Journals for e-readers

One thing that makes me cross is that despite the terrifying amount of money our library pays to buy back our research in the form of journals, they're still not terribly easy to read. I've got an e-reader now and I'd like to read things on that, just the sort of value-added that the publishers could do. Unfortunately everything is still just a pdf file only to be printed on A4.

There are some utilities for coping with this but it's not really ideal.

I wanted to see how tough it is. So I tried to convert my last paper into something that would look nicer on an e-reader (in my case a kindle). The paper was written for an APS journal using the REVTeX 4.1 package. This makes it very easy to write papers formatted for APS (and possibly some others as well). The answer is that this was the best I could get it using REVTeX.

Ashton2014_ereader.pdf
which originally looked like this:
http://arxiv.org/pdf/1401.2064v1.pdf
or here if you have access

It's actually not too bad! The abstract's gone a little wrong and the font is not strong enough, but it's not a disaster. It proves to me that the guys who make REVTeX could quite easily make a beautiful e-reader mode full of useful options. I made the citations clickable links for example.

To get this working I simply replaced this line

\documentclass[aps, prl, twocolumn,superscriptaddress,amsmath,amssymb,floatfix]{revtex4-1}

with these lines

\documentclass[12pt,a5paper,superscriptaddress,amsmath,amssymb,floatfix]{revtex4-1}

\usepackage[papersize={4.5in,6in},margin=0.5cm]{geometry}

Without the second one it doesn't seem to work very well. If you've got a better (and just as easy method) then leave a comment. I could have made it better by dropping REVTeX and customising every detail. Frankly that was proving a lot of work and that's not what I believe LaTeX should be about.

From now on I'll be uploading an e-reader version as well as an A4 version for my papers.

UPDATE:
Royal Society of Chemistry, with a bit of fiddling looks fantastic on the kindle:
Ashton2013_ereader.pdf
Had to dig about a bit to get this one-column (there's a \twocolumn[ half way down the page in the template that needs removing). Fiddled with the margins and widths a lot. See the .tex file here. Might go back to the APS paper and reduce the paper size even more. This seems to work quite nicely:

\usepackage[papersize={9cm,12cm},margin=0.5cm]{geometry}

UPDATE2:
Got the RSC send-to-kindle button working and this just sends the two-column pdf. I guess the best hope is converting the html version then.

FINAL UPDATE:
I've found the best way I think now. It's to skip pdf altogether and go via html. Using htlatex I compiled the same original latex file into this webpage:
http://people.bath.ac.uk/da246/papers/Ashton2014/
It's a bit broken here and there (you must use revtex4 and not revtex4-1, one day I'll go back through and work out all the settings needed to properly convert a revtex made file. Mostly it works.

Next step was to download the KindleGen utility and use that to convert the html to a .mobi file format. This is what I then put onto my kindle. If you download this and put it onto your kindle
http://people.bath.ac.uk/da246/papers/Ashton2014/Ashton2014.mobi
you'll see that this is basically perfect for what you want from a Kindle version of a paper. For sure some things need fixing, for example the equations are a bit small. I'll work all of that out and make a separate post.

The bottom line for this whole thing is that if I, a mostly lazy man, can get half way decent conversions of my LaTeX files onto an e-reader in an evening, then the journals could easily do this.

Meeting is good

Once again I find myself making some excuse as to why it's been over a month since my last post. My first reason is I'm finishing up my current postdoc. My other reason is I've been doing lots of travelling. This is much more exciting as I've been finding out more about all the cool soft matter / stat-mech work that is going on in the UK. Some of which I will blog about in time. I've also learned that half the people in soft matter in the UK have worked at some point in the Netherlands, which is handy because I'm moving to the Netherlands!

Getting to the point

All this travelling is related to the topic I wanted to get to today - the value of meeting. I was started off thinking about this thanks to Alice Bell's article in the THE on the value of the seminar. Here Alice calls for seminars to be posted online, something I agree with very much, as a way to reach more people (and to improve the standard a bit). From my experience I've had to use hundreds of pounds of grant money touring the country giving the same seminar. While I value that experience - meeting the people in the groups, direct interaction and so on - it's a shame that people at other universities can't see the talk as well.

Of course if people knew it was online they may not turn up, but hopefully not. I might start sticking mine up here.

The more efficient way of way of reaching many like-minded academics is of course the conference. A good conference can do wonders for your creativity and enthusiasm, it can give you an instant snapshot of the state-of-art and you can meet future employers/collaborators.

But they can be a bit stuffy and long. And expensive. So I'd like to fly the flag for a third kind of academic interaction, the informal science "retreat". Not long ago we had our annual Cornish Soft Matter weekend. A small group of physicists and chemists from a couple of universities got together for a more relaxed meeting. Talks were projected onto a sheet, we were sitting on sofas or the floor, and the start of a talk would be delayed due to people making a last minute cup of tea (usually this was me). All this in a really nice setting.

