one space or two?

One space or two after a full stop?  Many would have us believe two spaces is WRONG, and was introduced due to eeeevil typewriters, and we should return to the One Right Way. Heraclitean River delves into the history: it always was two spaces, until the eeeevil publishers and their Linotype machines demanded something simpler, and rewrote history!

Use one, use two, as you see fit – but do be consistent!

Read More

a new piling system

I write academic papers, and read a lot of other papers. What with hard copy scattered through filing cabinets, and soft copies on a wide variety of websites, it can be hard to keep track of what I’ve read, made notes on, made BiBTeX citation data, and referenced.

Nearly two years ago I had a go at using Mendeley, designed to help with this very task. But for some reason, it never gelled for me, and I gave up using it. Then, when I became an Evernote convert, I fiddled about with using it to store data on the papers: author, title, etc, notes, BibTeX, and links to the papers themselves. But it was clunky work-flow, requiring a lot of hand-effort. Only the note keeping part of it worked well.

Then a colleague raved about Paperpile on his G+ stream. I had a look. It has a similar concept to Mendeley and other such systems, keeping references, supporting tags, good searching, associated notes, and citation output in multiple formats (although I only care about BibTeX). Instead of being a stand-alone application, however, it’s Chrome-based, and uses your Google Drive as a repository to store your papers. It’s currently in Beta, and I thought I’d give it a try. I emailed off for an account, and about a week later I got one.

The first thing I did was import my dusty Mendeley data (with a single button click and a log on), so I started off with a well-populated, if slightly out-of-date, database. I decided to trial it on the paper I had just started writing.

I defined a tag for the new paper. As I was writing, each time I included a reference in the text, I checked if that reference was already in my Paperpile database; if not, I added it. (Since there is usually a fair amount of overlap between bibliographies of papers in a similar domain, this should get faster as the db gets more populated.) Then I tagged it with the paper’s tag, and any other relevant tags.

My current Paperpile db, with 321 entries

To generate the BibTeX, all I needed to do was select the tag, which selected all the references, and then export the whole BibTeX file in one go.

The real benefit showed up when I got comments back on a draft of the paper. One was about a short quotation I had included, and I needed to find the quotation in its original context in order to address the comment. Click the Paperpile tab in Chrome. Type the author’s name into the search box; the paper’s details appear. Click the “view PDF” button. Voila! The paper is on my screen! I can’t think of a faster way to achieve that, without using telepathy.

You can upload in various ways, including PubMed, arXiv, doi, navigating to a website, or just giving it a PDF.  When you upload a PDF directly, the system searches the web to find the right data to populated the various fields. It gets this mostly right, but there have been a couple of odd peculiarities. Still, the system is in Beta. I reported the couple of weird results, and got very fast and helpful responses from the team. (I like Beta testing. I can whinge about software, and feel virtuous about doing so!)

One thing I particularly like is that the uploaded PDFs are stored in my Google Drive in a very sensible way. The files have obvious names: <Author> <Year> - <Title>.pdf. So if Paperpile were to disappear for any reason, I still have all my PDFs in a very usable form. (I’m not expecting it to disappear; I’m just paranoid: I have my Google Drive synched to my hard drive at home, in case Google disappears!)

I haven’t used all the facilities, in particular, I haven’t exploited the Google Docs integration. The Paperpile team report that some people are using it to write their papers collaboratively in Google Docs. That looks potentially useful, but I don’t use this plain format: I write my papers in LaTeX/BibTeX, using TeXnicCenter.

One part of the system I probably won’t use that much is the notes field. It’s perfectly fine, but I like to keep more substantial notes, with formatting, sketches, figures, and the like. So I’ll continue using my Evernote “papers” notebook, but now just for the notes, not the entire paper and other detials. For a paper with notes, I add a link from the Paperile entry to the relevant Evernote note, using the URL field which gives a clickable link (and I add an Evernote tag, to make it clear to me that there is a note). Similarly, I have a lot of already existing book reviews on my website. So when I include a book that I own, I add a link to the review on my site.

