Chemistry blogs

One for the scientists again, I’m afraid.  I’ve been reading In The Pipeline for a while now, which is a well-written chronicle of the life of a medicinal chemist plus other matters of interest in the pharmaceutical industry.  He’s dealt with polonium posioning, a post on a new twist to RNA interference that makes a nice pair with one on Merck’s acquisition of Sirna, and something that I’ve laughed about before, the crap names of biotech and pharma companies.  Recently the author has been made redundant, which is something I have in common with him; the company I work for went breasts-skyward a few months ago, but I have potential employment with a company that is spinning out from the wreckage.  Of course, in contravention of the naming rules suggested in Lowe’s post, the new company’s name ends in an “X”; hopefully people won’t mind the cliche.

Another chemblog I’ve been keeping an eye on is Totally Medicinal, which is usually posts centred on recent publications in the chemistry literature, plus other synthesis highlights.  It’s definitely a case of a good writing style rescuing what could be quite turgid subject matter; for example, in Feeling Aroused?, TM writes

In BMC (2007, 15, 142-159) Pfizer are riding to the rescue of the sufferers of FSAD – that’s Female Sexual Arousal Disorder. [Stop sniggering at the back there!]. Far be it for me to suggest that this is in fact a bullshit, totally made-up, non-disease. Nothing to do with the fact that loads of people will want to buy these pills and make them loads and loads of money, even if they are only intended and approved for use in a very small subset of patients with a specific aetiology. This is a serious disorder, which demands serious medical attention.

I am looking forward to seeing the spammers latching onto this as soon as a compound makes it to the market.  And it’s rare to see a chemical series described as “a bit gash” in the literature.

Gene genie

Drosophila geneticists have always amused me.  They do lots of serious work developing models of human diseases and teasing apart the complex interactions of genes that happen throughout the lifecycle of the fly, then when the time comes to submit the paper they sit around and see who can come up with the worst pun describing the mutation; there’s a list of some of the best ones here.  There’s one particularly important one for my day-job’s purposes in there: the human homologue of the fly ether-a-go-go gene, hERG, is the new hot anti-target in drug discovery; if your promising new compound blocks hERG it’s not going anywhere near the clinic because this activity is associated with adverse cardiac events.  Human gene names are usually more utilitarian, e.g. BDKRB1 (bradykinin receptor 1), MAPK14 (MAP kinase 14, or more commonly p38 alpha, so named for its molecular weight), KCNA1 (voltage-gated potassium ion channel 1… and even that’s a homologue of the Drosophila shaker gene; guess what the mutant does?).  There are rare outbreaks of humour: the human homologue of the Drosophila gene hedgehog is called sonic hedgehog.  Of course, if any of these genes turns out to be disease-related, this can lead to some interesting patient-doctor discussions, a subject that is currently a hot topic over at HUGO; should potentially offensive gene names be changed?  The obvious answer is yes, for the patients’ sake, but this generates a headache for people researching the area due to the proliferation of synonyms for what is essentially the same thing, albeit in different species.  This is already complicated enough, because usually about three different groups find a gene at about the same time and each will independently name it and proceed to publish papers about it for several years using the name they made.  Eventually one will win out in a betamax vs. VHS stylee (rather than after a knife fight at a conference), but there’s still all those early publications out there.  At a push everything could stay as it is and clinicians can just use the gene symbol when discussing the disease – I doubt everyone with a mutated Ras gene is told that they have a mutation in their Harvey rat sarcoma viral oncogene homolog.  However, I’m sure that having to hide information from patients is not a good thing, and these days the first thing everyone does with a disease is look up more information up the internet, so they’re going to spot any comedy Drosophila homologues anyway.  This would mean that perhaps the fly guys and gals should choose less potentially offensive gene names.  I’m not sure what conclusion to come to here; personally I’d mourn the loss of a little corner of silliness in science, but with all this information now being freely available on the internet it would perhaps pay to be a bit more circumspect.  Though somehow the idea of having a mutation in one’s lunatic fringe does lend a certain levity to disease…

The Tritone Effect

The Tritone Effect is an interesting page demonstrating an audio illusion, which is the audio equivalent of the Necker Cube.  (On a side note, the psychology course I took in the second year of my degree had a brilliant Necker cube practical – the demonstrator handed out glow-in-the-dark wireframe cubes, then turned the lights out.  Holding the cube, we rotated it left and right; all was fine.  Then we were instructed to force our eyes to choose the other interpretation of the wireframe, so the front and rear faces were perceptually reversed.  Now when rotating the cube left, your eyes told you it rotated right, and vice versa.  This made your arm feel wrong.)  The tritone effect is based on Shepard’s Tones (that link is to another page on the same site).  Here’s an explanation:

Although pitch discrimination cues have been carefully removed from Shepard’s Tones, proximity information remains. Two consecutive tones are always separated by a single semitone. So although you can’t really determine which is higher based on the tones alone, your choice is that the second tone is either one semitone higher or eleven semitones lower in pitch than the first. It is natural for the smaller distance to be automatically selected.

