences student, but it's just the same in physical science.

Currently reading

2009-07-28T08:23:00.002Z

I've decided to scrap the currently reading pane on the RHS of this blog because it's fiddly and difficult to update - rather a challenge if you get through a fair few books and need to edit it frequently. Instead, I think I'll do a (semi)-regular posting.

So, as of 28.vii.2009, I'm currently reading

Dumas - The Count of Monte Cristo
Sayers - Busman's Honeymoon
Ball - The Self-Made Tapestry
Rosen - Symmetry Discovered

I'm also progressing well with my year-long project to read all of Allingham's "Campion" novels - I've just finished The Fashion in Shrouds

Hard books

2008-11-23T09:36:00.003Z

[sorry about the lack of postings ... I've been busy getting married, setting up home et c.]

I don't usually make any reference to my work on this blog, but I will make an exception here and recount the gist of a brief talk I made to the LVI last week on the subject "Why read?".

I suggested what I think are three important reasons.

It's fun. In many ways the quality and quantity of entertainment that can be dervied from reading exceeds that of other entertainment media (films, tv &c.) and the book is a very versatile and portable piece of technology. I added the advice that you should never buy a coat if its pockets are too small to hold a paperback book.
It extends study, giving greater depth to the courses that you take in an academic context. This has many benefits, but includes consolidation of ideas learnt and preparation for things to come.
It educates. Having a set of examination certificates does not, I argue, make you educated (although they may of course testify to being educated). What makes you educated is having encountered "the best of what has been thought and known" (Arnold: Culture and Anarchy). Books are the primary means to access the rich wealth of human thought and understanding.

In discussing (2) and (3) I suggested that students should be prepared to attempt books they considered hard for in so doing they will glean at least some insight and prepare themselves for further attempts at the topic in question.

Personally, I have long been a fan of "hard books", but I am now reading what I feel is likely to be the biggest challenge ever, namely Roger Penrose's The Road to Reality.

As of this morning, I am stuck at the end of chapter 7 (p134 of 1049).

Chapter 7 is about complex analysis, i.e. differential and integral calculus of functions of complex variables. My school and university knowledge of complex numbers only ever really extended to the idea of the complex plane and a struggle through the demonstration of Euler's formula (coupled with a lecture on how to pronounce [or more accurately how not to pronounce] 'Euler').

So now I have a choice - I can either

a) forge on to chapter 8 and get even more confused; or
b) give up this book as just too hard; or
c) find a primer to complex analysis and get to grips with the big ideas before proceeding.

Common sense rules out (a) as a waste of time. So it's between (b) and (c). I think that in many ways Penrose's book is that for which I have long been searching - a genuine intellectual challenge that will stretch me beyond the everyday grind of school teaching - so it must surely be (c), with the caveat that (b) can always come later!

As I seek to embark on this detour I only pause to wonder how many other readers (or dare I say it, reviewers) haven't got this far, have got this far or have got further. As a 'popular' science book it is highly unusual, being very tough going and yet reasonably priced (ca. £17). It has been very heavily marketed and, perhaps, shares something with Hawking's Brief History of Time - widely purchased but almost entirely unread.

I will endeavour to keep blogging with my progress.

First ferns of the season

2008-04-03T12:28:00.004Z

I've returned home today after spending a couple of days away to discover that the first of the fern spores that I sowed on Easter Sunday have already started growing enough to show up as green fuzzy patches. I don't think I've ever managed to get any to develop this quickly before, but my previous attempts have been in a cool north-facing room whereas they are now in a warm south-westerly facing room. Dyce says that they can appear within a week or two (or take months) so whilst this is unprecedented for me, its clearly nothing special. This knowledge does not, of course, make it any less exciting.

Species that have shown up are:

Dicksonia antartica
Dryopteris cambriensis
Dryopteris carthusiana
Dryopteris oreades

none of which I have grown before.

At the moment, the polythene bags preclude any good 'photos, but one there are some real prothalli to show, I'll take some pictures and upload them.

My A. hispidulum seems to be doing well and has really brightened up my desk. The new fronds (there are 3 at various stages of uncurling) are very pale, though, with no real brown colour to them. Altman says this may be a sign of too much water, so I'll hold back on the water for a couple of days - the compost is still just about moist to the touch at the moment.

Robert Harris: The Ghost

2008-04-02T22:03:00.002Z

WOW

read it!

That's all I'm going to say.

New Ferns

2008-03-31T16:21:00.002Z

Easter has also allowed a flurry of pteridological activity. I have sown this year's set of spores (40 pots, currently cluttering my home) and purchased a beautiful new Asplenium hispidulum (Asplenium bronze venus) from RHS Wisley.

More good books

2008-03-31T15:49:00.003Z

With the glorious relaxation of the Easter holidays I have been able to start reading my way through my birthday acquisitions from Foyles, which were somewhat substantial.

Having finally finished re-reading Eco's The Name of the Rose, I have sped through a superb Gervase Fen detective thriller by Edmund Crispin - Holy disorders which is a complex superposition of cathedral life, Nazi fifth columnists and devilry. In addition, I've been reading a rather beautiful volume by Hazel Rossotti (sometime member of the Inorganic Chemistry Laboratory, Oxford) entitled Fire - Servant, Scourge and Enigma. Originally an OUP edition (1993), it is now available as a Dover paperback (2002) that is an unabridged reproduction, though without colour prints. Rossotti divides the book in to five themes

fire, the phenomenon
fire for comfort
fire for use
fire as hazard
fire for contemplation

and takes with reader through a gentle whirlwind of everything fire-related. Rossotti has achieved the rare distinction of being readable and yet full of content and would engage the reader, whether scientist or layman.

Next in my sights are Robert Harris's The Ghost and a monograph on the historical development of the use of chloroform, mainly focussed upon applications in anaethesia. After those, there's an Eric Ambler thriller and a biography of Lavoisier so I should be busy for the rest of the week!

Traitor's Purse

2008-01-18T06:43:00.000Z

I have commented before on the wonderful service that Vintage are performing by keeping some of the country's most brilliant crime fiction in print. I have just finished Traitor's Purse by Margery Allingham, a novel that I had never spotted in the Penguin Classics series but has been released relatively recently by Vintage.

It is an amazingly compulsive read. The central idea is that AC wakes up in hospital to find that he has complete amnesia and that he quickly discovers that he is supposed to be saving Britain from complete disaster in the middle of the second world war. The reader shares all of Campion's bewilderment, frustration, confusion and fear as he races to re-discover his mission and prevent the destruction of Britain - for we see (or rather don't see!) everything from Campion's perspective. See this link for more comprehensive information, but beware the spoilers!

