Month: March 2012

The Beilstein Dictionary (German/English) was compiled by the Beilstein Institute’s scientific staff to help users of the Basic Series and Supplementary Series I to IV of the well-known Handbook. It has about 2100 entries and contains pretty much all the German words occurring in the Beilstein Handbook, apparently, as well as common abbreviations, alphabetically listed with their English equivalents. Copyright date is 1990, but it’s now online thanks to Stanford U with permission from Springer.

It’s interesting to note that until fairly recently, undergraduate chemistry courses usually had an obligatory German module because German was in some sense the lingua franca of chemistry and physics. Just look at a few of the research papers from the big names of the 19th and early 20th century: Werner Heisenberg, Erwin Schrödinger, Albert Einstein, Niels Bohr, Friedrich Wöhler and Emil Fischer, commonly published in German. My wife’s chemistry degree certainly had German as an option, but I got side-tracked with physics and advanced mathematics…

Beilstein German-English and English-German Dictionary.

The formation of a wave-like interference pattern when photons, electrons or other particles pass through two narrow slits and impinge on a screen or detector on the other side is the ultimate demonstration of quantum reality: individual particles behaving like waves.

This experiment, Young’s interference experiment, also referred to as Young’s double-slit experiment works with electrons, neutrons, atoms and even molecules. The odd thing is that classical physics cannot explain what happens. How do the individual particles passing through one or other of the slits “know”, what the particles that went before did?

We mentioned the latest example of the Young’s slits experiment on Chemspy earlier this week as Markus Arndt and colleagues have used nanofabrication and nano-imaging to record in real-time a video of the build-up of a quantum interference pattern from fluorescent dye molecules, known as phthalocyanines. One thing lacking from the various news reports was a video, so I asked Arndt to point readers to a suitable resource. Here’s the result: http://youtu.be/vCiOMQIRU7I

Higher resolution version and more information can be found on the team’s site here.

We already had Ph.Diddy…now we have Ph.Diva – Three weeks left to the conference deadline but on the gel is total mystery band…

The Royal Society of Chemistry once again hits on a novel way to capture media and public attention by drawing attention to a flaw with a recent episode of BBC forensic drama Sherlock. In the episode, a periodic table is seen hanging on Sherlock Holmes’ wall, but it’s a dusty ancient version, the RSC suggests. The org proclaims that pioneering chemist Dmitri Mendeleev would be turning in his grave to see the sleuth using such an outmoded version of his arrangement of the elements rather than keeping up with the latest tech.

The RSC is offering to send Sherlock a copy of its Visual Elements Periodic Table. But, Sherlock may already be using the RSC’s periodic table app on his smart phone and keeps the archaic arrangement on his wall merely as a reminder from whence he came.

UPDATE: 2023-02-01 The surgery did a bunch of other tests this year as part of a general healthcheck. My glucose and inflammatory markers were normal. My GGT was about the same as it was when I was in the Fenland Study (102 as it was 11 years ago). 0-54 is considered to be normal and alcoholics in hospital usually have a level in the 700s. I think my normal level is just higher than what is considered normal by clinicians. I know other people with GGT in the 70s with no problems. Anyway, they will want to test again, I’ve halved my omeprazole does in the meantime, as that can raise GGT too.

UPDATE: 2012-03-26 Two weeks off the booze. Follow-up blood test on Thursday. Given that the half-life of GGT (colloquially known as gamma) is 14-21 days or thereabouts, I am assuming that if my serum level of this enzyme has halved by Thursday from the value that was recorded at the Fenland Study, that the spike was essentially down to alcohol consumption the few days before that blood test rather than something like gallstones, liver disease or a muscle injury. Any of those things can raise one’s GGT levels and I don’t think I had any at the time.

Given my slightly worrying feedback from the Fenland Study, my neurotic brain latched on to the headlines today in which male 40-somethings seem to be dropping like flies, jaundiced and with failed livers.

The BBC reports: “Deaths from liver disease in England have reached record levels, rising by 25% in less than a decade, according to new NHS figures. The reports say that heavy drinking, obesity and hepatitis are to blame, with 37% of deaths due to alcohol abuse. Obesity is apparently on the rise, but why are liver problems due to hepatitis on the rise too?

Now, cutting back on fats, sugars, alcohol are probably a good idea for most people who indulge, but is it just a little bit of a coincidence that this report appears ahead of the government announcing a review of alcohol use, laws? Oh and that controversial issue of minimum pricing on booze that could rapidly net the government a few extra pounds to help it address the national debt and ultimately reduce NHS costs? As if politicians would care about our health…

Just for the record, I had a slightly higher than normal serum concentration of the liver enzyme GGT (gamma-glutamyltransferase) in my data back, which was flagged for referral from the Fenland team. Other readings were fine and my GP reckons it could easily be a blip and suggested cutting down on the sherberts and shandies a smidgeon.

BBC News – Liver disease deaths reach record levels in England.

