helen-louise's journal

Woo. I feel clever. I worked out that a certain molecule had to be put together in cells by polyketide synthesis. And the mechanism I sketched the other day appears to be basically correct, except I didn't know about a particular gene carrying out selective reductions.

I am recording this since research involves many episodes of feeling like you are the most stupid person on the planet and no one could possibly be as awful as you, and it's nice to celebrate those occasional moments when you get to feel pleased with yourself :)

In other and mostly unrelated news, I am Annoyed with the Pain Management Clinic at Kingston Hospital for failing to get back to me regarding the results of the MRI I had on 5th August. I have been chasing them up since last Friday. The receptionist suggested that the pain management doctor might call me at the end of his clinic on Monday, but he hasn't and - to be honest - nor did I expect him to. I just want to know what's supposed to be happening next, you know? Do I continue taking more and more gabapentin? Is there something obviously physically wrong that they might be able to treat?

Who wants to buy me this for Christmas/Yule/Newtonmas?

I need some brilliant people to come up with a solution to stop me hurting my back.

It's true that I am a lazy git who's been failing to do her physiotherapist-prescribed exercises for months on end, but the main reason my back is showing off now is because I've been doing things in the lab which are normal for chemists but not sensible for me. Specifically I've been standing up for too long, and bending down awkwardly to look at the meniscus of measuring cylinders.

Standing up for too long can be addressed - leaning on things to try to stay standing is putting too much strain on some parts of my spine. There are plenty of lab stools with back support in the lab. I just need to stop being embarrassed about the fact that I can only really stand up for a few (< 5) minutes at a time without pain.

But figuring out is some way of reading measuring cylinders without bending down is more complicated. I could get a "glamorous assistant" who doesn't have a bad back to read them for me (and have to trust that they're competent and have read it properly). My Disabled Students Allowance provides funding for lab assistance BUT I only need someone to help me for a few minutes at a time. I don't want to waste my funding paying for someone to be with me for 3 or 4 hours a day, when I only need help for about 15 minutes out of that. And not 15 minutes all in one go, either. There are other tasks later when I'll need an assistant with me all the time, and I'd rather save the funding for then.

A shelf, or box, would be a solution except that the meniscus that needs to be read at eye height is in a different place every time, since it's rarely the same quantity of liquid that I need to measure.

Can anyone think of something better than simply using a standard chemistry laboratory clamp stand to raise the height of the measuring cylinder? I don't want to do that because it's hard to clamp things perfectly perpendicularly, leading to parallax errors, and the extra clamping and unclamping is more effort on my hands. I'm sure there exist sturdy stands that can be slowly concertinaed up and down... except they probably cost a small fortune. Anyway, something like that, perhaps.

If you're a certain kind of geek, this is awesome: the new, 2011 definition of the hydrogen bond. Turns out all those school definitions involving a hydrogen covalently bonded to an oxygen, nitrogen or fluorine atom forming a second, weak bond with the lone pair of electrons on another oxygen, nitrogen or fluorine don't go anywhere near far enough...

'Cos three things make a post, right? (This is actually four).

[21:41] My ovary (or whatever) is really flippin' hurting again. I want to know when i'm supposed to be getting it scanned.

[22:53] I used the Hyperbole & a Half Pain Scale to determine if I needed to take my ovary to hospital. I decided it was about a "5", as in "Why is this happening to me??". It's not time to get it prodded in A&E until it's up to a 6 or 7 (I'm pretty sure I have to be crying with pain before it's worth going to the hospital in the middle of the night). I seriously need to chase up that scan though.

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[01:49] I don't mind molecules with a whole load of different names, but it gets positively insulting when there are a whole load of NUMBERING schemes. Geldanamycin is case in point - what IUPAC thinks is carbon 19 is what people using the old/ biochemistry/ natural product name think is carbon 17. Given that the IUPAC name is hideous then referring to it as geldanamycin makes sense - but it gets ever so confusing when you have names of derivatives based on adding and removing groups from carbon 17 - when the "official" name calls that carbon 19!

And I've just found a molecule (Radicicol) that can be numbered from 1-18 consecutively OR from 1-6 (round the benzene ring) and then from 1' to 12' (round the rest of it).

Mind you, if you ever want to have a fit of the vapours, try looking up the official IUPAC name for plain old glucose.

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[04:25] Gods, the weather here has been VILE for HOURS. Driving wind and rain non-stop since about 9pm (it's now nearly 4.30 am)

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[04:39] Did I mention that I'm wearing a pair of Richard's socks? The stupid boy was supposed to get my socks out of the washing machine & pair them & hang them on the line on FRIDAY. Today, I went downstairs with a load of dirty sheets and found them all still in the machine, smelling really revolting since they'd been damp since Friday. So I've had to rewash them, which meant I was completely out of clean socks.

Richard's socks are horrible & scratchy, & make my feet itch.

Of the reaction mechanisms I drew last night:
2 were completely right
1 was almost completely right (SN2 instead of SN1, something which I wouldn't have known because the textbook says that particular reagent, unusually, almost always goes via SN1 despite being primary)
1 would have been right if I'd trusted my instincts
and the last was bollocks only because I'd produced an extra C=C bond from nowhere and got myself confused. Without that, it would have made sense and I'd have been able to finish it.