In fact, I think that having a variety of tools that each does their own thing well, with links between the relevant parts, works better than trying to shoehorn all capability into every application. So in Evernote, for example, for a meeting note, I don’t copy the agenda from the email notification, I just store a link to it. Evernote Webclipper allows you to clip the whole email into Evernote, but that just seems to cause unnecessary duplication. It’s good practice to keep only one copy of data (except for backups, of course!), otherwise there is the potential for copies to get out of synch. When that agenda is inevitably later updated, and a new copy emailed out, I don’t have to do anything: provided it is sent out with the same subject line, the Gmail link pulls up the entire conversation, and I can select the most recent agenda. (One day, the agenda setters may start using Google Docs, and so everyone will always have the most up to date version – provided they haven't clipped it into Evernote!) With all these web-based tools, the URL can link everything together.

In summary: first impressions of Paperpile are very favourable. I’ve successfully and productively used it for writing a paper, and it being web/Google based means it’s available at work, at home, and elsewhere, without me having to do anything special. I’ll report on progress if and when it gets more deeply integrated into my web-life.

Read More

Typography in ten minutes

Yesterday I came across Butterick’s Practical Typography. It promises to make you “a bet­ter ty­pog­ra­ph­er than 95% of pro­fes­sion­al writ­ers and 70% of pro­fes­sion­al de­sign­ers” in ten minutes, by reading 5 rules (and, presumably, then following them). I instead read the whole thing – it’s fascinating (if you are fascinated by typography).

At one point, when advocating using wider margins, and making better use of white space, he sets an exercise, of making 2 documents with the same text.

Document A is the usual default style, and has the following format: “page mar­gins of one inch per side, font is Times New Roman, point size is 12, line spacing is “Double” [...], first-line indent is half an inch, and no space be­tween para­graphs.”

Document B follows Butterick’s strictures, and has the following format: “page mar­gins of two inch­es per side, font is still Times New Roman, point size is 11, line spac­ing is ex­act­ly 15 points, first-line in­dent is still half an inch, and still no space between para­graphs.”

He claims that B looks more like a professionally typeset book, is more comfortable to read, and contains more words per page. And he's right. Here are A and B (using Lorem Ipsum, so neither is particularly comfortable to read!).

(left) document A, default margins, double spaced; (right) document B, wider margins, better spaced, more text

Then today I had to write a 250 word “vision” document. I heeded what I had learnt. I initally wrote the text in the Word default layout. Then I tweaked it, by changing the font, and increasing the margins and linespacing. I made the margins as wide as I could, and still get all the text on one page. The result:

(left) 250 words in Word default format; (right) the same words, after some minor formatting tweaks

I’m sold!

Read More

the scientific process

There have been two well-publicised mathematical and scientific breakthroughs in the news recently, that have got the community all a-buzz, and that illustrate two quite different approaches to advancing understanding.

Yitang Zhang

In the first, a "virtually unknown" mathematician has made a breakthrough in the twin prime conjecture, a deep question in number theory.  A beautifully clear write-up from the Simons Foundation explains both the mathematical problem, and the process by which Zhang's contribution was handled by the mathematical community.  Zhang wrote a paper and submitted it to the Annals of Mathematics, a highly respected journal.  There is was refereed, and swiftly accepted, since, not only was it correct, it was "written with crystalline clarity and a total command of the topic’s current state of the art".  Being right is crucial, but being comprehensible to the community is also important: it is hard to check someone's work if they have written it in a language all their own.  So, kudos to Zhang for his achievement, and to the mathematical community for recognising it.

Eric Weinstein

The second well-publicised "breakthrough" is Eric Weinstein's "Geometric Unity", a contribution to particle physics.  Or is it?  Here we have another unknown worker, but this time his idea has been launched on the world through a public lecture and a newspaper article written by his sponsor and friend, mathematician Marcus du Soutoy. No publication, no journal submission, not even an unrefereed pre-print, and so no peer scrutiny is possible. Several commentators, including writers at New Scientist and Scientific American, and many science bloggers, have been highly critical of this process that amounts to "science via press conference".

Andrew Wiles

So, two announced breakthroughs by virtual unknowns, given two very different receptions.  Why the difference?  Well, because the conduct of science and mathematics is a process, not (just) a result. It's not some bizarre club, where you have to go through the right channels, jump through the community's hoops, in some arbitrary hazing process.  Those hoops are there for a reason.  It is so very easy to make a mistake, and the hoops are part of the process to help ensure that any mistakes are caught.  Remember the story of Andrew Wiles, slaving away in secrecy for seven years, proving Fermat's last theorem. Well, his first proof had a flaw. Fortunately, the error was correctable, after a lot of effort, and his proof stands. But other equally eminent mathematicians have thought they had made breakthroughs, only for peer review to determine otherwise.

