Avoid zig-zag and use parallelism

03 November 2017

Avoid zig-zag and use parallelism

This is the advice in a new ‘how to write’ paper by Mensh & Kording (2017).

Zig-zag is where you change subjects multiple times, or distract the reader by focussing on a subject that is not your central theme. This does not mean that you should not mention other subjects, just that you should not allow them to distract the reader by repeating or jumping back to unrelated ideas once you have arrived on your central theme.

Parallelism is around consistency with your topics or variables. Let’s say that you introduce three key variables in your introduction, and later want to discuss them. Parallelism requires you to use them in the same order and in the same way so that the reader can easily follow each of these concepts, even if they skip around in reading the paper.

I remember this same advice when having one of my papers edited. The editor complained that I had brought up three variables in the introduction and then used a different order in the methods, and yet another order in the discussion. Satisfying the editor meant re-writing all sections, and that never something that an author relishes. Thus, it’s a really useful tip to bear in mind in your planning. In this case, the editor had an inspiring message: I want this to be a highly cited classic paper.

We should all want our papers to be read and cited, and once accepted they can’t be easily changed (and certainly not re-written), so getting it right is important: even if you consider your work to be minor now, think of it as a future classic.

  Lab  Writing

Why do I like publishing with PeerJ?

23 October 2017

Why do I like to publish with the Open Access journal: PeerJ?

The academic journal PeerJ has now been going for 4 years. I learned of its existance early on in 2013, from a colleague at NMMU, and quickly started reading more about it. In addition to being Open Access and not impact focussed (the importance of which we'd learnt from PLoS-ONE), I was initially attracted by their policy of publishing reviewer and editorial comments. This was the transparancy that I'd craved for a long time. Credit and accountability for reviewers and editors, allowing them to take their game to the next level. All reviews can be cited as each carrys a doi. This is a great way for students to learn about the peer review process, and demystify it for interested members of the public.

Next, I was drawn by the novel idea of membership for authors. You can buy three levels of life-time membership entitling you to publish one, two or as many articles as you like for the rest of your life. The inital rates have changed somewhat (see here), and there are some extra requirements, but the spirit of PeerJ as a community continues. PeerJ has now added an Article Processing Charge (APC) which makes it look more similar to other Open Access journals (currently standing at US$ 1 095). This doesn't make the old memberships invalid, but allows for easier fiscal understanding of univeristy finance departments; not many of them understood the membership system. The PeerJ APC is also much more reasonable than that of most other APCs, but it continues to be out of my reach. Sadly, I can really only afford to publish on my existing membership (and with other members).

There is real care in the copy-editing process. The PeerJ staff are a pleasure to interact with, and they really do care about what is published under their banner. They will follow through with the last wishes of the handling editor and make sure that all of your permissions are what they claim to be. There is the real feeling that it's a quality product, and this draws community loyaly: it's certainly got mine.

Lastly, there are a bunch of extras that make PeerJ a pleasure to work with:

  • The aesthetically pleasing clean look to both their articles and website as a whole. 
  • The clear instructions and community guidelines 
  • The up to date policies and procedures
    • Copyright to authors
    • Clear requirements for who gets to be an author
  • Publication ethics
  • Data sharing

I've now published 7 papers with another already in review. I've edited a further 12 and you can see my current record here. The journal has published 4 041 papers, and there are a few spin-off publications in the same stable: PeerJ Computer Science and PeerJ Preprints. 

  Lab  Writing

SD or SE?

18 October 2017

Should I be using the SD or SE? Standard Deviation or Standard Error?

I’m surprised that there are so many poor answers to this question out there, so I’ve decided to write my own, just in case my poor answer helps you any better.

The Standard Deviation

The Standard Deviation is a description of how much spread there is around the mean. You can find the formula all over, so I won’t repeat it here. A small SD indicates that your data points are closely clustered around the mean, and the larger your SD gets the more the data is spread, in a normal distribution. However, there is some intrinsically useful information that the SD carries which may help you decide whether or not you should be using it. If your distribution is normal (and yes, you should have already tested for this), then the SD tells the reader that around two thirds of the data points in your data set fall within one SD of the mean: that is the mean plus 1 SD and the mean minus 1 SD. In addition, the units of SD are practically the same as the units that you have used to collect your data and display your mean. Thus, the SD is providing your reader with a descriptor of the mean that is quantifiable and can be easily interpreted.

You can report the SD in text as follows:

Our data show that males (n = 353) were larger (387.5 ± 49.37 mm) than females (n = 321; 245.4 ± 27.61 mm).

