Show me the data!

Failure to respond to a simple email – I’m not impressed

July 5th, 2012 | Posted by rmounce in Content Mining - (Comments Off on Failure to respond to a simple email – I’m not impressed)

I sent my local MP (Don Foster, Lib Dem) a simple, fairly short (~265 words), clear & concise formal letter 18 days ago – I blogged the draft of it which is virtually the same here.

It’s been at least 13 working days now by my count and I still haven’t received a proper reply, so I tweeted @DonFosterMP last night:


I soon also got a reply from Don Foster’s press officer, email below:


From: “ROBERTS, Nick”
To: “‘Ross Mounce'”
Subject: RE: Letter from your constituent Ross Mounce
Date: Thu, 5 Jul 2012 10:12:06 +0000

Dear Ross,

I’ve just seen your tweets to Don. Apologies for the mix up. acts as a middleman and forwards your query on to our casework folder as opposed to Don directly. There is nothing wrong with this, it just means that our acknowledgment email goes to them and does not get forwarded to you.

We did receive your email of the 17th and rest assured we will get that response to you asap. However, we get over 500 emails a day so as you’ll appreciate there are backlogs. This is especially true in the summer when there are staff holidays. Our small team then have to prioritise “urgent” cases.

Once again, please accept my apologies for the delay in Don’s reply.



Nick Roberts
Caseworker & Press Officer
Office of the Rt Hon Don Foster MP

31 James Street West, Bath, BA1 2BT
t: 01225 338973
f: 01225 463630

NOTE: Information in this email is confidential and may be privileged. It is intended for the addressee only. If you have received it in error please notify the sender immediately and delete it from your system. You should not otherwise copy it, retransmit it, use or disclose its contents unless permission to do so is explicitly stated. Views expressed in personal emails do not necessarily reflect the position or opinion of the Liberal Democrats.

Personally I don’t care if my MP occasionally receives 500 emails a day – he can still send confirmation of receipt messages automatically surely? It would have been nice to know that my letter had at least been looked at.

I can’t help feeling that I’m being fobbed off here.

But it appears I’m not alone in being ignored. According to 2008 statistics from
Don Foster only replied to 57% of letters sent to him with their service (and in fairness this makes him far from the ‘worst’ MP in terms of response rate for that year; stats here).

With so many young people today completely apathetic towards UK politics, myself included, this hardly sets a great precedent. It was my first attempt to engage, and so far it’s been largely unsatisfactory.

So what to do next? I don’t know frankly. I await a fuller response from Don Foster himself.

I’ll keep this post updated with any further relevant correspondences.


It’s that time again… time to write my monthly Panton Fellowship update.

The trouble is, as I start writing this it’s 6am (London, UK). I arrived back from the Hennig XXXI meeting (University of California Riverside) after a long flight yesterday and am supremely jetlagged. I still can’t decide whether this is awesome (I can get more work done, by waking up earlier), or terrible as I can’t keep my eyes open past 9pm at night!

At this conference I shoe-horned some of my Panton Fellowship project work into the latter half of my talk (slides below), as it fitted in with the theme of the submitted abstract on supertrees.

Supertrees are just one of many many different possible (re)uses of the phylogenetic tree data I am trying to liberate from the literature for this project. I tried to stress this during my talk, as a lot of people at Hennig aren’t too keen on supertrees as a method for inferring large phylogenies. In fact, there was a compelling talk with solid data from Dan Janies given later on in conference, critiquing supertree methods such as SuperFine and SuperTriplets, which were outperformed in most tests in terms of both speed and optimality (tree length) by supermatrix methods using TNT. That’s fine though – there are so many other interesting hypotheses one can investigate with large samples of real phylogenetic estimates (trees).


  • Do model-based phylogenetic analyses perform better than parsimony? [Probably not, judging by the conclusions in this paper]  –  I’d like to see this hypothesis re-tested more rigorously using tree-to-tree distance comparisons between the different method trees. Except we can’t currently do this very easily because there’s a paucity of machine-readable tree data from published papers
  • Meta-analysis of phylogenetic tree balance and factors that influence balance e.g. (this thesis, and this PLoS ONE article).  Are large trees more imbalanced than small trees? Are vertebrate trees more balanced than invertebrate trees?
  • Fossil taxa in phylogenetic trees – are they more often than not found at the base of the tree? Is this ‘real’ or perhaps apparent ‘stem-ward slippage‘ caused by preservational biases?
  • Similarity and dissimilarity between phylogeny and measures of morphological disparity as studied  by my lab mate Martin Hughes

So, I hope you’ll appreciate this data isn’t just needed for producing large supertrees.

I could go on about the conference – it was excellent as ever, but I’ll save that for a dedicated later post.