Peer review is an essential part of the scientific process.  It's not there to keep out "outsiders". It's there to keep out errors.  Put up or shut up.  And show your working.

Read More

thoroughly path breaking and novel

Last October, I blogged about a spam email soliciting journal paper submissions.

Yesterday, I got an even more ridiculous one:

I recently came across your research paper titled "."

Unsurprisingly, I don't actually have any publications with the null title!  Okay, so it's an amusing scripting error.  But the email continues:

In this everchanging world, where every new discovery refutes the previous ones,

"every new discovery refutes the previous ones"  Really?

your research is thoroughly path breaking and novel.

So novel that no title can adequately encompass it.

To provide more leverage to your work, I invite you to submit your upcoming research articles / papers for publication in [redacted], an international double blind peer reviewed research journal.

This may be noted that due date of forthcoming issue [redacted] is 15th March, 2013.

The process of publication is expected to be completed within two to three weeks. Our processes follow stringent quality control measures and comply international standards in journal publishing. 

Clearly, their "stringent quality control measures" don't cover proofreading their spam emails.

There's more, but I've stopped reading...

Read More

It truly is an excellent paper

A few days ago I received the following email (details redacted to protect the guilty):

This is from the editorial board office of Journal of [Totally Unrelated to My Research (TUMR). TUMR] is a peer-reviewed international research journal, devoted to supporting a global exchange of knowledge of [TUMR].
We found a paper you had published in “Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)”.
Title: An architecture for modelling emergence in CA-like systems
Author(s): Stepney Susan
It truly is an excellent paper that relates quite nicely to our journal.
To promote the communications of [TUMR] and broaden our journal’s global perspective, we cordially invite you to submit new research manuscripts to our journal before Nov. 29, 2012.
You can enjoy a registration discount if your paper is accepted.

The paper in question does exist. It is totally unrelated to the remit of the journal, however.

There are two big red flags in the email that there is something phishy.

First, no-one in the know says a paper has been

published in “Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)”

That rather unwieldy title is used only on the LNCS publisher Springer's website, from where I suspect it was copied verbatim.

Second, the claim that the paper "relates quite nicely to our journal" is not true, as could be spotted by glancing at the paper's content for a split second.

No-one did glance at it, however. This is just computer generated spam. I know what journal TUMR really is, so I can guess a crude bit of keyword matching glommed on to the word "architecture" or "engineering" in the abstract. These terms are used in the paper in a completely different context from that of TUMR.  Clearly the paper was found by a mindless web trawl.

The key phrase that flags what is really going on here is near the end of the email: "registration discount". TUMR is an Open Access journal, which means you have to pay to publish.  They are trying to flatter me into thinking that they like my work, in order to convince me that I should pay to publish in their journal.  Since they have clearly never even read my work, however, the result is not my feeling sufficiently flattered to publish, but sufficiently aggravated to blog. 

This approach is a distant cousin of the classic perfect prediction scam.  Spam a large population with a range of information (the classic example is stock market predictions).  It will be false for most targets, who will just bin it.  But, by chance alone, it will be true for some, who, not realising the extent of the scam, and the vast number of false hits, will be convinced by the truth of the claim in their case.  Here it is true for those few targets who will, by chance alone, have "an excellent paper that relates quite nicely to our journal".  The implication is that you have been carefully selected.  The actuality is somewhat different.

This is the first time I've seen the scam used in this way.  But I'm sure it won't be the last...

Read More

citation patterns

An academic's contribution to the community is made through publications.  And so we obsessively keep good records of what we have published, and neurotically check out if anyone has noticed.

To this end, I’ve been playing around with Google Scholar, tidying up my auto-generated publications list there. Although I still maintain my own publications page, this separate one is a useful resource, mainly because it includes citation counts and links.

Citation links are good for more than justegoboo and feeding neuroses, honestly! Citations indicate other authors who find my work relevant to them, so it's very likely that their work is interesting and relevant to my own research. It makes sense for me to check them out, and then also check out the other papers they reference, and also their citations, to see if there’s something interesting and relevant to me. Although it is a bit easy to get sucked into a never-ending death-spiral of link following: there’s just too much interesting stuff.

