It’s no secret that I’m currently somewhat vexed by The Borg, I mean Nature Network. Kristi made an insightful comment on my latest:

@ Cath: We need a good collective noun for blogs. A navelgaze?

I suggest a “stroke” of blogs, which could refer to genius, insight, lightning, ego, or … other things. In some cases I would also recommend the collective noun “bloat”.

In a stunning demonstration of one of the many things wrong with Nature Network, here is a snapshot of the ‘Featured Posts’ this morning:

Never mind the good writers making interesting posts, let’s tell the world how incompetent we are. At least they’ve finally got rid of the months old Local Hubs blog calling for new writers in Boston.

Yes, I’m whingeing. Deal with it.

So, just as an intellectual exercise, if I were to set up a community of like-minded bloggers, how to best go about it?

I envisage something like

http://example.com/ – aggregation page for blogs, recent content from fora
http://example.com/forum
http://example.com/blogger1
http://example.com/blogger2

etc.

OR

http://forum.example.com
http://blogger1.example.com
http://blogger2.example.com

Will the multiple user thing that WordPress do that? Or would I need separate WP installs, or Drupal, or what?

Let’s assume I can get chunky hosting (a reseller account, in fact) for this. All thoughts gratefully received.

Other considerations: each blogger to take responsibility for own blog w.r.t. design and plugins, but some subtle branding to be applied across all to identify it as part of the community.

No, not that sort of coupling.

I was writing up today’s Faculty Dailies, catching up on (yet) another paper about how ribosomes control the rate of transcription.

As has been known for decades, bacterial transcription and translation are tightly coupled. What’s interesting about the recent work is that the presence/processivity of the ribosome appears to feedback on the rate of transcription by stopping the RNA polymerase from going backwards. (I can’t help but think there’s also a link between this phenomenon and the observation that rare codons slow translation, but that’s something else to worry about.)

Now, when I was working on nuclear trafficking I managed to get our lab’s website into the first page of Google hits for that term (about third, I think). That’s irrelevant: what is relevant is that I left the field nearly five years ago, and at that time we all assumed that, just as in bacteria, translation and transcription were tightly coupled in eukaryotes. How can this be, seeing as they’re in separate compartments? Well, we figured that the messenger RNA was being exported through nuclear pores while the arse-end was still being transcribed. All the RNA-binding proteins seemed to interact with enough of each other that we could happily hypothesize a continuum from chromatin through RNA polymerase through the splicing machinery to the nuclear pore.

Besides, we couldn’t figure out what made mRNA go in one direction through the pore (i.e., out)—although we were pretty certain that it was ribosomes clamping down on the mRNA as it poked out of the nuclear pore, stopping it going back in, and equilibrium dynamics doing the rest (in much the same way this paper postulates that preventing back-tracking is how ribosomes control RNA polymerase)—so this made intuitive sense and seemed to answer a lot of awkward questions. The actual mechanics were simply a matter of time, we figured.

So, coming back to this morning, I was a little surprised to find the sentence

In contrast to bacteria, transcription and translation in eukaryotes take place in different cellular compartments and are not coupled

in a Research Highlight in Nature Reviews Genetics.

Um, has the field done a complete volte-face while I was noodling away at zinc fingers and websites? Were we wildly ahead of our time, or just completely wrong? What is the latest thinking on this? Anybody got a Stryer?
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A while ago (it was back in Sydney, so that’s at least a year and a half) I came across an analogy to do with mental health, depression, stress—something like that—and how we cope with stuff. It might even have been something to do with cancer. The writer was saying that she (pretty certain it was a ‘she’) had days where she just couldn’t cope with things, or people, and it was like teaspoons. She’d start the day with a limited number of teaspoons, but different events and people would cause differing numbers of teaspoons to be used up. On a bad day, she’d run out of teaspoons and just couldn’t cope with whatever it was that needed those teaspoons.

I found the analogy to be pertinent, but I didn’t note where I found it. Certain events recently led me to think of it again, and in explaining it I’d love to be able to find the source. A quick google throws up Shakesville, and a very useful but different analogy (essentially, you can empty the ocean if you have enough teaspoons = enough people doing small things will change the world) but that’s not what I had in mind.