Other activities this month included:

  • submitting my quarterly Panton report to the Fellowship Board
  • attending the OKFN Bibliohack session at QMUL’s Mile End campus (13th & 14th June) helping out with the creation of the OKFN Open Access Index, and learning how to use & debug a few issues with PubCrawler (a web crawler for scraping academic publication information, not a beer finder app!), with Peter Murray-Rust
  • discussing Open Access, Open Data and full text XML publishing with the Geological Society of London. The GSL have a working group currently investigating if/how they can transition to greater openness. Kudos to them for looking into this. Many a UK academic society may currently be hiding their heads in the sand at moment ignoring that the UK policy-wise is now committed to Open Access as the future of research publishing. It probably won’t be easy for GSL to make this transition as their accounts[PDF] show they are rather reliant on subscription-based journals and books for income. It’s hard to see how Open Access article processing charges could immediately replace the £millions subscription income per year from relatively few books & journals. Careful and perhaps difficult decisions will have to be made at some point to balance the goals of this charitable society, the acceptable level of income and the choice and amount of expenditure on non-publication related activites (e.g. ‘outreach events’).Interestingly, I note The American Geophysical Union (AGU) has recently decided to outsource their publications to an external company. Does anyone know ‘who’ yet? I just hope it’s not Elsevier.

Finally, the audio for the talk on the Open Knowledge Foundation and the Panton Fellowships, I gave in Cambridge recently, has now been uploaded, so I can now present the slides and the actual talk I gave together (below) for the first time! Many thanks for the organisers of the conference for doing all this work to make audio from all the talks available – it’s really cool that a relatively modest, small PhD student conference can produce such an excellent digital archive of what happened – I only wish the ‘bigger’ conferences has the resources & willpower to do this too!

…and if that’s not enough Panton updates for you, you can read Sophie Kershaw’s updates for June too, over on her blog

Taking inspiration from Cameron Neylon, I have written a DRAFT letter to my local MP urging him to support the recommendations in the Hargreaves Review of Intellectual Property.

[UPDATE: Letter now sent :) ]


Dear Don Foster,

As a graduate research student at the University of Bath, currently using textmining techniques to do scientific research in an efficient and comprehensive manner, I urge you to sign this early day motion (no. 151, tabled 11.06.2012).

Aside from my tweets to @DonFosterMP last night I have never before been moved to formally contact you, but this urgently requires your action.

Simple desktop computers can interpret vast amounts of digital information. The capacity, tools and eagerness already exist to enable scientists to do systematic reviews, knowledge syntheses, and innovative analyses on a scale never before imagined. But there is one barrier alone that stifles all this strong potential for good: current UK copyright law.

The exceptions for digital content proposed by Professor Hargreaves in his review would be a boon for research (; Chapter 5). It is galling that 87% of the research contained within UK Pub Med Central cannot be legally mined for information (p47 of the report). Especially exasperating when we are allowed to manually ‘human-read’ nearly all of this content. We just are not allowed to efficiently use machines to read the literature for us.

Current UK copyright law is outdated and is sometimes the *only* factor holding back scientific research. We need to remove this unnecessary artificial barrier to let UK scientists perform world-class research with modern and innovative tools and ideas. Otherwise we will be left in the Dark Ages, instead of the Bright, Shiny Digital Economy of the Future.
Yours sincerely,

Ross Mounce

PhD Candidate & Panton Fellow
Fossils, Phylogeny and Macroevolution Research Group
University of Bath,

Further resources:
* The Hargreaves Report
* PMR’s response to the Hargreaves report
* TechDirt – UK Publishers Pretend To Embrace Copyright Reform… In Order To Kill Copyright Reform
* Glyn Moody’s – Review of the UK Government Response to the Hargreaves Review



[A monthly update on my Panton Fellowship related activities]

Last month I was slightly late with my monthly report, so this month I’m going to get things back on track and write my post now, on this leisurely sunny Sunday afternoon…

It’s been a good month:

First of all, I had the chance to speak about my Fellowship work for the Ede & Ravenscroft Prize final. I made a few choice comments to our Pro-Vice-Chancellor who was present, about the plurality of benefits of Open Access & Open Data, and the difficulties of trying to do content mining research on subscription-access journals. I didn’t win the prize in the end, but getting to the final, and being recognised as one of the top 5 research students at the University of Bath was pretty cool. I then immediately went out and spent part of the £50 runners-up prize on Michael Nielsen‘s excellent Open Science book Reinventing Discovery. I gave it a read, then immediately passed it on to another lab for a friend to read, and it now resides with my supervisor who will also hopefully find time to read it (part of my not so subtle attempt to help spread the knowledge of how digital, networked, openness can hugely benefit research).

I bought some other books too, but this was the important one

Then on the 11th of May, PMR came Bath to give a talk to our Biology & Biochemistry Department. Those who came (including our subject librarian – thanks for coming!) were wowed with the ways in which PMR and colleagues have helped make semantically-enriched Linked Open Data available on chemicals for everyone, not just academic chemists! It’s brilliant to have an expert demonstration of the ways in which projects like CrystalEye have made the data underlying some chemical research publications far more easily searchable, open, and re-usable across many thousands of publications. There’s a strong, easily-justified need for more of this type of post-publication data scraping in biology (and palaeontology I might add!). We share a strong belief that research publications should be made open and explicitly re-usable without restriction.