I posted a photo of a rather melancholic sunset on Facebook and Google+ earlier this week and captioned it:  “just photons being scattered by atmospheric water vapour and dust…but still…” I think most viewers did with Trish Parnell suggesting that, ‘The whole is greater than the sum of its parts” and Harvey Leifert describing me as “an incurable romantic” and claiming he “wept while reading about scattered photons”

On Google+, Joe Repka suggested that “what some people miss is the depth that mystery somehow adds to a phenomenon. Mystery is like a promise for more, a door ajar, a beckoning. Fortunately for our epistemological hunger, any understanding is sure to bring even more questions to entice us with further mystery. How far down does the mystery go? I would guess, ‘Far enough’,” he said.’

I agree entirely, mystery is an enticement, curiosity, the exploratory instinct, all wonderful. The joy when one recognises an iteration, a small step taken towards a clearer understanding of some phenomenon cannot be beat, viz the “unweaving the rainbow”. The mysteries that process ultimately revealed are myriad from the spectroscopy of matter to the Big Bang theory! We’d know nothing of those vast mysteries without Newton having first “split” light…and the complementary, rival work of Newton and Hooke on gravity and other phenomena so eloquently and dramatically described by Stuart Clark in his latest novel The Sensorium of God, part 2 of the The Sky’s Dark Labyrinth trilogy. Incidentally, the tales of comet discoverer Edmond Halley, architect Christopher Wren, first Astronomer Royal John Flamsteed and others are all woven into the fabric of this pioneering period of scientific discovery and their lives and loves brought to life brilliantly by Clark.

In sharing my sunset photo I could, of course, have mentioned the biochemical wonders of lignin and cellulose in the foreground trees, the osmotic pressure, the transpiration and the photosynthesis all taking place as well as the vernalisation of the narcissi at the foot of the tree…

Jacob Cox described the notion (or the photo) as “Quite beautiful. Scattered photons a very beautiful thing” and Wendy Bailey posited: “Fabulous photons”.

James Brooks commented on G+ that he “will never understand how people can think that understanding a thing takes any of the beauty away from it,” while Erik Swiger emphasised the point saying that, “I think greater understanding brings more appreciation for the beauty of a thing.” Of course, they accused Newton of unweaving the rainbow, but it doesn’t stop the rainbow being as beautiful just because you know understand the optical principles manifest in the colourful arc. On the contrary, it adds an extra dimension to one’s appreciation of reality. It’s a truly Zen notion.

I hope things have changed a little since the bad old days when professors suggested that members of their research team ought to work all day, every day, including evenings and weekends, public holidays and could only have time off for a vacation if it had been well earned. It’s possible that an original letter reproduced a while  back was actually meant tongue-in-cheek, it’s hard to say but the letter sent to “Guido” lit a fire under the science work ethic debate.

Leaders in their field perhaps have every right to insist that their charges work as hard as they do. Was the letter, which told Guido: “In addition to the usual work-day schedule, I expect all of the members of the group to work evenings and weekends,” entirely serious? We may never know.

Interesting, that the notorious letter should come up again this week, given that once again the risks of working more than 40 hours a week has yet again surfaced in the media. It’s nonsense, of course, the notion of burning the candle at both ends is entirely relative, some people thrive on long hours, working weekends and never take a vacation. Others prefer an easy life, tipping the work-life balance in the opposite direction. But, who achieves the most in terms of life satisfaction?

More to the point, who was Guido? Did he stay in chemistry? Did he do well and does he still avoid working weekends? Well, the recipient of that infamous missive dated 1976 was allegedly none other than Guido Koch, Director in Global Discovery Chemistry Basel at the pharmaceutical giant Novartis. I suspect he worked quite hard to get to that position, whether or not that was down to the allegedly draconian rules on working hours or because he skipped weekends we may never know. Apparently, the letter’s author and Koch are still very much on speaking terms.

TL:DR – In 2012, I took part in a big clinical study on metabolism, weight, body fat, and liver function.

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UPDATE: 2012-05-08 Checked my weight again today, down about 5 kg on the weight they recorded in the Fenland Study.

UPDATE: 2012-04-18 It will be two months tomorrow since I took part in the  Fenland Study and got back the worrying metrics on liver enzymes, total cholesterol, body fat percentage etc. Since then, I have cut down on certain liquid refreshments, abandoned salted snacks and chip shop chips (with one lapse in Aldeburgh last week, well you have to, don’t you?). Last readings from GP for cholesterol (down from 6.5 to 5.0) and liver enzymes were pretty much fine and I’ve also shed about 4 kilograms, which isn’t bad and I haven’t had a gym-based workout for at least two weeks having opted for long hikes with the dog on our recent trip to The Cotswolds.

