@ 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.

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.

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?

Proshkin, S., Rahmouni, A., Mironov, A., & Nudler, E. (2010). Cooperation Between Translating Ribosomes and RNA Polymerase in Transcription Elongation Science, 328 (5977), 504-508 DOI: 10.1126/science.1184939

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?

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.

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.

PS. While looking for homeopathic non-remedies, I came across this comment on a wacko website:

homeopathic belladonna is safe so dilute that it contains no actual belladonna past 12c dilution.
You cannot poison yourself with it and it is highly useful as both a fever remedy and flue

The wrong, it burns.

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.

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.

But the trick is remembering those perfectly-crafted phrases, while waiting for Windows to log me in. I had time this morning, after entering my password, to go and make coffee, flirt with the MD, walk all the way back to my desk and ask loudly for a new hamster, mine is buggered, before I could start typing.

Thank God for iPhones.

Dedicated to a friend who is perpetually looking for Jamie Oliver spaghetti.

See it on Twitter: I had to remove punctuation to get 140 chars.

I like Nature Network. I’ve got a bunch of mates there, it’s possibly a bit cliquey but in a way that doesn’t exclude new, interesting people, and very few people are nutters, up their own backside or into the whole “let’s pick on creationists because it’s good for traffic” thing. A nice bunch, on the whole. Unlike the wankers at scienceblogs.com who bore me stupid.

So this cove has basically said ‘Thanks! I’m off to Scienceblogs.com!’ after a month or two. And points the NN bunch to his RSS feed.

Shrug. Yeah, whatever.

Dear Simon

You are no doubt aware of the case that the British Chiropractic Association brought against Simon Singh, the popular science author. Singh criticized the BCA for making medical claims [potentially libellious bit redacted] that have no basis in fact. Rather than demonstrating that Singh was wrong, the BCA sued him for libel (see here and here among other places).

This is no way for a supposedly civilized society to behave. Our country has a long history of encouraging ideas, and furthermore of debating those ideas in the public sphere. It is how new ideas are forged and progress is made. We are not some totalitarian regime where those who ask difficult questions are arrested or otherwise silenced: we rejoice in our ability to poke fun at the establishment, to draw offensive cartoons, to get ideas into the open and give them a good seeing to.

Singh was not sued because he was actually libellious, but because of potential defamation. The BCA were, apparently (and I am no lawyer) quite within their rights under UK law to bring this action, which to me says that the law needs to be changed. I am informed that even mentioning someone by name in a blog post could result in legal action, for example).

And Singh is not the only one. I keep a weblog at Nature Network, which is run by Nature Publishing Group: the same company that publishes the world’s leading scientific journal. In the last week another blogger on the Network―a professor at Imperial College and a personal friend―had a blog post removed on legal advice by Nature Publishing Group’s lawyers. We are still a little bit in the dark about this, but it might be because he suggested that certain people―certain well-known and certainly richer peopler―don’t have a firm grasp of what ‘scientific authority’ means. This is potentially defamatory, and could lead to legal action? In what sane and free-thinking world is that the case?

I’ve taken the liberty of attaching a saved copy of the blog post to this email, so you can judge for yourself whether such opinion should be censored―or be the subject of a libel action.

My fellow writers at Nature Network are interested in communicating with other scientists as well as in engaging with the wider community: to share what science is (and is not), how science is done, why it’s important; its limitations as well as its strengths and maybe, just maybe, to help people make informed decisions about how they live their lives. But if every time someone writes something that criticizes an idea or an attitude, they are under threat of legal action, what is to become of this ideal?

Research councils and funding agencies are waking up to the necessity of scientific communication within the community, and are currently looking at ways of funding and encouraging active scientists to partake in this. If part of scientific communication is saying what is and what is not science, and explaining why certain ideas are wrong-headed, or not scientific, or mistaken, or just plain dumb, then how can we do that if we need a lawyer to check everything we write? How can we, as scientists, engage with the lay public if we’re afraid to do so?

(It might be argued that Nature Publishing Group, which, presumably, is concerned with the dissemination of ideas and which, over the last few years, has tried very hard to make scientific papers more accessible, should try a little harder to defend the people writing for it. That’s not really the point though: if their lawyers don’t think they could win this case before the threat of an action has even been made, there is something seriously wrong with the law.)

This is not about free speech. It is not about ‘rights’. It is about the responsibilities that scientists have towards the taxpayer, the people who pay their salaries and fund their research; scientists’ responsibility to engage each other in discussion; their responsibility to give back to the community the fruit of their research. This is about the culture of scientific debate―open, honest, robust debate―that has existed (until now) in this country and the wider scientific community. This culture is now under threat, and will remain so until the law catches up with the 21st Century.

Yours faithfully,

Richard Grant

PS I will be posting the content of this letter on my own weblog. Unless someone threatens to sue me first.

(x-posted)

The following is a post that was removed from Nature Network, on advice of its cowardly lawyers. I dunno, guv, looks pretty much like fair comment to me.

I had been working on this post last week when all this Singh business blew up. But in a way it is allied to the topic that I wanted to write about: the meaning of scientific authority. The British Chiropractic Association, rather than relying on the authority of peer-reviewed scientific evidence, has decided instead to throw the law at the unfortunate science writer.

By scientific standards their recourse to law just doesn’t seem right. In part, the BCA may have taken this action because they don’t fully understand the origin of scientific authority. But perhaps we should be sympathetic because there are plenty of supposedly well-informed people out there who don’t seem to have an entirely firm grasp of it.