That's the beauty of Google Scholar.  it doesn't just have a list of my papers (a task I can do myself with relatively little effort); it also auto-generates links to citing papers (a task that would be ridiculously time-consuming to do myself).

More than that, it also provides neat little graphs of citations per year. These are quite interesting for publications that are several years old, where patterns have had time to emerge.

The typical pattern shows a peak a few years after publication, then a tail off into obscurity.

Slightly more gratifying is the pattern of a peak, followed by a drop, but then carrying on bumping along at about the same rate.

But the weirdest citation pattern must be to a paper written during my PhD, published nearly 30 years ago. It caused barely a ripple when published (I comfort myself that there was no Web in those days, and hence restricted access to it). But then there was a second (modest) peak of citations after about 15 years, followed by a drop-off. And then there was a third peak, starting more than two decades after publication.

Clearly, a paper ahead of its time!

Read More

Kindling

I've been debating whether to get an eBook reader like a Kindle for a while now.  So I was interested to read Jo Walton's blog post on this issue, as it covers some of my concerns.

The reason for wanting one is the convenience of being able to carry multiple books easily.  I had a three day trip to Greece recently (two days mostly travel, one and a bit days in Greece), and nearly ran out of reading material because I took only three books (two fiction, one non-fiction), yet those books were a significant fraction of my luggage weight.

A Kindle would help.  Even so, I was pleased to see in the comments phrases like: "I could take one fully-stocked Kindle and an emergency paperback".  This commenter is clearly sufficiently paranoid not to trust the battery life; good.  The fear of being without reading material is widespread; another commenter said: "it's a comfort to know that if I finish the book I'm reading in line at the post office I won't just have to stand in line at the post office without a book".

Being able to change (increase!) the font size is another advantage, which gets more advantageous as the years go by.

My major concern about eBooks, however, is that I absolutely positively do not want to even entertain the possibility of "losing" a book, either because the seller decides to remove it from the device (yes, something that can happen in this Brave New World, that has such vendors in't!), or because the technology becomes obsolete (hey, I've lived through the appearance and subsequent disappearance of cassette tapes, and pretty nearly by now VHS tapes).  Jo's solution is to buy the eBook when the hardback comes out, then the paperback when it comes out later (sometimes several years later: I feel aggrieved I have to wait this long, despite the fact that my reading backlog is several decades).  This is no more expensive than buying the hardback alone, so is a very reasonable approach (particularly since hardbacks are significantly larger than paperbacks, and the major cost of a book is not its cover price, but the space for storing it, which is why I prefer to buy paperbacks, despite the long publication delay).

However, my main amusement from the post was Jo's indignant reaction to Amazon's bragging about the battery life: the Kindle's battery will last for whole a month if you read for half an hour a day.  She realised she was not in the target market.  Who on earth reads for only half an hour a day?  My backlog isn't decades because of the amount I read; it's because of the amount I buy.  It reminded me of the time I saw a half height bookcase (so about 10 linear feet of bookshelf space, if that) for sale, which had a sign on it proudly proclaiming "ample for all your books".  I just fell about laughing.

Read More

scientific abstract

Scientific and technical writing is a little different from the kind of "creative writing" you are taught at school. There are different conventions. For example, "vary your vocabulary" is a complete no-no if you are striving for precision and lack of ambiguity. If you think using the same word several times may sound a bit clunky, and you decide to make things "read better" by using synonyms instead,  imagine the internal dialogue of your readers going something like this: "You talk about a thingumabob here, a thingamajig there, and a whatchamacallit in your other paper. What subtle distinction are you trying to make? I've been trying to puzzle this out for ages.  Oh, I see.  You are just varying your vocabulary. Come here and say hello to this two-by-four." That should help you decide not to do it.

One important part of a scientific paper is the abstract. It should be short yet comprehensive. It should tell you what the paper is about, the question the paper addresses, and the answer it discovers. It is not a spoiler to put the answer in. You are not writing a blurb for a whodunnit. Don't worry that you are giving away the punchline. The abstract may be the only part of your paper the reader even sees.

So I was delighted to see a paper with an excellent abstract quoted at Ben Goldacre's secondary blog. (Actually, it's only the perfect abstract when combined with the paper's title; techincally, abstracts should be stand-alone. But, hey.)

Read More