Richard P Grant and his BioLOG (biolog); the wee blog, weblog, or web blog; things not necessarily biology related. The anti-blogger.


5 September 2010

On Web 2.0

(Cross-posted from, 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?


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.

Filed under: Uncategorized — rpg @ 19:11

11 August 2010

Talking of stroking

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:

Featuring your own stuff

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.

Filed under: Uncategorized — rpg @ 10:58

3 June 2010

On coupling

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?

Filed under: Uncategorized — rpg @ 20:05

30 May 2009

Nature Network rolls over and exposes its belly

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

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.

Filed under: Uncategorized — rpg @ 8:42

7 August 2008


Telstra has updated your BPAY View Biller Code. You will receive a letter from Telstra telling you about this change. Once you receive this, to continue receiving your bill electronically via BPAY View you will need to re-register for BPAY View with your new Biller Code.

Details on how to do this can be found at the BPAY web site

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This is an automatically generated email advice. Please do not reply to this email.

This is the Telstra we’ve … just given the heave-ho and finger to, right?


Filed under: fools (!gladly),Uncategorized — rpg @ 7:17

31 July 2008

Sergeant Jonathan Mathews & Private Peter Joe Cowton

Poppies, in a field

It is with deep regret that the Ministry of Defence must confirm the death of Sergeant Jonathan Mathews and Private Peter Joe Cowton in Afghanistan.

Filed under: Poppies,Uncategorized — rpg @ 23:11

19 June 2008

From the “Have we got the right man?” department

Mark Thatcher famously got lost in the Paris-Dakar rally.

And now he’s accused plotting to overthrow a (admittedly very minor) government?

I think they might have the wrong man.

Filed under: Uncategorized — rpg @ 23:32


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