I cannot recommend this book highly enough. It is completely different from The Tiger in the Smoke and indeed from all her other novels. Absolutely thrilling.

==

I've also bought my first new book of the year - Pompeii (Robert Harris). I really want to read Ghost, but I'm waiting for the paperback!

LED electroscope

2007-11-25T09:52:00.000Z

In preparation for teaching electrostatics next week, I was searching the web for some demonstrations that were a little more exciting than combs attracting bits of paper. The LED electroscope is one of the ones I found, and I think it's really cool.

Its beauty comes from its sheer simplicity of construction. First, you take a normal 9V PP7 battery connector, slice off the top moulding and remove the wires (if you're careful, you can keep the plastic that you slice off and re-insert it later for a neater finish). You then solder an LED and a a FET (field effect transisitor) in series across the two terminals (making sure you have the correct polarity). The gate pin of the transisitor remains unconnected and acts as the antenna.

When you connect the battery, the LED glows with around 80% brightness (there's plenty of resistance across the transistor, that's also why you don't need a protective resistor for the LED). If you charge a plastic ruler and bring it within around 15-20 cm of the transistor, the LED goes out.

I built one with a highly directional green LED, but I'm going to try a super-bright, wide-angle blue LED to see if I can get a more striking demonstration, possibly pannel mounted, if I get time.

Reading policy U-turn

2007-10-30T06:21:00.000Z

I've cracked.

I just CAN'T stick to one book at a time - there are just SO many things I want to read.

Currently reading:

Oakeshott The Voice of Liberal Learning
Rousseau Emile
Sire Habits of the Mind
Arnold Culture and Anarchy
Woodhouse Very Good, Jeeves!

As you can see, there's a flurry of philosophy of education reading just at the moment, which I'm finding really interesting, although quite challenging to get to grips with. They are really forcing me to try and decide what I think about education.

There's also a new Allingham back in print from Vintage (what a marvellous service they are doing for society) which I want to buy and read, but I think I'll leave for my Christmas list since I really don't have time to read it at present! [I saw it in Borders, Oxford Street]

Last week I applied for my Waterstones Advantage Card. When ticking the boxes for "How many books do you buy each year?" M expressed surprise that I ticked the "20+" box. But then I don't drink or smoke - there are worse ways of spending your money!

PS viva was 3 1/4 hours! Passed with minor corrections.

Reading policy

2007-08-16T08:20:00.000Z

For many years (perhaps a little over 10) I have maintained a reading policy that has been described as "weird", "stupid" or sometimes more charitably as "strange".

It has been this: at any one time I have been reading number of books, usually along the following lines:

a work of fiction (alternating between serious literature and lighter fare, such as a crime novel)
a chemistry text or monograph
a science book (not chemistry)
a non-science non-fiction book (incl. biography)
a Christian book
anything else that I need to read for one reason or another (e.g. for teaching, research &c)

The advantages of this are several-fold:

if you are deeply engrossed in a number of books, it encourages you to spend more time reading
when you sit down to read, you have a choice of material to suit your mood or level of altertness (it's no good trying to read about quantum theory when you are tired - you want a nice Agatha Christie)
you have a choice of volumes to take out with you for journeys &c (a heavy Dickens or biography is not ideal for putting in a bag you've got to carry round all day)
plus it's just more interesting!

However the major disadvantage is that when there's a lot of pressure on your time it can be hard to keep the momentum going. When I was an undergraduate, I used to read for 3-4 hours a day or more. As a post-graduate it used to go in cycles, depending on how the labwork was going. Now that I'm starting teaching full-time, I think that I will very much less spare time to indulge this particular passion and so I think that I'm moving to reading one volume at a time. I hope that this will allow me to concentrate on it a bit more and feel like I'm making more progress. I may weaken on this resolve and keep a fiction and non-fiction going. But I'll try and just read one thing at a time.

If you read this blog regularly (who am I kidding??) then you should see the "Currently reading" panel dwindle away - but I'll leave the one's I've already started on there for now. From the previous post you can see that I've just finished the Hudson Taylor biog. I think that I will concentrate on the sunspots one next.

Hudson Taylor: A Man in Christ

2007-08-16T08:11:00.000Z

I've just finished reading Roger Steer's Hudson Taylor: A Man in Christ (Paternoster /OMF: 2001; 1850784086). It is an amazing story about an amazing man - one who thought of himself as the little servant of a great Master, yet one who started a missionary society that pioneered the evangelisation of inland China and saw the baptism of over 18,000 Chinese Christians in about 50 years.

I was somewhat hesitant about reading another Christian biography, after finding Walker's work on Calvin very hard-going. But this book is engaging from the first page and the short chapters made it ideal for reading on the London Underground (where I seem to be spending a fair bit of time lately).

I cannot do justice to this book here, however hard I try. All I will say is this: READ IT!

End of an era ...

2007-05-29T09:02:00.000Z

I now have in my possession a yellow slip of paper that proves that I handed my thesis in at the Examination Schools at 12:13 on 1st June, 2007. That event draws a line under my graduate research in Oxford and I've now turned over and begun to fill a blank page with a new chapter in my life.

On Saturday I relocated to London and I am spending this week observing lessons in the school that have appointed me to teach chemistry from September. It seems a little bit strange returning to a life governed by 'the bell' - but in many ways it feels like coming home and I'm very much looking forward to starting properly in September. I think that it would be unprofessional to share personal views on my work in an open forum such as this (though please be re-assured that I'm getting delusions of grandeur thinking that anyone actually reads these ramblings). Henceforth, therefore, I hope to cut out the (really rather dull) autobiographical stuff on this blog, and return it to being what it says on the tin ... a blog about Chemistry, Ferns and other musings ...

A publisher's mistake, but still a cracking novel ...

2007-05-29T07:17:00.001Z

I have just finished reading The Mysterious Commission by Michael Innes. The chief characters are a portrait artist (Charles Honeybath, RA) , Inspector Keybird, and a bunch of criminals. However, having read this book from cover to cover, it is most manifestly NOT an "Inspector Appleby Mystery" - as the publisher blazes across the cover.

Apparently, this error by House of Stratus has been noted before (and drawn to their attention) as described by this excellent website, which fills in a little more detail about Michael Innes and his work.

I'm inclined not to be too hard on HoS, though, because they are at least keeping these works in print and available for the public (Penguin seem to have decided that classic crime novels aren't worth producing anymore - those beautiful green and cream covers are fast disappearing from the shops).

