A quick post

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!

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

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!

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

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

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

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

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

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

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

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 ...

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

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

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

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 ...

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!

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

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!

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

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

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

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

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

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!!!!!!!!

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!

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 ...

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

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

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?

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

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

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

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.