Note that I’ve not used the terms mean or standard deviation in the text above, this is because you should set this up in your material and methods section. If you need to change between the SD and SE in your results, then you will need to indicate which is which when you report it. I have used different levels of accuracy (decimal places) for means and SD. This should be relative to how you actually measured your data. In this case, I measured animals to the nearest mm, so report the mean to one decimal place and the SD to two. Although there is no strict rule, you should not be reporting a mean with far greater accuracy that you actually measured it (e.g. to four decimal places). Note also that the sample size is given for each set. It is very important to provide this information somewhere. There may be instances (such as an experiment) where these numbers are set throughout the document, and so don’t need to be repeated in the text each time you report a result. 

Standard Error

The purpose of the Standard Error is to inform the reader on the likelihood of the mean. In many biological studies, we take the sample from a population that is much larger because we can’t measure all individuals. In our example above, we see that males were larger than females, but how likely is it that the mean we obtained reflects the true mean of the entire population, both sampled and unsampled?

By now, you should have come to the conclusion that the SE is useful when comparing means. In a graph or table where you are interested in demonstrating whether or not the means are different, you can use the SE as error bars around the mean. Note that the convention is that you have plus or minus two SE in error bars (two SE above and two SE below the mean). This is because 2 SE is equivalent to a 95% probability that the mean falls within this range, meaning you’d be very sure. Showing 1 SE either side only shows that you are 68% sure, which doesn’t help much if your test statistic is 0.05. Either way, just make sure that you clearly indicate what you have done in the figure legend. In addition, you will probably want to conduct some statistical test to show that the data are indeed different. Interestingly, statisticians are moving away from many of these tests (or at least the test statistic). If you have used the SE correctly, your graph should speak for itself and there is no real need to carry out a test. In cases where it appears marginal, a test can be useful. Alternatively, you should go back and measure more animals!

In summary

In summary, the SE is telling us about the variability of the population mean (in relation to the one we measured), while the SD is giving information on the variability of the data points that we collected around their mean.

Standard Deviation or Standard Error?

To try to answer the original question posed above. You are most likely to report the SD in your text when describing the data you collected, and the SE on a graph demonstrating how likely it is that the means you obtained represent the entire (only partially sampled) population.

Read on...

If you didn’t understand the above, or want to read more on the (relatively) simple logic of how and why the SD and SE are calculated and derived, I suggest that you look for:

Streiner DL (1996) Maintaining Standards: Differences between the Standard Deviation and Standard Error, and when to use each. Can J Psychiatry 41:498–502.

I am indebted to Don Kramer for pointing me toward the above paper.

  Lab  Writing

A rant for Open Access week

15 October 2017

I put my journal behind a paywall, so why am I talking to you about Open Access?

It is easy to forget who does what in the world of publishing, so I begin by refreshing the minds of older readers, and informing younger ones. I will take the process of submission, peer-review and editing as understood. Although I dismiss it quickly here, this is really the crux of the work involved in science, and what follows is simply the recording of this process.

Academics are not (usually) superstars, nor looking for enormous numbers of readers, but there would be little point to recording our work if we had no readers, or if our work were inaccessible, and so publishing is a necessity. However, we have got into a state in which much of our work is behind a pay wall, and thus inaccessible to most. Whether or not we need our work to look pretty and appealing speaks more to our readers as humans than academics. Perhaps it goes without saying that an audience is likely to be larger the more appealing the presentation, and that’s not just the writing style but the layout and presentation of the text itself. And this is not new.

Right back to the first scientific journal, Philosophical Transactions in 1665, it is clear that the papers were type set and presented in the manor of a book, perhaps analogous to a collection of short stories. At the start, these were reports of studies that were presented at meetings. Producing proceedings of learned societies became the way in which most scientific journals began. Only later did it become possible to submit a manuscript that had not been presented. And later still when publishers began to manufacture their own scholarly journals in the absence of any academic society.

Being the editor of a society journal means being elected by members of that society, and being responsible to an editorial board, normally made up of the society’s members. Until very recently, and I’m thinking back to my first interactions with editors for my first few publications, submitting to the journal meant producing three (or sometimes more) double spaced copies of a manuscript and mailing them to the editor. Editors of bigger journals had secretaries dedicated to handling the administration of the paper. Following a telephonic enquiry, the copies were sent out to referees by post and sent back to the editorial office with a typed report often together with the marked up manuscript. Once the editor had received all reports, they communicated their decision back to the corresponding author (i.e. the one to whom correspondence was addressed) and, once accepted, the article went into production. Prior to personal computers being commonplace (only 25 years ago), each journal would have had to have had a publisher to set the type and print the pages. Clearly, this was beyond the scope of individual societies and the publisher was a necessity. Libraries had to pay for copies of journals, as the cost of publishing had to be offset by the society.