Anybody any idea at all what I’m talking about?

Jenny has a new shiny. It’s a device for imaging chemiluminescence–a standard procedure in any lab that works with proteins. The traditional way of doing this is on film, but it seems a lot quicker, safer and environmentally-friendlier to do it with one of the imaging gizmos.

Except…

Except I’m a little bit worried. I was reading a paper just now, trying to figure out how to summarize it for our Faculty Dailies, and came across this figure:

Now I have no idea how this image was obtained (the Methods section mentions neither film nor fancy-schmancy new devices), but either way that is one butt-ugly blot (BUB for short). I am worried that it is obtained with a FSND, because you really have to be a bit of an imbecile to get that level of pixellation when digitizing a blot by scanning a film. I wouldn’t ever want to publish something that looked like that–accusations of over-processing aside, it simply looks wrong.

Are we likely to see more BUBs as FSNDs gain in popularity? Is a whole way of life and aesthetic pleasure at stake here? Say it ain’t so, Jenny.

Say it ain’t so.

It’s just not funny any more.

This tweet:

Dangerous advice. Fever of +105F go to the ER! RT @homeopathyworks: Hot baby, less is better for your Children’s fevers http://om.ly/jgzJ

made me fall off my chair. The argument is that if a child has a fever of 105°F (40.5°C) or more, you should give them … water. The retweeted twitterer (‘twat’?) ‘@homeopathyworks’ says in her profile

Joette Calabrese is a certified homeopath, she has become a trusted voice in achieving robust health that is decidedly educated, experienced and committed.

Tell me, would you trust someone who recommends giving just water to your feverish child?

We should note that homeopaths often take the moral high ground, attacking ‘big pharma’ for selling drugs and making lots of money of the back of illnesses. It’s been pointed out time and time again by people with two brain cells to rub together that the homeopaths are also making money, and indeed their profit margins are probably much greater (because there’s no active ingredient).

But I didn’t realize just how much more money homeopaths are making.

Take this fever ‘remedy’ for example. On the Boots website, you can get a packet of ‘pillules’ for five quid. That should clear your fever within five days according to the dosage instructions (let’s ignore the fact that most, non-life threatening, fevers are self-limiting over that period anyway). And most homeopaths will tell you that you should go along to their ‘surgery’ and get the stuff made up the ‘proper’ way, which means you’re looking at substantially more dosh than that.

Aspirin caplets are 75p. If you take them at the recommended dose a pack will last you two days. Even if you bought three packs (to last five days) that’s still only £2.25; plus you get an active ingredient.

So who are the immoral money-grabbers now: ‘big pharma’ or homeopaths?

But seriously, if you have a temperature of 105 you should be in hospital already. As another twitter friend of mine put it,

They’ve obviously not read the book – stupid people are supposed to remove themselves from the genepool, not innocent children.

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I’ve not ironed more than one shirt, or a couple of hankies, in a single session since I can’t remember when. K would expect me to iron her stuff as well as mine, which would be fine except she’d never do my shirts in return. I got really annoyed about it, and ended up not ironing anything. This wasn’t a problem while I was still an academentic; if ever I needed a smart shirt I’d just do one.

Nowadays I like to look a bit smarter though—I even wore a tie to work a week ago, which really got people wondering—and so my nice or dress shirts are getting a bit crumpled. Jenny is away at a lab retreat tonight, so I’ve put some of my fave tunes on the Bose, poured myself some cider and got down to it.

I’ll… be back in another seven years, maybe.

This is called “I remember“:

A cold, wet night, by candlelight—
Our love as strong as death—
Your soft, warm thighs and soul-dark eyes
Sweet wine upon your breath.

‘This train is destined for Wembley Park’
No more illusion of free will
But destiny’s arrow missed its mark:
We jumped ship at Dollis Hill

The first line is an exact quote from a platform announcer on the Jubilee Line. We were held at Southwark and he wibbled on in a very plummy voice for about five minutes. But that line stuck in my memory. See my twitter feed.