Apparently I am not actually stupid at organic chemistry. I just need a lot more practice so that I trust myself in unfamiliar cases.

Having given up and gone to bed two and a half hours ago, work is now happening. Well, WHATEVER - I don't care what time the clock says if I have a concentration span and am able to get useful work done. However, I am now reading an article by this man who is obsessed with the word physicochemical, and it's annoying me greatly. I'm not joking about his obsession - on the same page, we have:
"the physicochemical features of protein folding"
"the physicochemical basis of protein folding"
"the same physicochemical features of the polypeptide chains" and
"under the physicochemical conditions found in the living systems".

The reason it's annoying me is that physicochemical is a horrible kludge of a word. Technically, it means "relating to physics and chemistry"; but in practice, the features that are being described are entirely physical - as in "relating to physics". But they don't use the word "physical" in these papers for two reasons:

1) Virtually no one reading the paper would describe themselves as a physicist. You'll get a lot of Physical Chemists, a few Chemical Physicists, and a few Biophysicists - but no unmodified Physicists. (Also, the word "physicist" now looks like it's spelled wrongly through having been typed too many times, hmmm). The author doesn't want to alienate readers by implying that these mysterious but very important properties are all to do with physics - even though they are! (We're talking about very basic properties such as electrostatics, here - opposite charges attracting and same charges repelling. Electrostatics cover at least 90% of the "physicochemical" features being referred to in this context).

2) When people read the word "physical" next to "features", many people will jump to thinking in terms of what the molecules look like. After all, my physical features include brown eyes and long hair. Non-physicists don't immediately associate the word "physical" with physics!

So instead, this horrible made-up word appears to try to stop biologists and biochemists^* freaking out at/being confused by the mention of physics.

Have I mentioned recently how much I hate the division of science into three main and a handful of ancillary subjects? There's a huge amount of physics in chemistry, a huge amount of chemistry in biology, and even quite a bit of physics in biology (though I'm not sure there's too much biology in physics); while materials science crosses over everything. Students tell me "I love biology" / "I hate physics" without being aware of how much of one subject is in the other. Tell me you hate a topic - I'll happily accept "I hate electricity" / "I hate Newtonian mechanics". But don't tell me you hate an entire discipline until you've learned how much nifty cell biology and functioning of the nervous system is due to basic physics.

This rant has been brought to you by the letter P for physicochemical, and the letter C for cold. Which it is. 2.4 deg C outside right now, brrr!

^* Interesting note: I no longer know what I am. I used to be a Physical Chemist. Then I was either an Atmospheric Physicist or an Environmental Chemist. Now I could be a Biochemist or a Molecular Biologist or a Chemical Biologist or a Medicinal Chemist... Woo, interdisciplinary!

Three snippets of recent conversation:

Richard (getting dressed & pulling clean underwear out of a drawer): "I think these pants have had it. Look at the elastic! It's not elastic any more, it's undergoing plastic deformation!".

Me: "Hooke's Law in action!"

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Tim (coming into our room as we were getting up): "Oh, you've got the big bear in bed with you!".

Richard (rolling over sleepily): "This is my bed! I always sleep here!".

Tim: "Perhaps I should have said 'the big bear (white)', to distinguish him from any big bears (brown)".

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Peter (talking about somewhere they'd eaten recently): "It's quite a smart pub. They have games. We drank a bottle of wine and played Scrabble."

Tim: "Only the pieces were muddled up like they came from several different sets."

Peter: "So you could draw a Q and put it on the board, and then draw another Q."

Tim: "There was one tile which was the same size as a normal Scrabble tile, but had letters on both sides. And another one which was 1/4 of the size of a normal Scrabble tile, with the number 4 on it."

Richard: "For all of those words with a 4 in, obviously."

Tim: Maybe it was from a set of Chemistry Scrabble!

Richard: "You could have double and triple atom score, and double and triple bond score..."

Tim: "But would you be allowed free radicals? That's the question."

Me: "I don't think so. Anything can be a radical - CH3 dot would be too cheaty. It would have to be actual molecules and compounds only."

Richard: "You'd be screwed if you drew helium, though."

Me: "I guess it would have to be no Noble Gases."

Richard: "It would be even better if it used organic notation with all those zigzag lines. You'd be able to add a benzene ring to the end of any atom on the board!"

Analgesics (painkillers) that I have personally taken - with bonus educational bits! Big image. ( Read more... )

Richard just brought in a couple of tetrapaks of "So Organic chick peas". Apparently Sainsbury's have decided that tetrapaks are more environmentally-friendly than cans - I'm guessing because the mass of the tetrapak is much less than that of a steel can, so less energy is needed to transport food in tetras. Anyway, on the back they say:

Ingredients: Chick Peas, Water.
Of the ingredients that can be organic, 100% are organic. Water cannot be organic.

Sainsbury's, you are absolutely right - but probably not for the reason you think.