Clouds

2007-05-04T06:53:00.001Z

I have just finished reading a rather interesting little book called The Cloud Spotter's Guide, by Gavin Pretor-Pinney (Sceptre, 2007).

I must confess to having been avoiding bookshops for a while, mainly due to the distinct lack of book-buying funds which is part and parcel of being a 4th year graduate student in the UK. I am, therefore, probably one of the last people to hear about this book (the 2006 HB edition was selected as the Sunday Times Bestseller). Whilst I won't go so far as to endorse the Sunday Times review comment, (which was 'Go cloudspotting: it's the new religion') I will go so far as to say that I think it is an excellent book, being by far the best treatment of cloud classification and identification that I have ever come across.

Most meterological books tend to jump from the Janet-and-John-level [This is a cloud. A cloud is made of water. When the water falls from the cloud it is called rain] to the mind-blowingly complex this is a Cirrocumulus lancunosus undulatus cloud in a matter of a couple of paragraphs. In The Cloud Spotter's Guide, however, Mr Pretor-Pinney takes us gently through all the cloud types, explains their Latin names, and just when you think it might be getting a bit heavy diverts you onto a human-interest story.

I really recommend this book to anyone who has ever been interested in clouds, even for a split-second. I also own (and have read) Uman's classic text on lightning (kindly kept in print by the wonderful Dover Publications) but that's a much harder read, though just as worthwhile.

If you are in any doubt ... have a look at the Cloud Appreciation Society website, especially the photograph gallery.

The only question now is what to read next. Perhaps this is the time to bite the bullet and actually read Bryson's A Short History of Nearly Everything.

FINISHED!!

2007-02-08T11:23:00.000Z

Finally - I'm out!

I finished yesterday evening at about 6pm. My fume cupboard is beautifully clean, my bench space cleared and you can once again see that I really did have a desk, rather than just a mass of paper piled up from the floor.

I'm feeling really quite relieved. All I have to do now is write the thesis. Ahem. Writing proper starts tomorrow!

And now, on my first day of not-having-to-get-up-and-go-to-the-lab, there's 4-6" of snow, which would definitely have kept me at home. Hey ho. A nice walk is in order later, I think.

The end is in sight

2007-01-30T16:18:00.000Z

It has felt like a very long month. When I started back (see my last post) I was facing a month of labwork in order to finish. Three and a bit weeks later, I'm getting close (probably another week to go). At times it has felt as if I've been getting close to the end, only to find it waves at me before running off into the distance again, but I really and genuinely hope to be out of the lab by the middle of next week.

And then ... the thesis beckons!

Back in Oxford

2007-01-07T17:41:00.000Z

For the first time in nearly three and a half years, I've managed to spend 3 weeks away from Oxford (well, almost - I came back for a day because we were moved out of our laboratory at very short notice). I spent most of that time at home, but also went twice to Norfolk. It's been a restful time, and I have made some progress on my thesis (I have at least started all the chapters now). But today - amidst a flurry of packing up, driving down, unloading and supermarket shopping - I'm back in Oxford.

I'm sitting in the lab now, filling in some time before going to church and pondering on what the next couple of months have in store.

First and foremost, they must see an end to the lab work. I have a little bit left to do, but as is always the case with research, one can never quite be sure how it is going to work out.
Secondly, I need to get on with writing my thesis - I don't want it dragging on for ever.
Thirdly, I need to get on with the review article I'm meant to be writing.
Fourthly, I need to find some employment in Oxford to carry me through until the summer.
Fifthly, I need to work out what I'm going to do next year (though I have made a little progress on this)

It's going to be busy!

A quick post

2006-12-24T18:38:00.000Z

I've been feeling really guilty (well, OK, perhaps not really guilty - but at least slightly guilty) about how long it's been since I posted to this blog. I was trying to transfer some photos from my phone to talk about our lab move, but the technology seems to be against me, and since it's Christmas Eve, I really can't be bothered to spend all evening fiddling with it ...

I have, however, updated my blogs to the new version of Blogger, and updated the template, including a photo from my new webcam (Christmas present from my housemate, intended to help keep in touch with M), so that's all quite cool (except that my book notes have gone, but I'll restore them soon (or at least soon-ish)).

With a bit of luck, I'll post something at least slightly interesting here before too long ... I got some cakes to go and ice now.

Happy Christmas to one and all!

At last, another post!

2006-10-27T09:20:00.000Z

It's been a long time since I last posted to this blog, and a lot has been going on in my life ... if you don't know what I'm referring to, you can email me and ask. Suffice to say in this public arena, life is going very well and I'm very happy at the moment :o)

Two posts ago, I was musing that autumn had arrived and as I look out on South Parks road now, I can see that well over half the leaves have fallen from the Lymes , and cycling in this morning was certainly colder than it has been for a long while.

I'm poised to head home this evening, to spend most of Saturday helping my parents re-decorate my old room, and trying to salvage the data from their mal-ware infested computer. One thing I'm particularly looking forward to is trying out my new oyster card on the bus home from the station. I am particularly proud of having bought my oyster card online (I'm not a big buying-things-over-the-internet fan) and having had it speedily delivered in time to try it out this weekend (I was particularly aiming for the weekend after). The main advantage is the huge saving on fares (some are reduced by as much as 50%) but there's also the convenience.

One real niggle, though, is that the suburban train companies haven't really got on the oyster band-waggon, so although I can use it on buses in greater London, getting the train to-and-from town is still going to require me to buy a ticket or travelcard at the station, which given the queues is usually a great big faff; the only way round it being to carry around enough heavy coinage that you can use the self-service machines. I think this is just stupid: if the system can work across the whole tube network it shouldn't take several more years to roll it out over the rail network. But at least most of South West Trains' services run vaguely on time (when there aren't derailments at Waterloo!).

Raspberry flavour

2006-09-11T12:52:00.000Z

The supermarket where I buy much of my shopping do an interesting line in budget cakes. Some of them are really poor quality, but others are not so bad and they are ideal for over-running grad students! I quite like the Raspberry Flavour Tarts. These are jam tarts with red jam and they do taste of raspberry BUT the ingredients listing makes it clear that they have never so much as waved to a raspberry from a distance. There is some apple as well as the usual gelling agents and preservatives and that old stalwart glucose-fructose syrup, but the flavour comes from just 'flavouring'. Today I've discovered what this mystery compound probably is.

Meet 'raspberry ketone' aka 'rheosmin' aka 4-(4-hydroxyphenyl)butan-2-one.