The demographic was largely PhD students and postdocs, and everyone had to give a short talk. If it overran, fine, if people had questions they'd asked them right away. Students were encouraged to ask as many questions as possible and academics resisted the urge to tear anyone to bits with their sharpened critical skills.

Scientifically it's great. I got to hear from the people who make all these synthetic colloids that I always cite. Their concerns weren't always about phase diagrams or dynamic arrest, sometimes it was simply how much stabiliser or chemical X do I need to get the polydispersity down. These are problems I don't usually get to hear about and it's particularly nice to get it from the people at the coal face.

Because the atmosphere is more relaxed you can give a different kind of talk. In a conference you're so worried about being jumped on that you tend to take out all the personality from a talk, all the wild speculation and, well, then fun side of science. Here we could kind of let rip. If we wanted.

Socially it is also a good thing. It's easy to get a little isolated with your own little problem, especially when your doing a PhD, so it's nice to mix a bit. Science, like most jobs, requires a degree of networking. While I hate this word and all that it implies, these informal gatherings are a much better way to get to know people than conferences. People at conferences are always trying to look smart and generally suck up to the established professors. Makes me shiver just thinking about it.

A snappy conclusion

The main thing that made this meeting nice was the atmosphere. I highly recommend anyone to organise something similar if it's possible. Sure, it was no Copenhagen, but the science was good and it helped create that sense of being in a scientific community.

While it's not free it's a lot cheaper than a conference. I guess you don't need to go all the way to Cornwall but it is nice to get out the department for a couple of days - especially when you usually sit at a desk all the time.

Thoughts of a first-time peer reviewer

Most of my time is spent tirelessly chipping away at the scientific rock face, probably bogged down fixing a bug in my code or staring at some noisy looking data. Every now and then it all comes together and I want to tell people about it. So I write up my results as best I can, spend hours tinkering with figures, another few hours getting the fonts right on the axes, and after drafts and re-drafts, eventually I'll send it away to a journal to be published. This is where I become caught up in the process of peer review.

Usually it goes like this: The editor of the journal will check that the paper is basically interesting and then send it out to two reviewers who are chosen for their expertise in your area. These reviewers, or referees, will then read the paper, check it for basic errors and then comment on its originality and its pertinence to the field. This is sent back to the editor who will decide whether or not to publish. Usually the referees make you fix something, sometimes nothing, sometimes you can have a right old ding dong.

The main point is that the process is anonymous and behind closed doors. This is good and bad. Better blogs than this one discuss different options. It's not really my intention to criticise or support peer review, just to share my experiences.

Recently I was sent my first ever article to review. I can't say anything about the details, but it has been strange crossing over to the other side. I've had to ask questions that I have never thought much about before. So I wanted to put it down before I forget what all the fuss is about.

Reviewed

Up to now my only experience has been on the reviewed side of peer review. I've certainly had mixed experiences here. The first paper I had reviewed went through after lots of useful comments by the reviewers. It gave us more work but it made the paper better. Good experience. Another time a reviewer spotted a small error in our equations - also a good experience.

My worst experience involved two bad scenarios. Our first reviewer had not understood the paper, nor taken the time to follow the references that would allow him/her to do so. Instead of passing on to someone more qualified they just said it didn't make sense and was not interesting. The second referee had some interesting points but appeared to block it mainly on the basis that it didn't agree with other (presumably their) results. As you can see, I'm still bitter about this paper! It took 18 months to eventually get it through by which time it was thoroughly buried.

Of course, I'm biased, our paper could have been crap. Either way, the experience was bad enough that I was close to leaving science because of it. Receiving sneering anonymous reviews is a crushing blow to your ego - even if they're right.

Reviewer

So now I've reviewed my first paper. I won't say what I did, most of the questions I found myself asking would apply to any paper.

I'm quite used to reading other people's work, occasionally making a scoffing remark, or more likely not fully understanding it. The prospect of checking a paper for errors and assessing its quality filled me with dread. The only way I could deal with it was telling myself that it doesn't matter if I don't understand absolutely everything. The main thing is to check that they haven't done anything completely stupid.

This part of peer review I think is not too bad. There is an element of trust that someone has collected their data properly, but checking that it's not completely upside down is not too difficult or controversial.

Where it starts to get subtle is questioning the interpretation. Pulling someone up on their conclusion requires quite a bit of guts. Or I suppose an over inflated ego - of which there are many in science. This is related to another question, when should a scientific argument happen before publication and when should it happen afterwards? If the signal to noise ratio is to kept reasonably high then some things will need to be filtered out before hitting public view. I have not worked out an answer to this.