Sadly, most of the biological literature in my domain is neither open, nor re-usable without permission (more of which in a later post) – which makes my highly integrative data-focused research, that much harder than it otherwise could be. As I’ve said before on the internet – I have all of PLoS on my USB stick, I’ve no doubt I could put all the relevant papers I need & scrape data from them, on just my desktop computer hard drive – yet subscription-access paywalls, and current copyright law prevent me from doing this for much of the literature (PLoS and other Open Access literature aside). I can understand how we arrived at this strange situation (we didn’t used to have such computational power to analyze large volumes of data, nor the Internet with which to freely & easily distribute research) but now we *do*, it seems like utter madness to continue to publish research in ways (e.g. subscription-access, copyright-transferred to the publisher) which make it very hard to analyze or re-use en masse.

The Panton Principles

So I’ve been joining the nascent OKFN working group Skype calls on Content Mining and soon we will hopefully have some interesting things to announce…

PMR also got the chance to meet my PhD supervisor and the rest of the lab which is great since I’m doing this fellowship work concurrently with my PhD work on fossils & phylogeny.

Later on in the month, I suggested the excellent Panton Discussions be made more amenable for podcasting. An OKFN group are now working on producing an audio-only version of all of them, and making them more easily integrable on personal listening devices (mobile phones & MP3 players).

Finally, the past week has been a whirlwind:

On Tuesday (22nd May) I was at the Natural History Musuem, London to talk with Dr Mark Wilkinson about some PhD project-related work – he’s kindly supplied me with some source code (among other things), so I can recompile his programs to run on my linux machines. I told him all about the OKFN & Panton Fellowship and he was very supportive of the goals. Time and time again, I encounter such enlightened, high-up academics and wonder why & how academic publishing is still in it’s current state – it’s not for want of researcher support for Open Access in my experience!

On Wednesday, I was back with PMR in Cambridge hacking PDFs, focusing particularly on BMC literature as this is BOAI-compliant Open Access and we can do what we want with such material. Towards the end of the session we had a think about what metadata would desirable to extract from the text of the papers and figure labels that might add context and information to the phylogenetic analysis performed, and phylogenetic tree presented in each of the papers. By coincidence the Open Tree of Life group have also just republished the MIAPA working group list of desirable metadata for phylogenies. We certainly won’t be able to get all this information, and the information we can extract may not necessarily be interpreted and associated 100% correctly, but it will certainly be hugely valuable as this information would otherwise take 4 years to re-digitise(!) by some estimates.

On Thursday, I went to ProgPal (Progressive Palaeontology), a conference also in Cambridge. There I gave a short ‘announcement’ talk with slides to explain to everyone there a) what the Open Knowledge Foundation are about, and b) why they might be of interest to academic palaeontologists. I touched upon Open Access and Open Data issues in palaeontology and encouraged those with an interest to visit the website, join the Open Science mailing list, listen to or watch the Panton Discussions, and consider applying for a Panton Fellowship next year if they had any innovative ideas for paleo-data. This talk tied-in very well with the other announcement talks for Palaeontology Online (a new free outreach & education initiative) and Palaeocast (a new paleo podcast).

Which reminds me, I should really pop them both an email to explain why they should post their content with a Creative Commons Attribution Licence, so their materials can be re-used, re-posted and remixed as Open Educational Resources

Best of all, on Friday I travelled down to London to my alma mater to attend & furiously tweet the Open Access debate at Imperial College London, in the very same lecture room I sat most of my undergrad lectures! There were rather a many palaeontologists also there, including Tori Herridge and Nick Crumpton and a large volume of tweets under the #OAdebate hashtag were sent (archived here if you’re interested). Graham Taylor of the Publishers Association said some rather provocative things that got me rather hot under the collar including:

…we [publishers] are the stewards of genuine science…

Which I think could all too easily be misinterpreted to overstate the importance of the role that publishers play in organising peer-review, spell-checking, typesetting and other such tasks. I also couldn’t help laughing out loud at Graham’s straight-faced proposal for subscription-access publishers to offer ‘fee-waived walk-in access at public libraries‘ as a way to provide taxpayer access to taxpayer funded research. Stephen Curry (also on the panel) thankfully quickly interrupted to state how ridiculous that was. I’ll leave it to Mike Taylor’s post here to explain just how ludicrous that proposal is in light of 21st century technology. I will however give Graham Taylor credit for further disavowing the Research Works Act, he said of it [and presumably his organisation’s initial support for it]: “the RWA was not such a good idea, don’t ask me to defend that one”, which elicited a pleased response from the audience.

There will be another debate held after the release of the Finch report which I suspect will be rather more exciting. A lot of the issues were aired at this debate, but the brevity of the time slot allowed for the event meant that there was not enough time for in-depth discussion IMO.

That’s just about it for the month. I can’t wait for what the next month will bring!