Apparently this is what they add to get a raspberry flavour. Being a good synthetic chemist it doesn't bother me in the least that chemicals are added to my food, since I'm well aware that 'natural' ingredients are just cocktails of chemicals anyway. I do, however, still find it fascinating that such a small molecule can give rise to such a distinctive taste. It's a 10-carbon unit and hence probably a biosynthetically produced as a monoterpene with post-condensational aromatisation.

A little gentle googling informs me that it's a white crystalline solid (though if I made it I'd probably end up with a yellow oil!), it is insoluble in water (but soluble in fats and alcohols) and the taste threshold is 40 ppm. It is apparently a major component of real raspberries (Rubus idaeus) and has been shown to be an effective anti-obesity drug - which seems like a good excuse to keep eating cake!

Next time you see 'Raspberry Flavour', think raspberry ketone!

Autumn has arrived!

2006-09-10T07:23:00.000Z

It's been feeling really rather like summer this past week in Oxford, though in the evenings there has been a coolness in the air and birds have started flocking. However I've woken up this morning to find really thick mist shrowding us in Botley - I can't see the far side of the crescent.

I suppose that Keats is responsible for the association between mists and autumn, since as a meterological phenomena, they happen all year round. I'm not a huge Keats fan, but I do like To Autumn (and also La Belle Dame Sans Merci). For those of you that aren't familiar with it, To Autumn starts like this:

Season of mists and mellow fruitfulness!
Close bosom-friend of the maturing sun;
Conspiring with him how to load and bless
With fruit the vines that round the thatch-eaves run;
To bend with apples the moss'd cottage-trees,
And fill all fruit with ripeness to the core;
To swell the gourd, and plump the hazel shells
With a sweet kernell to set budding more,
And still more, later flowers for the bees,
Until they think warm days will never cease,
For summer has o'er brimmed their clammy cells.

Yes, I rather like it.

The oak leaves on the tree opposite my window are starting to turn too: 'Summer's lease hath all too short a date', as Shakespeare has it.

That's probably enough literature for this time on a Sunday morning. Suffice to say that I have decided that it's now officially autumn as far as I'm concerned.

I used to really like autumn above the other seasons, but as I've grown older I've come to appreciate the stark beauty of winter (even in the absence of snow), the freshness of spring, even the heat of the summer - my affection for autumn is now matched with an admiration for the rest of the year, which I consider to be something of a blessing, since each year will inevitablty expose me to all four!

Lake District

2006-08-29T13:07:00.000Z

It's been rather too long since I last posted to this blog. I believe that there are many blogs out there which, rather like this one, are enthusiastically started but then fall to the wayside as the novelty wears off. I hope that the past few weeks will turn out to be a momentary dip.

Anyway ... I had a few days away from Oxford, holidaying with friends in the Lake District. This was my first visit to Cumbria and I was quite overwhelmed by the scenery. My friends with digital cameras took some good photographs, some of which are included below.

We left Oxford at ~6.15 am and reached Grasmere in about five and a half hours, stopping only once on the way. We spent a pleasant afternoon visiting Ambleside, seeing a little of the village at Grasmere and taking a gentle stroll up the fell on the western side of the lake. My friends had asked for the first day to be fern-free, which I found to be relatively easy, despite them all continually trying to start conversations about ferns with me: it seems that a walk without fern commentary isn't that exciting after all!

The next day was mostly spent climbing the Old Man of Coniston. It was quite steep, but well worth it for the views over Coniston and Coniston water.

View over Coniston Water
[Photo by David Lowry]

View towards Lake Windermere
[Photo by Peter Baker]

There were several ferns of note - fine stands of Oreopteris limbosperma and Pteridium aquilinum everywhere. As we got above 300 m clumps of Cryptogramma crispa began to appear. One thing that struck me, though, was the relative absence of lycopods: Huperzia selago being the only one I found. At similar altitudes in Snowdonia there is a much wider variety to be seen.

The penultimate day saw us doing a very steep ascent over Grasmere via Alcock Tarn.

View over Grasmere on starting the ascent
[Photo by Peter Baker]

The ascent left us a little worn out, but again it was worth it for the views over Grasmere, Rydal and then further away to Windermere and Coniston water.

The top ridge that we reached
[Photo: Peter Baker]

View towards Windermere

[Photo by Peter Baker]

We were all beginning to feel a bit tired - though David was keeping his cool as usual - but Richard wasn't having any of this sitting-down stuff, not when there was banoffee pie to get back for.

[Photo by Peter Baker]

On getting back down, the weather was beginning to change for the worse - Peter took this excellent photo of the storm gathering over the lake.

Our final day was somewhat damp but the poor weather was discounted by meeting up with some old friends. We went for an abortive row on Lake Windermere (returning within half an hour due to the heavy rain) and then returned to shelter for the afternoon.

It was a great time with great company: here's the obligatory comedy group photo

[Photo by David Lowry]

I was very sad to be back in Oxford afterwards, but I've got some great memories to keep me going though the next few months. :o)

The Birthday Weekend Break

2006-07-17T10:51:00.000Z

This post has been a little long in the editing (and it's nowhere near beautifully written), but here it is at last ...

Yesterday (16/7) was my mother's 50th birthday. As a surprise, my father had booked us into the Victoria hotel in Sidmouth. I was doing some church PA stuff on Saturday morning, so I took the train afterwards and met them at my Uncle's house in Woking. When we left there my father took the 'wrong' turning - towards the southwest rather than towards London.

3 hours later, we arrived at Sidmouth and swept up the drive of the hotel. My mother was very surprised - my father and sister had executed a perfect conspiracy. The rooms were very well appointed and the hotel was tastefully furnished throughout.Dinner was excellent, as was breakfast.

Having spent the night at the hotel, we set out to make the most of the day, starting with a walk up Salcombe Cliff (on the east side of Sidmouth).

It was very very hot, but there is plenty of shade going up. There were also plenty of ferns. Altogether there were Dryopteris dilatata, D. filix-mas,
D. affinis affinis,
and Asplenium scolopendrium.I looked for D. carthusiana but did not find it. Previous excursions at Branscombe (a little east of Sidmouth) showed mainly with only occassional carthusiana so I wasn't really that hopeful. In addition there was plenty of Pteridium aquilinum
After the walk, we cooled off in the Connaught Gardens and then braved the beach for a few hours, which was quite pleasant. I was even induced to stand with my feet in the water for a little while. At the end of the day we headed back to London and finished the weekend with birthday cake on the patio at home.

