30 March 2014

Word cloud view of my publications

Since switching to Zotero for reference management I've been exploring its features, native or implemented via extensions. Among those, Paper Machines looks neat (I'm not yet sure about useful). As a first example, here is a word cloud visualization of all my research papers:

29 March 2014


This concept got its name from Daniel Dennett, who defined it in 2009 (in Intuition Pumps And Other Tools for Thinking) as:

A deepity is a proposition that seems both important and true—and profound—but that achieves this effect by being ambiguous. On one reading it is manifestly false, but it would be earth-shaking if it were true; on the other reading it is true but trivial.

The category is so useful (I have already invoked it on this blog) that it must have been discussed before Dennett. The only reference I can find that goes pretty much in the same direction is Wittgenstein's Tractatus (propositions 4.46-4.4661):

The truth-conditions of a proposition determine the range that it leaves open to the facts. (A proposition, a picture, or a model is, in the negative sense, like a solid body that restricts the freedom of movement of others, and in the positive sense, like a space bounded by solid substance in which there is room for a body.) A tautology leaves open to reality the whole—the infinite whole—of logical space: a contradiction fills the whole of logical space leaving no point of it for reality. Thus neither of them can determine reality in any way. (4.463)

That is if I understand the text correctly, which is not the obvious assumption here, and even so Wittgenstein considers logical limitations rather than errors in reasoning. So, who was really the first to discuss deepities?

[UPDATE 27/10/2014] Some other discussions of the term (posterior to Dennett's):

22 March 2014

Meeting duration as a function of the number of participants

My conjecture is that a meeting involving \(N\) participants takes a time \(T\) given by:
\[T(N) \, \text{[in hours]} \, = \exp (N/\; 7) -1\]This only applies to unstructured meetings (with no official hierarchy) and is fairly insensitive to the topic at hand. The time ranges from 20 minutes for \(N=2\) to 4½ hours for \(N=12\).

For any meeting larger than about ten attendees one should either designate a chairman or schedule a lunch break.

16 March 2014

My six-word research talk

Here is my attempt, inspired by #6wordchemtalk:

Inclusions in membranes repel each other

More details: 1, 2, 3, 4
...and we're still working on it.

9 March 2014

The open data controversy

As of March 3rd, open access publisher Public Library of Science (PLoS) requires authors publishing in one of its journals  to make publicly available all data relevant to the conclusions drawn in their papers.

After the wave of protests (just check #PLoSFail) that PLoS delicately called "an extraordinary outpouring of discussions" or "[a] flurry of interest", the publisher changed its position, see updated original blog post and the more recent explanation. The requirement was downsized from 

"...any and all of the digital materials that are collected and analyzed in the pursuit of scientific advances" 


"...if you are providing graphs, it would indeed be helpful to provide the spreadsheet from which you generated the graph. If you think some other form of the data would be useful to other researchers who might want to understand, replicate or build on your work, please do include it. Conversely, if it is usual in publications in this field to provide only the summary information, then that remains sufficient now."

In short, they attempted a revolution before quickly returning to the status quo. Still, it's a good thing they insist on making available the raw data for graphs: squinting at ten superposed curves in log-log scale is hard on the eyes...

As to their more ambitious goal of opening all the relevant data, it is much too early for that, mainly because scientists see their (painfully acquired) data as valuable property, to be converted into publications. Giving it up for free to colleagues (and competitors) is not an economically viable model. A very lucid presentation of this point of view was given by Terry McGlynn, in a (long) blog post.

I am sure a default policy of open access to all scientific data (with reasonable exceptions) would be a Very Good Thing, but we need to work out a way of formally crediting the initial authors. The only solution I see is co-authorship, but that would pose some serious problems:
  • Merely collecting the data is not sufficient for authorship. PLOS ONE, for instance, requires active involvement in all stages of the work.
  • The original authors might disagree with the conclusions of the second team, or even compete with them by writing their own, separate analysis.
  • The number of authors on scientific papers is already quite large; do we need to increase it? This point might be solved, or at least mitigated, by a detailed description of each author's role.
I'm looking further to the development of this story, in particular to the response of the more established journals.