To be frank, I’ve decided that you really don’t need to know my detailed waist-to-hip ratio, my weight, body fat percentage or any of the other details I am now poring over thanks to the good people at the MRC Epidemiology Unit. None of them are particularly bad…none of them are particularly good. I think I’m in the middle of the ranges for almost all the metrics they acquired, although the DEXA data shows that I’m proportionally rather more fat by percentage body mass than I’d hoped to be by the time I reached my mid-forties. My total fasting cholesterol is bit higher than it should be but the ratio of “good” to “bad” cholesterol is very good (my GP showed me I’m well into the green zone for cardiovascular risk. Nevertheless, she still advised me to cut out the saturated fats and eat more fruit and veg though (isn’t that part of the GP’s standard script, anyway?). She also advised me not to worry about the spurious liver test result mentioned in part 1 and simply to cut back on the old chianti a tad (but, that’s also part of the script, isn’t it?).

Meanwhile, with the specific data in hand, I turned to various health risk calculators on the web all of which take as input BMI, weight, cholesterol, blood pressure, body fat and other measurements as input. It’s interesting to see that even if I lost 10kg, cut my total cholesterol in half and reduced my waistline by an inch or two my 10-year risk of having a cardiovascular event would fall by very little. These things are all risk factors, they are not terms of predestination.

One CV risk calculator puts it more graphically (pardon the pun) on the basis of blood pressure, total cholesterol and HDL. It says my current risk is about 8.4%. That means that over the next decade I have an 84 in a 1000 chance of developing cardiovascular disease, with its associated risk of heart attack or a stroke. The risk of actually having such an event or dying in that time are different again (lower thankfully). Nevertheless, by getting my cholesterol level down, losing a bit of weight and reducing my systolic blood pressure reading by about 10 mmHg (which should happen with the weight loss), I could reduce my risk, according to the calculator to about 5%. That is actually a change in odds from about 11:1 to approximately 25:1. Is that a good enough reason to revise my diet and exercise regime when the chips are down? I think so…

Of course, it could be that the total cholesterol was up because of a spot of unusually rich living and partying the week before the Fenland tests. That would also explain the fact that without effort my weight had shifted down within a week of the tests by a couple of kg. That’s my excuse and I’m sticking to it. Similiarly with the liver test. Indeed, given that the other values were all fine it makes me wonder whether I am one of the 9% of people who have a permanently raised reading on that test regardless of alcohol consumption or what meds they are on.

Regardless, I’ve got a follow-up cholesterol test booked with my GP for a couple of weeks time, hopefully that cholesterol risk will be down of its own accord before then (I’ve had a week of vegetarianism and a hepatic sabbatical so far and have not touched any crisps for at least a week). Then, I would have to simply focus on shuffling some of those other percentages. I reckon my normal total cholesterol is probably closer to what it was the last time I had it tested, which was fine and gives me a current risk of closer to 6% than 8% (15:1 risk of CV disease). Nudge it down a little and knock off another 2kg and I could reduce that risk to about 5% about 20:1). Of course, one of the worst things to do is to raise stress hormone levels by worrying about all those kgs, mmol/l and mmHg. I’d take a chill pill if I thought it wouldn’t affect the liver tests…

Regular readers will know that I was recruited via my GP to take part in the Fenland Study. The study is taking a sample of the population born between 1950 and 1975, and carrying out a raft of blood tests, body stature measurements, DEXA body fat and bone density and tests for diabetes, cholesterol, liver and kidney function etc.

I had a callback from my GP to discuss the blood results. Two liver enzymes were slightly raised and my total cholesterol is above what she would like to see (although still in the green zone for my personal risk of cardiovascular disease, thankfully). Of course, I’ve spent the last two days worrying that those enzyme spikes were going to tell me I had something seriously hepatically amiss.

My GP reassured me that none of the medication I take could be to blame but rather generous she suggests that a couple of days of birthday celebrations the week before the blood tests could have raised the enzymes in question: GGT (gamma-glutamyl transpeptidase,) and ALT (alanine transaminase). The latter was only marginally raised and she was not concerned with that. The former, is the classic biomarker for alcohol use. I admit there had been some the week before, and in denial mode I suggest that the spike was down to that week’s celebrations and not being a Geordie journalist (two synergistic aspects of my heritage determined to make me keen on the effects of EtOH).

Nevertheless, it’s what they usually refer to as a “wake-up call”. Another good reason to take part in the study if you are given the opportunity – better informed than ignorant when it comes to one’s health.

The spike wasn’t so high as to be a major concern and was certainly not indicative of any liver damage, but it is a spike, nevertheless. My GP reassured me that reducing the weekly intake of said EtOH should be enough to bring the GGT level back into the normal range within a week or two and that there’s no reason I should deny my heritage. The liver, she says, can regenerate itself very well given the opportunity regardless of whether one is a Geordie or a journalist, all that is required is to reduce, or better still, remove the toxins one has a wont to ingest and it can carry out all its marvellous metabolic processes unhindered.

Then there was mention of eating more fruit. Wake-up call or not that’s a suggestion too far for most Geordies and a lot of journalists too…

I should get the other data from the Fenland Study team soon and will outline my metrics in a little detail and the health advice they offer in Part 2.