We all had a really great weekend - many thanks to Dad for organising it!

Vegetable chemistry

2006-07-04T12:23:00.000Z

I've been looking at Organic and Biomolecular Chemistry, Vol4, issue 12. The cover has a picture of a bunch of carrots, a blender and a reaction, and refers to the article on p2348 which is entitled "Daucus carota L. mediated bioreduction of prochiral ketones". Basically, these guys have taken some carrots, chopped them up and then put them in a reaction to effect the chemo- and stereo-selective reduction of ketones. The general procedure reads:

Carrots were obtained from a local market. The external layer was removed and the rest was cut into small thin pieces (1 cm long slice). Ketones (100 mg) were added to a suspension of freshly cut carrot root (10 g) in 70 mL of water and the reaction mixtures were incubated in an orbital shaker at room temperature. The suspension was then filtered off and the carrot root was washed three times with water. Filtrates were extracted with ethyl acetate, organic layers were dried on sodium sulfate, filtered and evaporated. The crude products were purified by flash chromatography.

The amazing thing is that they get good yields and high ees!

Why didn't I think of this?

A busy few days

2006-07-03T15:59:00.000Z

It's been really busy these past few days. The good news is that my finger is healing up well. When I took the steristrips off on Saturday morning it really didn't look pretty, but it has dried out quite well. I thought the doctor did a pretty good job of closing it up, since the original wound was about twice as wide. I was talking to a friend who is a doctor yesterday night and he thought a stitch or two might have helped it, but that it didn't matter much either way.

Saturday was spent playing around with PA stuff at church. We re-organised the equipment at in the control desk cupboard and fitted new patch cabling. We also identified the cable runs for at least 2 older PA installs and checked which sockets worked around the church as well as some supposedly new cable installations. This was all occassioned by the need to install a brand new mixer desk (a Yamaha MG24/14) which is really cool. A long but fun day.

Yesterday was a typical Sunday but with the added panic of 2 deadlines to be met today (Monday): my quarterly progress report and a book proposal review that I had agreed to do for a publisher. I've been working away at both of them for a week or so, but only finished the review at 1.30pm and the report at 4.30pm.

Phew.

Just everything else to catch up on now ... I hope my finger will be sufficiently better than I can do some labwork on Wednesday. One other exiting (if slightly geeky) thing that I've done is to edit a .wav file for my mobile ring tone. Now it plays Noel Coward singing "I'm old fashioned" (my theme song) whenever I get a call. I like the irony of that!

My kitchen is more dangerous than my lab

2006-06-30T14:10:00.000Z

There's been something off a lull in my posts this week because there's been something of a lull in my general activity. This, in turn, has been caused by a nasty accident on Monday. I was washing up a tall glass at home, pushing a spontex around the inside with my middle 3 fingers. Unfortunately the glass spontaneously broke and the resultant sharp edge sliced a chunk off the side of my right ring finger. Ouch.

It wasn't too big a cut (about 5mm x 15 mm x 1-2mm) but it wouldn't stop bleeding and in the end I had to get my housemate and his financee to take me up to the A&E department. I had it cleaned and dressed and it seems to be healing quite well.

Some photos are below - if you're very squeamish, I suggest you don't look. The second shows it after 2 days, with the bandage removed but the steristrips still in place. I have to take those off tomorrow, which I think will be a bit painful.

It just goes to show that it is much more dangerous at home than in the lab!

Crazy, wasteful packaging

2006-06-22T16:48:00.000Z

I bought a box of 100 new test tubes from our departmental stores yesterday. They came in a cardboard box which, when opened, revealed layers of test tubes separated by cardboard partitions. Nothing new there. Except that each layer of tubes was held in place in a vacuum-moulded plastic tray. What a waste of plastic - a little bit of tissue paper would have been quite adequate.

Well done Fischer Scientific!

In fairness, I must admit that they are quite good test tubes.

Windows Vista - LiveKernelReports

2006-06-17T20:48:00.000Z

My housemate has temporarily installed Windows Vista on a virtual machine in order to see what it's like. On the whole, it's just like XP except things have been moved around a bit and given a glossy make-over with extra frills and animations.

Personally, I think GUI's are for wimps and I ran a command prompt and started nosing around the file system. The directory tree has been tidied up a lot, with only 4 at root level. The Windows directory is as voluminous as ever and several directories contained files with what appear to me to be new file name extensions.

The one really intriguing thing, though, was the directory "C:\Windows\LiveKernelReports". On trying to open this,

C:\Windows> cd LiveKernelReports
Access is denied.
C:\Windows>

Eh? I looked at the security properties under WinExplorer and found I had all the necessary permissions. Double clicking from with Explorer gave me 2 alerts, but clicking [continue] on both allowed me into the folder. It was empty. Having done this, the cmd prompt allowed me into the directory.

Why all this fuss? I really hate being told that this or that directory contains files that are important to my computer and that I really musn't fiddle. Hey - it's my (or in this case my housemate's lab's) computer!

Update - it's been a few days ...

2006-06-16T09:38:00.000Z

A very exciting thing has happened - I've had my mobile 'phone upgraded to the sleek, modern, stylish and ultra-'hip' Motorola PEBL. This means that I'm now able to take pictures of reasonable quality, transfer them to my computer by USB and upload them to my blog.

Just to prove the point, here's a picture of my Osmunda regalis that is doing extremely well in the garden in Botley.

Considering that I had given it up for dead after it withered last summer, I was delighted to see it producing fronds of 18-24" this year!

Here's a close-up of a diamorphic frond with the sporangia. I think these ferns are really cool. They are quite difficult to propagate because the chlorophyll-bearing spores are only viable for a short time.

I once visited an extraordinary stand of Osmunda with the BPS in the New Forest. The plants were growing in a knee-deep bog and were taller than me (I'm 6'2"!). The sporangia were ripe and we were almost choking in the dusty spores that were being released each time we jogged a plant.

My sporlings are doing pretty well from when they were potted on. I've taken the cover off the greenhouse because it was too difficult to water them. I will try and get them out of the greenhouse and onto the patio floor. Here's a picture of most of them.

Last night, whilst routing through my letter rack I found a whole pack of spores that I misplaced last year. I think that I'll be sowing them soon so that I can grow them on through the winter and put them out into the greeenhouse in the spring.

