Evolving notes, images and sounds by Luis Apiolaza

Category: research (Page 7 of 8)

Should I reject a manuscript because the analyses weren’t done using open source software?

“Should I reject a manuscript because the analyses weren’t done using open software?” I overheard a couple of young researchers discussing. Initially I thought it was a joke but, to my surprise, it was not funny at all.

There is an unsettling, underlying idea in that question: the value of a scientific work can be reduced to its computability. If I, the reader, cannot replicate the computation the work is of little, if any, value. Even further, my verification has to have no software cost involved, because if that is not the case we are limiting the possibility of computation to only those who can afford it. Therefore, the almost unavoidable conclusion is that we should force the use of open software in science.

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If one were to invent scientific journals today

While taking a shower I was daydreaming about what would happen if one were to invent journals today, with a very low cost of publication and no physical limits to the size of a publication. My shower answer was that there would be little chance for a model like traditional printed journals.

One could create a central repository (a bit like the arXiv) taking submissions of text format of the article + figures, which are automatically translated to a decent-looking web format and a printable version. This would be the canonical version of the article and would get assigned a unique identifier. The submitters would get to update their article any number of times, creating versions (pretty much like software). This way they could fix any issues without breaking references from other articles.
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When R, or any other language, is not enough

This post is tangential to R, although R has a fair share of the issues I mention here, which include research reproducibility, open source, paying for software, multiple languages, salt and pepper.

There is an increasing interest in the reproducibility of research. In many topics we face multiple, often conflicting claims and as researchers we value the ability to evaluate those claims, including repeating/reproducing research results. While I share the interest in reproducibility, some times I feel we are obsessing too much on only part of the research process: statistical analysis. Even here, many people focus not on the models per se, but only on the code for the analysis, which should only use tools that are free of charge.

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Publication incentives

(This post continues discussing issues I described back in January in Academic publication boycott)

Some weeks ago I received a couple of emails the same day: one asking me to submit a paper to an open access journal, while the other one was inviting me to be the editor of an ‘special issue’ of my choice for another journal. I haven’t heard before about any of the two publications, which follow pretty much the same model: submit a paper for $600 and—if they like it—it will be published. However, the special issue email had this ‘buy your way in’ feeling: find ten contributors (i.e. $6,000) and you get to be an editor. Now, there is nothing wrong per-se with open access journals, some of my favorite ones (e.g. PLoS ONE) follow that model. However, I was surprised by the increasing number of new journals that look at filling the gap for ‘I need to publish soon, somewhere’. Surprised until one remembers the incentives at play in academic environments.

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My approach to presentations

I give a fair number of presentations per year, some to university students (in classes from 6 to 90 students), some to people from industry (in groups from 4 to 20), and others in conferences (100+ people). Despite that I have stage fear for most activities (and I could not save my life by acting) I have to admit that I do enjoy giving presentations (a lot, really).

Once in a while I like visiting Presentation Zen, which is one of the best resources providing a critical appreciation of different presentation styles and tools. I guess that one of the typical mistakes is to accept one ‘style’ or method as THE absolute truth. I believe that a ‘horses for courses’ approach works best and will shamelessly borrow from different methods as I see fit. Aiming to make clear to myself what works and what doesn’t I decided to write down a few notes about my experience giving presentations. I want to make something clear: this is what works for me that does not pretend to be a one size fits all recipe.

Although many comments on this post refer to presentations using slideware (either Keynote of PowerPoint) it is important to remember that they are only support tools. When giving a presentation one is basically selling an idea (or product) to the audience. One is acting as an intermediary between the idea and the audience, and success will be measured by how people buy (understand, learn, adopt, take ownership) the idea. These people may be students, customers, clients, etc but the elements are essentially the same: the idea, the presenter and the audience. No, PowerPoint is not on the list.

The resources that I use the most are:

  1. Analogy, presenting new concepts relating them to something familiar to the audience. This is an excellent way of presenting complex topics, although it requires some care to avoid stretching the analogy too far and misleading the audience.
  2. Humour, using a lighthearted approach to my topic. I am not talking about the typical opening joke, but of finding ways of making the presentation memorable through the use of interesting associations, the occasional joke and showing that one is having a good time presenting.
  3. Images, lots of them. In my experience, diagrams work better than bullet points and good quality pictures make the presentation stand out. I use some of my own pictures (photography is one of my hobbies), iStockPhoto, Flickr and a few Getty stock photos too.
  4. Slides for questions that I am expecting. At the end of my presentation I normally insert a blank slide followed by two or three slides that explain questions that I think may arise from my presentation. I have rarely used them, but when I have they have been a real bonus.

