Wahey. I’ve just installed the ‘Notify me of followup comments via e-mail’ plug-in for your delectation and delight. If I’m going to use this place as an alternative to Nature Network for your comments, it can only make life easier, right?

(Cross-posted from http://blogs.nature.com/rpg/2010/09/05/on-web-20, for ease of commenting)

As promised yesterday, I’m going to write down my notes from Saturday’s final panel session of Science Online London 2010. But first, I want to say a couple of things about the Research Information Network report that Rob Procter discussed, If you build it, will they come? How researchers perceive and use web 2.0. (These concerns were raised in the twitter feed at the time, but for reasons I won’t bore you with, we didn’t have time to discuss them at the meeting itself.)

In the last half of 2008 I consulted for the Science Advisory Board (SAB) on a study looking at How Online Media Affects Traditional Publishing Methods. This study was, like the RIN one, a survey of scientists and their use of social media, or ‘Web 2.0′ (by the way, there was a tweet on the #solo10 hashtag mentioning the Britishness of saying “two point nought” rather than “web two point oh”. Was that really me?). This was an international study, rather than the British-centric RIN one, and surveyed 1500 scientists (vs 1300 in the RIN one).

What perturbed me on reading the RIN report was that the SAB study found that it was the younger and more junior scientists who were making more use of Web 2, whereas the RIN report seemed to imply that it was being driven by older scientists. In fact, one of my conclusions was that as the older guys died off we’d see more uptake. (Both studies bemoaned the low overall uptake of Web 2 tools, although the SAB was more upbeat in its assessment).

But as I sat on the Tube on the way home last night, I realized there were a couple of major flaws with the RIN study. The RIN sent its survey to 12,000 scientists in the UK, and got a 10% response rate. That’s a pretty lousy statistic. Here, we’ve selected for people who have both the time and inclination to respond to a random survey. Most of the SAB respondents were selected from the SAB’s membership (currently nearly 50,000) to receive the questionnaire, and were rewarded for their participation (the SAB operates a points system: if you respond to questionnaires and whatnot you can accumulate points which can be exchanged for physical goodies). The response rate was a lot higher (I don’t have the exact numbers to hand) and we might assume that the quality of response was correspondingly higher, too.

A more worrying question, however, is how were those 12,000 people (who received the RIN survey) selected in the first place? Turns out that these are ’scraped’ email addresses, which makes me think there was already some bias towards older, more well-established scientists in the first place. Young researchers not only have had less time for their contact details to be established on an institutional website (and indeed, pre-tenure, have probably moved around a lot, relatively speaking. Google me, for example; the second hit is me but the email address in it was defunct five years ago) but are possibly also more security conscious and less willing to have their email address available for scraping.

I think those two concerns might well go some way to explaining the ’surprising’ results from the RIN study.

So, what did I say at SOLo 10, after all that? Here’s my notes (like Ed Yong, I have to refer to my Moleskine notebook. No copy & paste here, and it’s not a transcript!):

< fx: English accent, ginger hair>

This is a room full of very special people <fx: laughter>. If we didn’t believe in online technology, the value of it and the coolness of it, we wouldn’t be here today.

And over the last couple of days we have seen some very neat stuff. This morning, Aleks talked about the Growing Knowledge project; Peter Murray-Rust showed us a really cool experiment this morning, and we’ve had a whole heap of open- and linked- data stuff–semantic web, if you like. Real nerdgasm stuff.

But, we have to remember, we are special. We are the early adopters, if you like. To borrow a phrase from technology business development, we haven’t yet crossed the chasm to mainstream adoption of these cool toys, as Rob has just pointed out.

The vast majority of jobbing scientists simply haven’t signed up yet, perhaps for the reasons Rob listed. We, here in this room, are a load of technology evangelists, there are a few companies here who share that vision and who have demonstrated some of their toys, but people as a whole?

No.

Of course, they’re into Web 1–email and websites and whatnot, but Web 2, Web 3? Not so much.

We’ve given reasons over the last two days why people should adopt these technologies, but there’s been a lot of stick, and not enough carrot, I feel. What should we do? Encourage–or bully–people into using this stuff, just because it’s there, just because it’s cool?

I don’t think so.

I think, rather, that it comes down to two things, and my thesis is very simple. People, as a whole, will only adopt these new technologies for one of two reasons.

First, these new tools allow you to do something necessary, something you have to do anyway, something that exists outwith cyberspace but that you have to do, but that is made so much easier, so much more efficient with internet tools that people will WANT to do it.

Obvious examples are PubMed–anybody remember Silver Platter?–and online journals themselves. When did you last use a photocopier to copy a journal article?

Say what you like about PDFs, didn’t life get a lot lot easier in the late ’90s and early 2000s?

The second thing that works is something that adds value, and that value can include ‘fun’, but a value that just can’t be gained from anywhere else. A compelling value. For example, Facebook and Twitter are great Web 2 tools that allow people to communicate in new and exciting ways.

It’s slightly less Web 2, Web 1.5 perhaps, but Faculty of 1000 I think is such a tool. We’re addressing the filtering, the information overload problem, adding value to the published research. We don’t care, actually, whether it’s Open Access or where it’s coming from: we’re just providing editorial, if you like, content on top of the literature. And you can’t do that, effectively, without cyberspace. It won’t work.

The challenge, really, is not to have a smart idea. There must be oh, how many people are here? 120 bright ideas in this room alone. But you have to figure out where that value is, that compelling calue that will make the vast majority of scientists want to use this stuff we’ve been talking about.

This includes things like blogging networks, like data visualization, like linked datasets.

and then we were out of time. There was some ad-libbing in there, but that’s the gist. Oh, and I had no slides.

I’ve just got back from a tiring but awesome couple of days at the Science Online London conference (which—conflict of interest declaration—I helped organize). I’ll be writing up my speaker notes for the final panel tomorrow, I hope, but in the meantime I’ve just been challenged by Ruth Seeley on twitter to explain the scientific method:

I’d LOVE it if ONE scientist would take on the challenge of CLEARLY explaining the scientific method. Wikipedia sure doesn’t.

Martin Robbins took up the challenge straight away, but in the interests of clarity (and non-jargon) I’d like to see suggestions that might replace the Wikipedia entry. As far as I’m concerned, these explanations should be lay-readable; understandable to a high school student, say.

Please feel free to have a go, and then, seeing as the Wikipedia article is the first Google hit for ’scientific method’, let’s edit the bloody thing to something more like.

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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