The advent of desktop publishing changed the need for publishers and brought many small society journals onto a larger platform where they could produce attractive content (over the typewritten documents that had been stencil duplicated or similar) and sent around to members. However, for small societies there was no professionalism involved as it devolved to the editor to publish society material. This is where I entered the stage in 2009 when I took over as editor of the African Journal of Herpetology. Thankfully, email had taken the place of the postal service, but once a manuscript was accepted I was the one who needed to type-set the documents (in Quark) and send out proofs to authors. Once proofs were corrected and the issue was ready, I had to find quotes from 3 printers, deliver discs and ultimately collect boxes of printed journals. Back at home, I also packed all of the copies into labelled envelopes (with some help from friends) and carried the boxes once again to the post office.

  

After the first issue, I realised that I could not do all of this work indefinitely. I knew that there were publishers who were interested in acquiring the journal into their stable, and I contacted them and started negotiations. In 2011, the first copy of AJH from a professional publisher emerged, and allowed me to go back to editing the content through peer review.

At the time, I was aware of Open Access and considered this as an option for the journal. Open Access would have required that someone pay for the type setting, and the society would still have to pay for an online dissemination platform, given that they did not have their own platform. This would have meant that authors paid for getting their manuscripts into print. And then, like today, the decision was that our authors would not be willing to pay. Other, richer, societies were able to go Open Access with the costs being covered by their members. For one, Salamandra, this became an incredibly successful model, with submissions increasing as well as their Impact Factor. But it did become too much, and eventually a charge is now levied to the authors (albeit small). However, they (and other societies) demonstrate that Open Access is possible on an independent platform.

Why don’t all society journals do without publishers, and go Open Access independently?

The first problem is that societies generate income from journals. Subscribers to print or virtual copies pay the society, and this can defray a large part of the cost of publishing otherwise carried the members. Going Open Access means losing this revenue, as well as taking on the extra costs.

The second problem for many societies is that their members are paying, and the councils or committee’s elected to represent the members do not feel that it is fair for their members to pay for open access for everyone else. Part of the privilege of being a member of the society is having a free (or more accurately paid through membership) copy of the society’s journals. The costs are not high, and the exclusivity of members having Open Access while it is denied to others is perhaps just a hang over from the days when the only other copies were in the library. Certainly, the costs are nothing like those which authors are now charged by publishers to turn their accepted manuscripts Open Access.

In my opinion, the current situation is truly crazy. Tax-payers (in the main) pay for science to be conducted at universities and other institutes. In places where Open Access is mandatory, the tax-payer pays again to have the research published at a cost that is far inflated from the actual production costs. Publishers are getting fat, and the losers are the scientists (whose funding is reduced to pay publication costs) and the tax-payers who end up feeding the greedy publishers.

What will it take to break the vicious cycle?

We need new models for publishing. Society journals are still kings in this game and ultimately hold the cards for moving away from filling the pockets of publishing companies. What we have seen in recent years is that journals can come from nowhere to become dominant players in the system. Think PLoS ONE, and the even more recent Scientific Reports. These mega Open Access journals didn’t exist 10 years ago. And they don’t need to exist 10 years from now. What is needed is for governments to fund societies for the actual costs of publishing their own content. This could cover type-setting and the additional IT infrastructure (on-line submission system and online dissemination platform). Most (if not all) societies are not-for-profit organisations, and only need to cover the costs of publishing.

Why would a government in one country pay for the costs of researchers from another publishing in their sponsored journal?

Soft power. It is not in the interests of governments to have any scientific content behind a pay wall. The relatively small costs of grants to societies, together with some simple accounting for papers published, would be tiny compared to the current costs that many are handing over to publishers. Have your country’s logo stamped all over the pages if you must, but it really wouldn’t cost what you are currently paying. Think of the soft power involved in diseminating peer reviewed independent science.

Clearly, scientists in some countries might be worried about handing their publications to their government to disseminate. For this reason, perhaps governments might not be the correct long-term solution for many scoiety journals. Instead, there is potential to obtain grants from philanthropic societies: The Open Society Foundations might be one such source.

But wouldn’t that put all editors back in the position that I desperately wanted to get out of in 2009?