In the case of Shepard’s Tones, what would happen if the proximity cue was removed? In other words, what would you hear if the second tone played was either half an octave higher or half an octave lower than the first? (The midpoint of the octave is called the tritone, hence the name of the current illusion.)

What tickled me is that I experience the 110Hz illusion in the opposite way to what most people hear, so I think tone 1 is lower than tone 2.  I also can’t do what Kyla could, which force myself to hear it the other way around.  Besides being further evidence that I’m weird, the illusion is mainly of interest because apparently it is very repeatable in a non-time dependent manner; the way you hear the illusion today is the way you’ll hear it in a year’s time, which would indicate that everyone has perfect pitch.  Perhaps I’ll find some freebie ear-training software and see if improving my pitch recognition turns out to be useful.

Balloonmolecules

Waste money on expensive computational modelling of molecules?  Don’t!  Balloonmolecules will save you time and money (well, maybe just money), and interest a whole new generation of kids in chemistry at the same time.  Check out the model of DNA at the bottom of the gallery page; awesome.

Beer v. prostate cancer

Between this and the old curry fights cancer story, by rights I should be immune to cancer.  Sadly it probably means that I’ll die of liver failure and dyspepsia instead, but you can’t have it both ways.

But don’t rush out to stock the refrigerator. Xanthohumol, is present in such small amounts that a person would have to drink more than 17 beers to consume the same amount found effective in the study

Damnit, there’s always a catch.

Wiki trawling for hairy balls

After a brief discussion over lunch about what’s denser than lead (yes, we are scientists; sometimes we talk about football, but often we slip and end up talking about geeky stuff), I turned to my favourite source of background information, Wikipedia. Yes I know it can often be badly written or just plain wrong, but I have found it a useful source of historical information, e.g. on the break-up of Yugoslavia or the formation of the state of Israel. In addition it’s fun to follow links around with no real idea of where you’re going to end up. So this lunchtime I started with depleted uranium, which I knew was denser than lead, moved on to Tsar Bomba, the most powerful bomb ever tested by man (with an output at detonation 1% that of the sun), which was designed in part by Andrei Sakharov, whose name was familiar to me for some reason, perhaps because he was one of the people who first came up with the idea of a tokamak design of fusion reactor. It was there that I learned that the reason a tokamak is toroidal is because this shape facilitates the creation of an irregularity-free magnetic field, for reasons explained by a mathematical problem referred to as hairy ball theorem. It is this theorem that gives us a wonderful truth: you can’t comb a tennis ball. From depleted uranium to combing hairy balls in one glorious info trawl. Time-wasting has never been so educational.

Science vs. the media

I just read an interesting article over in the Guardian by Ben Goldacre, who writes their Bad Science column, entitled Don’t Dumb Me Down. (I’ve no idea how I’ve managed to miss the Bad Science column until now, as I read the Guardian… maybe it’s only in the weekday editions that I rarely buy, or possibly it’s far enough back in the paper that I’ve lost interest by that point. If you’re interested there’s an archive of his articles over at badscience.net, which also has this wonderful bio:

Ben studied Medicine at Magdalen College Oxford where he also edited Isis, the Oxford University Magazine. He left in 1995 with a First: before going on to clinical medicine at UCL, he was a visiting researcher in cognitive neurosciences at the University of Milan, working on fMRI brain scans of language and executive function, and was also funded by the British Academy to do a Masters degree in Philosophy at King’s. He is, as you can see, a serious fuck-off academic ninja.

Anyway, back to the point.) The article sorts bad science reporting into three categories, wacky, scares and “breakthrough” stories, then makes the point that it is the simplistic way in which science news is reported that is really at fault.