Things that I avoid:

  1. I avoid as much as possible breaking thoughts on bullet lists. There are very few cases where I think that they are really useful, but diagrams tend to take their place in my presentations.
  2. Corporate templates with logos on every slide, which are a distraction and take too much space. I use Keynote’s ‘Modern Portfolio’ template because it is quite neutral and I can adapt it to many different types of presentations.
  3. Complex transitions, flying objects, etc. However, some times I use transitions for only a few slides just to show off the mac to my colleagues
  4. Equations, unless they really add value. In my job I have to use fairly advanced numerical and statistical approaches, but I always keep in mind that the concepts (rather than the formulas) are what really matter to my audience. I leave the equations for publications in professional journals and endorse the ‘Look Ma, no equations’ approach for presentations.
  5. Using too many slides: I tend to use between 12 to 18 slides for a 45 minutes presentation. I know, some people like Guy Kawasaki advocate ten as the optimum, but once you count overlapping objects he is probably close to 15. I have seen excellent presentations with 50 slides, mostly pictures and diagrams, but one really needs to be an excellent speaker to pull that one off. If in doubt, drop the slide from your deck (another use for those slides is point 4 on my list of resources).
  6. Overestimating the audience: even if you are in a room full of experts they want to hear a good story showing that one knows where the topic is coming from. I first read this advice in A Ph.D. is not enough: a guide to survival in science by Peter Feibelman.

Handouts

Considering the way I prepare my slides, there is no much point on using them as handouts for the lecture. I tend to prepare a handout starting from my notes for the presentation or the presentation notes from a well written handout. I avoid like the pest preparing a deck of slides without having something written first. The length of my handouts varies from two to six pages, depending on the audience and the complexity of the topic.

A typical question is when do you hand out the notes? It depends. If I am talking to students that I will see again over several lectures I will give the handouts either at the start of the lecture or even several days before. On the contrary, when I am giving presentations that are completely self-contained (not part of a course) I tell the audience that I will hand out the notes at the end. I do this to ensure their full attention, particularly considering that I may not see them ever again.

In case you are using a mac/linux

When I am teaching I can always use my own laptop. However, in meetings with industry, conferences and the like all presenters usually have to put their presentations in a machine running MS Windows. For these cases I usually have two additional versions of my presentation exported from Keynote: PowerPoint and PDF (note: in 2015 I moved back to PowerPoint. Now in 2024 I use mostly PowerPoint withe some Keynote). I used to always test the PowerPoint version in my windows box and if I was not satisfied with its appearance I would use the PDF version. (Now I do not have a computer running windows, so I test with PowerPoint for mac). In many projectors, presentations look better using PDF rather than PowerPoint (and there are no problems with missing pictures). Still, Keynote is much better than any of the alternatives with its presenter screen displaying current and next slide, notes (with a few key points to remember) and a clock.

Odds and ends

I always take with me a laser pointer/remote control (lost my old, trusty and cheap $3 laser pointer that was given to me in 2000. Note: I lost it somewhere in 2018); I have been in many meetings where the pointer runs out of battery. My laptop battery is fully charged before presenting (just in case). I carry copies of my presentation and handouts in a USB disk and, when traveling away from work, I also load copies of the files in my web server. If talking to industry I take printed copies of the handouts in good quality paper (with a yellow shade, like Moleskine paper). It is a bit more expensive, but I think it is $10 well spent.

Most times I do not practice my presentation, but I only read my presentation notes a couple of times and go over the slide desk a few times trying to remember key points for each slide. I do not memorize the notes (my memory is not great), but try to convey the gist of them. Thus, if I give the same presentation twice there is a fair amount of variation between versions. I think this is a good thing and I always think of it as a jazz performance: the core is the same, but there is a good amount of improvisation. Anyway, I try to know the presentation material quite well, so I can give my talk even if all audiovisual material fails (it has happened before!). I never apologize if things don’t go perfectly, except if I arrived a bit late by some delay outside my control (this has happened only a couple of times).

Finally, I smile. A lot. I walk quite a bit looking at different persons in the audience as if I were talking only to them. This helps them to pay attention and to me to gauge how I am doing on keeping them awake and interested on the topic. I always tell myself ‘remember to have fun’ before presenting.

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