Retrosynthesis II

2006-06-09T09:47:00.000Z

Yesterday evening we held our second informal retrosynthesis session in St. John's bar. It was quite good, though the molecule I chose was a little hard. It provided some good discussion with each of us coming up with different approaches, so I think it was quite a useful exercise. The sum of our deliberations was to disconnect the 8-membered ring first and then open the aminal-type centres to amines and carbonyls, envisaging reductive amination as a synthesis. I wondered whether you could disconnect them all at one and stew it up to get the cyclisations you wanted, though we seemed to agree that this might just be wishful thinking.

For the isolation, see JNP 2005 258.

Picture

2006-06-08T09:38:00.000Z

I've decided there aren't enough pictures on this blog - so here's one that I recently had developed and have scanned in. It was taken in North Wales, somewhere a little SW of Snowdon. I think it's a really beautiful landscape and would work well in watercolours.

Note the Pteridium aquilinum everywhere!

Potting on

2006-06-07T07:04:00.000Z

I had a great evening yesterday potting on the rest of my ferns. The species that I have are:

Asplenium adiantum-nigrum
Asplenium trichomanes subsp trichomanes (?)
Athyrium filix-femina
Cystopteris fragilis
Dryopteris affinis subsp affinis
Dryopteris affinis subsp borreri
Pellaea andromedifolia
Polypodium interjectum
Polypodium australae
Pteris cretica
Woodsia ilvensis
Woodsia obtusa

Plus a couple of randoms that are supposed to be polypodys but look like Dryopteris to me!

I reckon I've got about 180-200 plants in around 180 pots now. I have a 3-tiered metal-framed PVC-covered greenhouse which gets about 40 pots per shelf as well as a similarly constructed cold frame that is now full to bursting - I've put all the affinis affinis in there but there are also some cuttings from my parents' garden that I'm trying to propagate.

They all looked a bit bedraggled last night, but they've perked-up somewhat overnight and I think they'll be OK.

The only problem is that getting a watering can in between the shelves of the greenhouse is really difficult, so I'll have to get the pots out each time they need watering, which given the current weather is going to be often. The plan is to water them all again tonight, and then work on them in rotation - one shelf a day. I don't believe in excessive watering - it just engenders a dependence that can't be practically maintained.

Unfortunately, having started at 7.30 (after getting more pots from Homebase) I wasn't through until 9.45 and so I have to go and make jam sandwiches for today because I haven't any more cheese and didn't make it to the co-op: sometimes you have to suffer for the things you love!

Out of the living room into the greenhouse ...

2006-06-01T08:50:00.000Z

I'm talking about my ferns, of course!

I got home yesterday and saw that they were beginning to get just a little scorched by the evening sun coming through the (north-facing) patio window. This, coupled with their now well-developed sizes (mostly - my polypodys aren't doing so well) made me think it was time to start hardening them off.

Today is a fairly average temperature day, though there's a cold breeze. I have a small metal-framed PVC-covered 3-tier greenhouse in my back garden. I have it against the east side of a wall, which means it's pretty sheltered and out of direct sunlight except in late mid-summer, when it gets a little in the evening. My plan is to leave it open (there's a roll-up front cover) during the day but close it at night for at least the first week (or if frost is likely - which can happen right into mid-June in Oxford).

I will need to pot most of them on soon because at the moment there are 2 or 3 plantlets per 3" pot, whereas they need to be one-per-pot really at this stage. I hope to put some photos on here soon!

Submitted - YESSSS!

2006-05-30T09:36:00.000Z

After a tense hour or so this morning I was summoned to see my supervisor. He was satisfied with the HPLC trace and so, after an agonising few moments, I have finally clicked [send] and it has disappeared into the cyberspace aether, winging its way merrily to Harwood at Reading.
It is such a relief to have submitted it.

This morning I'm actually doing the Ru-catalysed hydroborations ... more on that story later, assuming no pesky undergraduates turn up for their practicals.

Bank Holiday

2006-05-29T20:18:00.000Z

Bank holidays are always a bit strange in the lab. All the people who are sallaried seem to regard it as an unalienable right to take a day off, despite the fact that many of them will regularly work on Saturdays and/or Sundays out of personal choice. Most of the D.Phils were in, except those who have boyfriends/girlfriends who are in paid employment.

I was somewhat frustrated that my supervisor wasn't in, since my paper is sitting in his pigeon hole waiting for him to OK it for submission. At least it is dated 28.v and I hope he'll take the point.

I spent most of the morning thinking about rhodium catalysed hydroboration reactions and the rest of it looking for Rh(I) catalysts which seem to have been scattered around the stock system in a bizzare mixture of systematic, semi-systematic and trivial catalyst nomenclature. D's stock of catalysts are all kept in one dessicator but I'm not sure that works unless all the catalysts are kept there.

The afternoon was divided between trying another titanocene reaction, columning some old stock contaminated starting material, and brushing up my biochemistry in anticipation of teaching it to my sister next weekend.

The weather is playing some serious tricks on us, changing from blue skies to stormclouds in the space of 20 minutes and then back again. This evening has been beautifully clear. The setting sun falls on the oak opposite our house and makes it glow with a warm radiance that transforms it from an ordinary tree to a thing of beauty, and reminds me how much I like living in my house, and how blessed I am to be able to stay here for another year.

HPLC - done!

2006-05-27T22:00:00.000Z

I've finally got a set of HPLC traces that I think are good enough to show to my supervisor. There's clearly only one enantiomer of my enantioenriched product, so we'll go for >99%. I also noted that in preparing a new batch of the alcohol for this analysis that my best yield has improved from 67 to 84%!

The original date for the submission of my paper was to have been 5.iv - so it's taken nearly 2 months to sort this out but it's done now.

I spent most of the day at work. Firstly finishing the last-Friday-of-the-month clear-up that I started yesterday (including polishing my fume hood metalwork with Brasso), secondly writing up the HPLC stuff and the titanocene-mediated epoxide opening that I've worked on so far and thirdly looking at biochemistry topics to help my sister with her A2.

This evening has been spent looking at some more of the Bagley Wood mosses. I have looked at Campylopus introflexus for the first time and it is so beautiful. Bryophytes must be the most under-appreciated part of God's creation.

Highly Problematic Liquid Chromatography

2006-05-26T14:38:00.000Z

is definitely the definition of HPLC.

I got in at 0610 this morning and ran the analysis properly set up and with the right eluent and ... 4 hours later: nothing - or rather something very wrong - peaks but with strange profiles!

Then I ran it again (1120-1520): no peaks at all - my sample had broadened into the baseline.

So I've given up trying for the 0.1 conditions and am running at 0.2 mL min-1.

1530 start, should be over by 1830! It had better be, since I need to be home at 1915 to meet the landlord and sign next year's lease, which is a scary commitment but nowhere near as stressful as HPLC.