Yes, clearly there needs to be a not-for-profit clearing house that societies can use to pass on their manuscripts. Such places exist. Most governments have their own governmental publishers. Although it would be understood that academic freedom might fly in the face of some governments being held responsible for publishing content. Many countries have institutes with publishing wings. We could even use commercial publishing houses, if we could only curb their greediness.

Alternatively, we could get more savvy as authors and start using La-Tex software to compose or at least submit manuscripts. Most of us have become too dependent on word processors, and we could step up to submitting in La-Tex. Submission software could allow us to cut and paste our content into La-Tex editors online. It’s all possible. I think that many academics would be happy to submit via La-Tex if this meant that their content went Open Access.

Can we afford not to change?

If you are from a rich country or institution, then you can probably afford the current system. Those who cannot are researchers in disadvantaged countries. In some cases, the cost of publishing Open Access is greater than the cost of the research. These are insurmountable costs for many researchers. We have a massive hole in scientific contributions from the poorest of nations, and the current Open Access models will see their work being the most hidden from view, while the countries paying for their work do so disproportionately. But even developing countries could be winners in a new Open Access model. By sourcing the relevant IT skills in country, governments of middle-income countries could facilitate the content of their own society’s with relative comfort. In my opinion, everyone should publish work from scientists in the poorest countries as Open Access without any charges.

What is needed for this change?

  1. Societies need money. Editors can’t be publishers.
  2. We need free software. We desperately need good, free editorial management software. There are some free versions out there, but what we need are free versions that are at least as good, if not better, than existing platforms (e.g. ScholarOne; Editorial Manager).
  3. We need a free La-Tex interface with robust templates for all societal journals. Ideally, this would be packaged with the above editorial management software. This must have the ability to cope with figures and equations, and the unusual demands that some society journals have.
  4. We need a solution for hosting and disseminating the Open Access society journals (and their supplementary information if not hosted elsewhere) in perpetuity. This last point is perhaps the most expensive, and almost certainly requires government assistance. Maybe this is an interesting use of the block-chain with libraries keeping the data. It would be an interesting way to build a doi with editor and referee unique IDs, and the document's information hanging off. 
  5. We need to take back our content stuck behind pay walls. Yes, it’s time for you to all to dig up those old submitted manuscripts and submit them to an institutional repository where it can be accessed for free.

  Lab  Writing

No paper should be a puzzle

28 September 2017

Did you ever feel that reading a paper was like trying to solve a puzzle? I did.

During my PhD I read a lot. My study species was the subject of tens of thousands of papers, and I was convinced that I'd find what I'd need somewhere in those musty old reprints and heavy volumes that came from the library shelves. It was easy to believe that the authors of those papers had set great puzzles for me to try to understand their content. The realisation that this is not the best form of communication came as a personal epiphany some years ago.

“The goal of good writing is straightforward: to make your reader's job as easy as possible” Kevin W. Plaxco (2010).

This great quote from a paper by Plaxco (2010) cuts to the heart of why it’s essential to write well. As an editor, I once experienced an author who thought the opposite, and for me this was an epiphany. The submitted manuscript was an impenetrable mess. I could tell that there was good work in there, but as an editor I felt that the information had been made so obscure by the authors that my readers were unlikely to get much out of it. The author was a colleague, and so I decided to phone him and chat about the need for much greater clarity in his manuscript. Experience with email has taught me that they can often be taken in the wrong way; usually in the worst possible way.

The response I got surprised me. The author recognised that his text was dense and was unapologetic. “Let the reader work to make sense of my data,” he said. My epiphany came not because this was a totally alien concept, but because during my PhD days this was exactly how I had thought scientific writing should be done. I had spent so many hours slogging through dense and dreary papers by well-respected figures. The reward when I finally understood what it was that they were trying to communicate felt so great that I believed the puzzle they had set me was what I should set my own readers. Happily, my advisor didn’t feel the same way, but for years I continued to believe that a paper should be a decent puzzle for my readers to crack.

There are still authors out there who attempt to set puzzles for their readers, but they aren’t in the mainstream any more. Instead, biological sciences has some inspiring writers, and many more are taught how to inspire future generations towards communicating great science. That’s not to say that there are no puzzles left. Much of what we do requires great puzzle solving abilities. However, let’s keep the puzzles away from communicating with our audience, make their job as reader easy or even pleasurable, and they’ll keep coming back for more.

Plaxco, K.W., 2010. The art of writing science. Protein Science19, 2261-2266.

  Lab  Writing