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Another test

All my ’serious’ and ‘not-so-serious’ blogging will henceforth be at Confessions of a (former) Lab Rat, http://occamstypewriter.org/rpg.

Please do the thing with your bookmarks and RSS feeds.

Praise for Occam’s Typewriter

“HOUSTON, WE ARE GO FOR LAUNCH!”

we need to pay you more

I will happily buy you a pint

grumpy old scrotum

hope wikileaks isn’t hacking us

When did Richard ever *not* ask for trouble? Trouble is what he likes. Trouble with a capital T.

Would just like to mention that @rpg7twit is a genius :) #occamt

Edited to add: Nature Network is NOT mentioned here: http://www.nature.com/nature/journal/v468/n7326/full/nj7326-993a.html but the spamming ResearchGATE enterprise is.

Also, I’ve just heard that Nature Network blogs will be getting google analytics for stats. Welcome to the 21st Century, guys.

You see, what I would do is release some information to them: a good mix of real intel (that, despite its appearance, wouldn’t hurt that much), some stuff we know everybody knows already, and some made-up junk.

I mean, let’s face it: you’d be disappointed if, as the ruler of a foreign power, the US wasn’t spying on you. And we already know that politicians are the scum of the earth, and that Silvio Berlusconi doesn’t get enough sleep. People say nasty things about other people all the time; down the pub, in email, and in the embassy. How about some information that, actually, makes us look good—Hey, the Saudis asked us to nuke Iran, and we haven’t. Aren’t we good citizens?

As time goes on, I’d release more info, and successively weight the mix towards the third sort of material. I’d do this through multiple sources. Eventually, Wikileaks is publishing shite, and then you can discredit them publicly, throwing doubt on everything they’ve ever done.

Before that stage, however, I’d get the Secretary of State to stand up in TV and announce that we were taking ‘aggressive steps’—to shut down Wikileaks and increase internal security.

Who could blame us for that?

The trick now is to photograph the Street View car and match it up with the photo it takes of you.

You may remember that last summer I was strolling along Cleveland Street in search of some lunch, when the fabled Google Street car passed me, and looped the block. Indeed, I offered a drink to the first person to spot me.

It looks like I might have to buy myself that drink. Here’s a photo I took:

and here is me, about three seconds after taking it:

Check out Google itself for the full picture. If you look to the right you’ll see that chap in the white shirt has passed the pale concrete slab, and on the left those two pigeons have taken off in the time between my shot, and the Street View.

Hah. Gotcha, Google.

Context. A year ago today.

Thank you for signing Early Day Motion 767. This implies you support continued (if not increased) public funding of scientific research, along with many of your colleagues in the Coalition. Today we learned that your science funding has been ring-fenced for the next four years. While I am happy that science funding has not borne the brunt of the CSR’s bad news, it is disappointing that your administration has not seen fit to invest in an area proven to deliver economic growth.

But that is not why I am writing today. I helped organize the Science is Vital campaign, which saw over two thousand scientists and their supporters demonstrating outside the Treasury on Saturday 9 October. We arranged a lobby of Parliament and filled Committee Room 10 with over 100 constituents and some two dozen MPs. More MPs sent representatives. We delivered a petition of nearly 34,000 signatures to 10 Downing Street two days later. I wrote to you asking if you would care to meet me at the lobby—as did at least one other member of your constituency. We filed a green card to let you know we were there. You did not turn up, nor even have the grace to send a message.

Now, I know that Vince Cable was speaking to the House at that time. We waited until questions had finished, waited until the chamber had emptied. You, I am told by somebody who saw you, met with other members of your party in the committee room next door—yet you did not attempt to meet me.

I also wrote to you last May, about libel reform. You didn’t respond to that letter either. But you did send me a Christmas card. I’m not quite sure what to make of that.

Do your other constituents wait in vain for a response from you on matters important to them? Do they, like me, make the effort to come to Parliament to talk to you (taking time away from their own work or family or leisure), only to be ignored, without being offered even the most basic courtesy? A message that you were unavoidably detained would at least have signalled you were aware of my existence.

There is no room for complacency in democracy. If the people of a constituency feel that their MP no longer represents them, they will replace that MP with somebody else. This is not merely their right, but their duty. And the lesson I have learned from the Science is Vital campaign is that in a democracy, determined groups of quite unlikely citizens have extraordinary power.

Yours sincerely

Richard P. Grant

http://www.cbc.ca/video/#/News/TV_Shows/The_National/1233408557/ID=1618838637

It’s bad enough when an unaffiliated Nature staffer who does not have an active blog on Nature Network (and yet maintains a presence on the private forum) weighs in and completely misses the point. It is far worse when one of the admins says something patently untrue—and then implies that the user shouldn’t be so silly as to ask for pretty basic features.

First, WordPress comes with an ‘Admin login’ straight out of the box. Second, I have used a Moveable Type install where the login link was in plain sight—and connected to an entire University’s user database. They managed to solve the ‘logging in across different sites’ problem that seems to be beyond Nature Publishing Group’s ken. Third, bookmarks are not necessarily “always in a fixed location on the screen” as anybody with more than one bookmark will be able to verify for themselves.

And let’s get to the nitty gritty here. It’s one line of code we’re arguing about.

The comment made on 27 September was, actually, pretty good and said all that needed to be said for the time being (I suspect that was Lou). There was an apology, an understanding of the issue, and what looked like positive moves in the direction of working things out together with us, the users. Compare and contrast with what followed.

But apart from Lou, Nature Network isn’t that good at communicating with its users. Take this new Microsoft group blog for example: I know that a few people have been thinking “Pepsi“—but all we have heard from the Network is that “there’s no commercial connection here”. What does that mean? Does that mean Microsoft aren’t paying NPG for the privilege—and if not, why not?. Will Microsoft products or Microsoft-funded research never be mentioned in “The Fourth Paradigm”? At this stage, you know as much as I do, which is a truly woeful position to be in (and I should know).

Has Nature Network lost its way? Who is steering the ship? And is anybody left rowing?

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’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.

@ 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.