I'm so pessimistic about this that I've bought a new bottle of heptane. I've now eluted nearly 2.5 L through the HPLC trying to get the ee from this reaction. That is so depressing.

Arrrrrrgh: HPLC horror

2006-05-25T20:18:00.000Z

I've decided that I really don't like HPLC. I never really considered it to be one of those exciting techniques that makes children say to their mothers at bedtime 'when I grow up, I want to be a chemist', but now it's really in my bad books.

I have spent most of the day running the HPLC of my asymmetric compound. I had 2 sets of conditions separating the racemate, one with a flow of 0.2 mL min-1 and the other with 0.1
The 0.1 is slighlty better but takes a lot longer. What I hadn't realised was how much longer my single enantiomer would take to elute compared to the racemate. I think I have a hand-wavy argument for why this is, but it doesn't include the words 'theoretical plates' so it's probably wrong.

The long and the short of it is that due to 3 mistakes in a row I still don't have the ee of my compound. I'm going to get up super early and try and get in and get it running before 8am. That way I might actually have the answer by lunchtime. From what I've seen today, it's looking good with only one peak in the asymmetric product implying >99% ee.

Tomorrow's the day - it just has to be.

The suspense is unbearable

2006-05-25T09:59:00.000Z

No posts since Tuesday because I've been frantically busy. I've made the enantioenriched ketone and am now running the HPLC analysis.

I haven't been this tense about work for a long time: I've edited the text of my paper all ready to insert the data, print it and give it to my supervisor. There's still another 2h to go, though.

Update to follow later ...

Nothing to demonstrate

2006-05-23T10:39:00.000Z

Junior demonstrating is one of those things that D.Phil. chemists are ambivalent about.

On the one hand, it is a really boring experience where you get to watch a bunch of incompetent and inept undergraduates make a complete hash of really easy experiments, break countless items of glassware and if you're unlucky, injure themselves in the process. Most of the time it is about as exciting as watching paint dry and it usually turns out that your demonstrating slot coincides with the day that you have the most other stuff that really needs to be done now.

On the other hand it pays. In fact it pays rather well: about £70 per day (usually 4-6 hours with 45 minute lunchbreak). Pay is something that no grad student (especially if it looks like he'll over-run) can afford to turn down. It's much better than tutoring since there's no preparation, no non-contact time marking, and you can usually take an entertaining book to read (I've been taking PG Wodehouse this term (see:Wodehouse: the non-Jeeves stories)

Just occasionally, though, there will be a really, really good day where nobody turns up! Since experiments have to be started by 1130 (in order that they have a reasonable chance of finishing them) if no one has turned up by then the demonstrators can leave, but they still get paid (they can be called back to sign someone off if required).

Today has turned out to be one of those glorious days! So it's back to the lab for all the column chromatography anyone could wish for. There had to be a downside, didn't there?

Monday in the lab

2006-05-22T17:17:00.000Z

Quite the most exciting thing today was the HPLC trace (see previous post), but I've also managed to make another target (a bicyclo epoxide) for a test reaction. I've even characterised the epoxide and launched the test reaction to run overnight. Slick or what? It makes a real difference getting in before 0830 - I seem to get so much more done in the mornings.

The HPLC's not looking quite so promising. I'm making the enantioenriched to test in comparison, but I'm still looking for that elusive better separation. Oh well.

We had a group meeting this afternoon during which I struggled to stay awake. Sitting in a warm darkened room straight after lunch, listening to a talk your not particularly interested in is not a recipe for staying awake!

I've felt quite tired all day but that might be due to having woken up at 0510 coupled with the fact that I have increased the distance of my morning run. I'm not sure how far it is exactly, but I think it's now a little over 2 miles (so about 3.5K) up and down a very big hill! For someone who generally avoids physical exertion I think I'm doing OK. It does seem to improve my mood, so perhaps all the people who talk about endorphins and serotonin levels being boosted by exercise are actually right.

HPLC - success!!!!!!!!

2006-05-22T11:02:00.000Z

Finally, I've managed to resolve the enantiomers of my racemate by HPLC.

Quite long retention times (~100 minutes), but you can drive at least a medium sized saloon (if not quite a bus) between the peaks!

Very happy indeed.

Bagley was fun!

2006-05-22T07:58:00.000Z

I got down there at about 6.20pm and had an hour and a half of very exciting, though at times quite damp, fieldwork. It was very tranquil - I met one guy out walking his dog about 30 seconds after entering the woodland and then no one else for the rest of the time.

I walked around the edge of the section I was recording and then made my way across it a couple of times. The map that has been made available to me is somewhat out of date, and some of the paths that are marked as minor have become major thoroughfares for (I guess) landrovers whilst other apparently once major tracks have been abandoned and become overgrown.

The area I was looking at was a mixture of birch, norway spruce (with beautiful carpets of old pine needles and moss), mixed oak/beech and also some more open heath-like areas, which promise to become quite overgrown with bracken as the year progresses (at present the new crosiers are just beginning to unfurl).

I made 15 stops for collections, collecting 1 or 2 spp at each site, so I've now got about 20 species to identify! I made a start on Sunday afternoon, looking at just three of them. One was Mnium hornum, which is a very common woodland moss, but it's been a while and I wanted to make sure. Another I managed to ascribe to the genus Bryum but Smith's keys stated explicitly that I couldn't get further than that without having the spore capsules - so that one will need to be re-visited at some point in the future. The third one I looked at (only briefly) was really difficult. The leaves were about 2 mm in length, very narrow and also highly incurved, making microscopic examination quite difficult. I'll have to look at that one again.

I hope to work on these over the next 10 days and then head back to Bagley sometime during the weekend after next. I didn't manage to do any sketching (at one point when it started to rain heavily I considered pausing under a tree and having a go, but the rain eased very quickly and I was back to the mosses). I did take some photos, however, of what I believe to have been Polytrichum commune - there were huge stands of it bearing immature capsules which were very striking. The light wasn't good and I used my camera's automatic metering and flash - but I'm hopeful.

A bonus was meeting some deer. They were in shaddow and too far away to be certain, but I think they were probably fallow deer, rather than muntjak but I'm not sure.

Anticipating some botanising later ...

2006-05-20T13:10:00.000Z

I'm writing this post in odd moments between doing lab stuff - it's Saturday afternoon, so I don't have to be working all the time :o)

I'm meant to be doing a survey of the bryophytes in Bagley Wood (a large area of woodland to the southwest of Oxford owned by St. John's College) . That is to say that I was encouraged to embark on this project, obtained permission, did a bit and then ignored it for a long time. After finishing in the lab today I hope to get down there for the first time in ages. I've noticed that my permit is up for renewal in November and in order to have it renewed I think I'll need to be able to produce some data!