The final problem I had was with the question, "is this work of sufficient quality to be published in journal X?". Again this is really tricky, scientists can be real bitches when deciding what is or isn't interesting. On the other hand some scientists can try and get away with putting out any old crap just to lift their publication count. I found being asked to be the arbiter of quality quite stressful. Most results need to be on the scientific record somewhere, but should something be blocked for being too "incremental"? I suppose this is the journal's decision.

Is it worth it?

Apart from some initial stress I found the whole experience quite enjoyable. It makes you feel part of the scientific collective and it really tunes your critical skills. It will be interesting to see what becomes of peer review in the web 2.0 era, I would quite like to see it open up a little. I worry that unregulated, open anonymous comments, could be unhelpful. People are arseholes when they're anonymous, just ask a peer reviewer.

Brno - best poster spot ever

It's 10pm and I'm writing this during a talk on modelling water. In case you didn't know water is about as far from a simple liquid as you can get. It's very interesting, although from the baffling number of water models you'd think it's been solved by now, but they do keep going. And going...

Anyway, I'll talk more about the science later, in general I had a couple of thoughts today. First, and most certainly without naming names, there is a huge gulf in standard between the good talks and the bad talks. Experience seems to be a factor, the two best talks by a long way were the invited speakers. The best talk introduced a new subject to me, which is on coarse graining, and I felt like I had a good idea how it all worked when he finished. The worst talks I lost attention within a minute.

It surprised me that people can do this for years and still be no good at it, I guess they don't care. But it's so so important that you can tell people what you're doing! Not to be negative though, the good ones were good and they really make it worth being here.

Second thought is that this poster fiasco is heading to the ridiculous. I was lucky enough to get the board at the back of the room, facing a wall two feet away! Not exactly a prime spot as you can see from the photos. At A0 I doubt they'll be able to focus on it from that distance! C'est la vie.

I'll let you know how many punters I get.

Conferences

Seems like it's been a very long time since I've posted anything. This is mostly because things have been a bit of a blur recently preparing a paper, a talk and a poster for some up coming conferences. As soon as conference season is over I'll be back on the regular posts.

The science poster is a bizarre and demoralising ritual. You know that hardly anyone will see it (at one of my conferences there will be something like 500 posters), but you daren't not do it properly just in case. So you spend days putting this thing together, £30 getting it printed, only to have hundreds of people walk straight past it. Who knows, maybe you can catch one or two people who will write down a reference.

Anyway, this is what I'm going to be standing in front of next week, I think it's quite pretty:

It occurred to me that I haven't really blogged about my own work (is it not done?) but I'll start doing so when I return. In the meantime, it's all on the poster!

On the off chance anyone is going to Brno next week then come and find me and say hello.

How should we teach Maths

I came across this new feature in the NYT via Science Blogs by Steven Strogatz. You may remember him from his paper with Duncan Watts on small-worlds that arguably kick started modern network theory. It looks like it's going to be a regular series so I highly recommend adding the feed to your rss reader.

The article that first caught my eye was called Rock Groups. It starts by differentiating between the serious side of arithmetic and the playful side. This is something I've long gone on about but never quite had the nice way of putting it like these guys do. Maths teaching for kids is like torture. I was having a discussion a while ago where I questioned whether we really needed to recite endless times tables aged 10 years old. A suggestion that drew scorn from my opposite number. But really, why?

The book that is heavily quoted in the article, "A Mathematician's Lament" by Paul Lockhart. It starts with a musician having a nightmare that children are not allowed to touch an instrument until they have mastered the theory of music and how to read a score. Only after many painful years are they allowed to lay their hands on an instrument.

This is a powerful analogy. You don't have to learn all the nuts and bolts of mathematics before you can start playing with numbers. Back in the Strogatz article he shows how much you can discover without being able to do any addition at all, just by grouping rocks. I wish I could quickly multiply two large numbers in my head but it wouldn't make me a better mathematician. It's like arguing that the best playwright should be able to spell every word in the dictionary.

The beautiful thing about the rocks is that it shows how much you can learn about number by pushing things around with your hands and being creative. Perhaps all those people who complain to me that "oo I could never do maths me" would have enjoyed it more if it was based on this rather than being expected to master "a complex set of algorithms for manipulating Hindi symbols".

Make sure you keep up with the Strogatz series. I found a pdf of the essay that inspired the Lockhart book. If I ever get through my Christmas backlog I might get around the getting the book.

Quorum decisions in bacteria

Stumbled across a few nice things related to quorum decision making recently. Remember how sticklebacks make their decisions? Well bacteria do it too, below is a great TED talk by Bonnie Bassler on how they communicate and how they decide to act as an enormous group.



Also came across this article on humans making group decisions in a Kasparov vs The World chess game. It gets the saliva flowing on how you can engineer good decisions.

Addition: Incidentally, I also think this talk is a great example of how to give a science talk. It's a little rushed (probably nerves) but the enthusiasm is fantastic and the use of visual aids is perfect. I'm giving a workshop on presentations so I've been thinking about this stuff a lot recently.