Karol Sikora, “one of the UK’s most-quoted cancer experts and arch-critic of NHS cancer care” has just been found out for claiming a professorial affiliation with Imperial College that he does not have. On one level, as an Imperial prof myself, I am gratified that such a claim might be perceived as an effective way to boost your authority on weighty matters of medical science! But only if you are the real deal. And even then, how are people to know you can speak with authority?

There can be little doubt that Professor Susan Greenfield, director of the Royal Institution, is in a position of scientific authority. And she is very good at engaging the public. Judging by the number of hysterical headlines in the UK press of late, fed by her commentary on the possible negative effects of computer use on the developing brains of the young, she is certainly getting her message across. But as Dr Ben Goldacre has pointed out on his excellent Bad Science blog, there doesn’t seem to be too much substance to it.

According to Goldacre, when pressed on the matter she concedes to “a lack of evidence and an excess of panic, that these are merely ideas, speculations, hypotheses”. Though a neuroscientist herself, Professor Greenfield seems to have no program to tackle these potentially important questions. One has to wonder if part of her motivation for keeping such issues before the public is due to her endorsement of a expensive ‘mind-training’ computer game, the benefits of which have not been published in any peer-reviewed journal, as far as I can tell.

I can see two potential problems here. Firstly, whatever her motivation, the product endorsement seems to me to undermine her scientific authority on the question of the impact of computer usage on brain development. And secondly, what is the director or the Royal Institution doing endorsing products that claim a scientific legitimacy but have not passed the gold standard test of peer-review?

George Monbiot is a polemicist, not a scientist. As such, he is perhaps allowed more license to pontificate but I find his output in The Guardian a little wayward and in several instances lacking in authority. A recent outburst, sub-titled “Science research in Britain is now all about turning knowledge into business, rather than the beauty of exploration”, is a case in point.

Like any good polemic there are a few kernels of truth. But unlike sound scientific writing, those truths are so cherry-picked that the piece becomes fairly worthless. He has picked up on the fact that the UK research councils all have former industrialists have as their chairs and connected it to the recent introduction of an ‘impact statement’ on all grant applications that, according to Monbiot, requires researchers to “describe the economic impact of the work they want to conduct”. From this he has spun a tale of woe about the corrosion of universities in the UK and the death of the wonder, insight and beauty that comes from science.

Not quite, Mr Monbiot. True, every government of every hue has made noises about making sure that science funding ultimately benefits the UK economy. There is a real debate to be had about this subject. But even a cursory glance at the web-site of the BBSRC (the research council I am most familiar with), would have brought him to this part of the FAQ on the new-fangled impact statements:

Does this focus on impact and benefits imply a shift away from blue-skies to
applied research?
No, we acknowledge that “blue-skies” research is essential to underpin future
advancements in science and will continue to fund high quality basic research. The
scientific excellence of the research proposal will remain the primary criterion for
funding.

I can confirm that these are not empty sentiments since I recently sat among my scientific peers on a BBSRC funding committee scoring grant applications. It was very hard work, especially given the breadth of the science emanating from all corners of the UK. But I am happy to report that UK science is in rude good health. Not only was there a wealth of superb applications but the first, foremost, primary, and predominant consideration in judging each application was: is this good and exciting science?

And it was fantastic to see the enthusiasm of committee members for the scope and genius of the applications that excited them. For sure there were sometimes tensions in the room, arguments to and fro, forthright debate. But at the end of the process I sensed that most people were happy with most of the applications that ended up at the top of the pile. The process is by no means perfect and this was itself the subject of our deliberations at the close of the meeting: what steps could we take to enhance the judging process? Again the discussion was robust, informed, open.

Simply put, this frankness, this readiness to critique and be critiqued is the not-so-secret foundation of scientific authority that, strangely, remains a mystery to many. I have this on good authority, ladies and gentlemen. But please feel free to disagree.

I soon found more recipes than there are Italians, and then one on the pack of Savoiardi (Ladyfingers); so decided to extract the best from each and essentially make it up as I went along. So, for posterity:

rpg’s tiramisu recipe

Ingredients

• Six eggs, separated
• 200 g sugar
• splodge real vanilla essence
• pack of Savoiardi
• small pot strong espresso
• 1/2 cup brandy
• 500 g mascarpone

Protocol

1. Prepare a pot of espresso (about a cup/4–6 servings) and allow to cool
2. Beat yolks together with the sugar (hand balloon whisk) until pale yellow and smooth and creamy, and most of the sugar is dissolved. Mix in the vanilla essence
3. Fold in 250 g mascarpone and beat for a couple of minutes. Add the rest of the mascarpone and beat again until smooth and all the sugar is dissolved
4. In a clean bowl beat (electric whisk) the egg whites and a generous pinch of sugar until stiff peaks form
5. Gently combine the meringue with the yolk custard, a little at a time, until completely mixed
6. Pour the espresso into a shallow container (e.g. Chinese takeaway box) and stir in the brandy
7. Dip each ladyfinger, sugar-side, into the coffee/brandy for about 2 seconds, and place on the bottom of the serving tray, dry side down, until the base is covered
8. Cover the base with 1/3–1/2 the custard (cream). Sprinkle cocoa over it
9. Repeat for a second layer of savoiardi; followed by the rest of the cream. Sprinkle cocoa (through a tea strainer)
10. Refrigerate overnight

Tiramisu, ready to go

We’ll see how it goes tomorrow.

Isn’t that just neat?

(and one day I’ll figure out how to embed movies in WP…)

It’s a frigging praying mantis. In my frigging garden!

As if the snakes and spiders and UV weren’t enough.