Bagley is quite an interesting place. It's mentioned by Arnold in The Scholar Gypsy:

In autumn, on the skirts of Bagley Wood—
Where most the gypsies by the turf-edged way
Pitch their smoked tents, and every bush you see
With scarlet patches tagged and shreds of grey

(I like Arnold's work, but don't think I understand very much of it!)

For a long time the Oxford Forestry Professorship was associated with St. John's and in consequence the whole wood is a massive collection of forestry experiments. Every 100 yards or so, the trees change completely! An ideal situation for high bryodiversity and therefore a lot of fun for a bryologist. I would be happy to describe myself as an amateur pteridologist, since I can identify a good chunk of the British fern flora, however the title of 'amateur bryologist' can't really be applied to me, since I'm still at a very basic level with my mosses. I am able to execute the survey, though, with the help of some good keys. I use mainly Watson, but also have Smith on hand for a more detailed desciption of species, especially those that are only sparsely described (and in smaller type too) in Watson. I also have ex-Library copies of the 3-volume Atlas of British Bryophytes (my best value book buy ever @ £3 total!).

Doing a full transect-method/ quadrant weilding survey is beyond my expertise and time available, and previous records are constituted by a checklist, so that is what I'm going to aim for. I've divided the wood up into areas and am hoping to produce a checklist of species for each area (and perhaps sub-divide each area to smaller sectors), so as to produce an overall checklist for the whole wood with some element of distribution data. Today I hope to do a first sweep of an area I haven't looked at before. Each area will need several visits because mosses are small enough to be easily missed, plus some species will be more identifiable (e.g. bearing capsules) at different times of the year.

I'm also taking my camera and sketchbook. I haven't done any photography or sketching for ages and I'd like to get back into it at some point. I'd also like to work on my watercolour technique, but I think that will have to wait until after I've written-up my D.Phil.

All in all, I'm quite excited about going today, which is good since my enthusiasm for the whole project has been low for so long. Of course the fieldwork will need to be backed up by a lot of microscope work tomorrow in order to get identifications of all the specimens I collect today. The temptation is always to start as soon as you get them home, but I think an hour of the Calvin biography that I'm reading followed by an early night is much more in order. Perhaps I could fit in an hour first thing tomorrow before church.

Windows vista

2006-05-19T13:18:00.000Z

I've just read that the new Windows release (Vista) that is due for Jan 2007, has minimum hardware specs that include 15GB of HD space!

What on earth are they doing with all that?

Windows has long been known for being untidily written, but that's just plain rediculous when compared to a bootable Linux release like Knoppix, where a whole OS and program suite fits snugly on a 650MB CD.

I dread to think how much space Office will require once it is Vista-ised - 40GB seems not unlikely!

Kinetics of free radical chain reactions

2006-05-19T11:29:00.000Z

I've been thinking a lot about the kinetics of my radical reactions this morning. Even modelling the initation is tricky, since my method uses the slow addition of initiator via syringe pump, which gives rise to a differential equation that I don't know how to solve:

d[In]/dt = k1(t) - kd[In] where k1 is the rate of addition and kd the rate of decomposition.

The thing that has become overwhelmingly apparent is that my abilities in the solution of differential equations (which were never very extensive) have diffused away over the last six years, and trying to skim through the big maths for physical scientists books doesn't seem to be much help.

Given that I also add the chain carrier and the electrophile via syringe pump, I think that this is going to be a nightmare of analysis. It is interesting that the kinetics texts never seem to treat chain reactions in any depth. Maybe it is too hard a problem.

Not going to be beaten yet, though.

Progress?

2006-05-19T01:50:00.000Z

Another day in the lab draws to a close and I'm looking forward to heading home to eat, read and play the piano.

I'm not really sure if I've made any progress today.

The HPLC seems to be playing up and giving me weird step-like plots of random wanderings up and down the scale. I don't think my compound eluted at all, despite having previously shown a retention times of 10-40 minutes. Not sure what I'm doing wrong.

My efforts to crack dicyclopentadiene directly into my reaction yesterday seemed to have worked to some extent - I think 40% of my tosylacetylene underwent Diels-Alder (by NMR) but I think I'll try a bigger scale cracking/distillation of cyclopentadiene tomorrow, to be sure I've got some good stuff.

I found some more of the alkyne in the freezer but it looked really scummy, though recrystallisation from EtOAc/pentane produced a fine crop of fluffy yellow crystals. Waited all day for the NMR to come back because our fast 200 MHz machine is down. Again.

I've tidied my desk - at least I managed that.

I've also been thinking about kinetics of free-radical chain reactions. Last time I thought about this seriously I think I concluded that it was a very hard mathematical problem. My supervisor also thought it was a waste of time. I think, though, some theoretical analyses would look well in my thesis, so I'm adding it to my 'things to do in my copious free time'.

Platensimycin

2006-05-19T00:43:00.000Z

In today's Nature (2006, Vol 441, Issue 18, p 358) there is a report of a novel antibiotic with activity against MRSA and vancomycin-resistant enterococci.

However, as far as I can see, it's a real monster of a structure to synthesise, with two quaternary stereocentres and a polycylic core with no handles for stereocontrol.

Wodehouse: the non-Jeeves stories

2006-05-18T20:46:00.000Z

I've long been a fan of P. G. Wodehouse, but my main exposure has always been the Jeeves and Wooster stories. Recently, though, I've been exploring his other novels and have found them to be brilliantly funny.

What is so admirable in his writing is the effortless way that the scene descriptions unfold with the maximum gentle release of suspense for comic effect, and the little throw-away clauses tacked on to the main sentences that communicate so much.

I'm currently reading the Lord Emsworth short stories, which are just the right length to be read over a lunchtime break.

Definitely worth reading!

First post

2006-05-18T18:35:00.000Z

I've thought about starting a blog for a while, but haven't got round to it through lack of time. I still don't have the time, but hey - sometimes you've just got to get on with things ...

FYI "Ferntastic" is a contraction of "ferns are fantastic".

If you're in any doubt, then see http://www.nhm.ac.uk/hosted_sites/bps/ and be convinced.

Mosses are cool too.

Botany is sadly just a hobby - I'm an organic chemist by training. I expect some of the trials and tribulations of chemistry will become a feature here too.

Better go and check my reaction.