Because papers think you won’t understand the “science bit”, all stories involving science must be dumbed down, leaving pieces without enough content to stimulate the only people who are actually going to read them – that is, the people who know a bit about science. Compare this with the book review section, in any newspaper. The more obscure references to Russian novelists and French philosophers you can bang in, the better writer everyone thinks you are. Nobody dumbs down the finance pages. Imagine the fuss if I tried to stick the word “biophoton” on a science page without explaining what it meant. I can tell you, it would never get past the subs or the section editor. But use it on a complementary medicine page, incorrectly, and it sails through.

I’d say it’s a bit of an unfair comparison; an exciting science breakthrough is actually news and so is expected to be read by a wider audience than a book review, which is usually only looked at by someone who’s interested. The dumbing down of science reporting is obvious and I even caught it in action recently. I can’t remember the exact scare story, but I believe it was some work showing a link between leukaemia and living near powerlines. On Radio 4 it was reported as being based on a very small sample set and the actual risk being very very small indeed, and that these two points were clearly made in the paper. By the time it made it to Radio 1, all these caveats had been lost. The main reason for this kind of thing happening is perhaps a more general problem with the media, in that they’ve realised that to sell papers/advertising time they must entertain or shock their audience. Well reasoned, balanced, arguments, which most science consists of, isn’t exciting. Cf the political media in America; fat obnoxious opinionated people make better entertainment than anyone trying to see both sides of an argument and admit that no answer can be completely correct.

Freezing hot water

I sat in my car this morning, flicked the wipers to clear the dew off the windscreen, then watched ice grow across the screen from the edges in neat little parallel lines. It’s cold out today. This reminded me about the general advice that you shouldn’t clear ice off your windscreen by pouring hot water on it, because 1. if you’ve just boiled the water you’re liable to crack the windscreen due to thermal shock, and 2. hot water freezes faster than cold water. Reason 2 always struck me as mumbo-jumbo, but apparently it is true, and is called the Mpemba effect. The linked article says that the effect isn’t fully understood, though is probably due to a variety of reasons:

• Hot water evaporates quicker, so by the time it freezes there is less ice formed than if the water had started cold
• Hot water already has convection currents in it, which aids the cooling process
• Hot water contains less dissolved gas than cold water (which affects the nucleation of ice crystals, I surmise)

There’s another article on the effect here, though the content isn’t really that different to the first one. What’s most important about freezing boiled water is that the ice formed is free of bubbles (boiling degasses the water), so your G&T looks reet posh, like.
All this serves to remind me that I really must buy some de-icer, scraping windscreens on a freezing morning is dire.

Sex

Birds do it, bees do it, even educated fleas do it… but leave it up to the duck-billed platypus to make it complicated:

In most mammals, including humans, sex is decided by the X and Y chromosomes: two Xs create a female, while XY creates a male. In birds, the system is similar: ZW makes for a female, while ZZ makes for a male. But in platypuses, XXXXXXXXXX creates a female, while XYXYXYXYXY creates a male.

Lucy

Was looking into the 5HT (serotonin) receptor at work, and consequently came across information about LSD, which binds to the serotonin receptor. A particularly interesting site is that of Albert Hofmann, the scientist who first made LSD back in 1938. Initially the compound had been disregarded as it apparently had no interesting pharmacological effects. However, after resynthesising it in 1943, he made the following report:

Last Friday, April 16,1943, I was forced to interrupt my work in the laboratory in the middle of the afternoon and proceed home, being affected by a remarkable restlessness, combined with a slight dizziness. At home I lay down and sank into a not unpleasant intoxicated-like condition, characterized by an extremely stimulated imagination. In a dreamlike state, with eyes closed (I found the daylight to be unpleasantly glaring), I perceived an uninterrupted stream of fantastic pictures, extraordinary shapes with intense, kaleidoscopic play of colors. After some two hours this condition faded away.

He, and others in his department, went on to perform a series of “self-experiments” on LSD and its close chemical relations. Fascinating stuff! He also alludes to the effects LSD has on spiders, which can be seen here (OK, it’s a pdf; if you want jpegs just google for “lsd spiders”). Also on the Hoffman site, he quotes Werner A. Stoll’s paper “Lysergsaure-diathylamid, ein Phantastikum aus der Mutterkorngruppe” [Lysergic acid diethylamide, a phantasticum from the ergot group], describing the visions he experienced under the influence of LSD:

An evening sky of an unimaginable pale blue over the dark roofs of a Spanish city. I had a peculiar feeling of anticipation, was full of joy and decidedly ready for adventure. All at once the stars flared up, amassed, and turned to a dense rain of stars and sparks that streamed toward me. City and sky had disappeared.

Now I can see why the 70s were so tripped out!