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BusinessWeek has an interesting post on how adolescence could be a failed social experiment and we should let 13-yo kids take adult-level responsibilities.

While the idea is good, I still find it troublesome in a society that works more than ever and has less spare time even when technology should provide abundance of resources otherwise.

The idea of rushing kids into adulthood does sound a bit like getting them to be productive as soon as possible. What happens then with those years where you experiment and test new things? While they may appreciate the new-found responsibility at first, long-term consequences of this decision are unpredictable. Will we have less creative people? I for one didn’t know what I wanted to do with my life at 13. If adolescence was a social experiment that enabled upper-class to take their kids out of sweat shops, then removing adolescence will land them into a new "intellectual sweat shop" environment. Take China for example. Kids (only kids!) are under a lot of pressure to be the very best at some specialized domain from very early in life. I would be surprised if this has no consequences. As Cal Newport wrote, there’s a general obsession with productivity that seems to be preying on our youngest. And then, the feared academic crisis.

So we translation from physical sweat shops to intellectual ones.  How is this better? We seem to bring our children into a world where most of us are time-poor, even though there is a (theoretical) abundance of resources since the industrial revolution.

Most people accept laughable payment for their time (that includes academics). So time is the scarce resource. During adolescence, we are granted an oasis of time -that in retrospective, may feel wasted-. Do we want to rush teenagers out of it?

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How do we know it’s not more productive? Well, it’s a slippery problem. Observe that it must be a slippery problem, or it all would have been debunked fair and square by now. But it’s exceptionally difficult to measure software developer productivity, for all sorts of famous reasons. And it’s even harder to perform anything resembling a valid scientific experiment in software development. You can’t have the same team do the same project twice; a bunch of stuff changes the second time around. You can’t have 2 teams do the same project; it’s too hard to control all the variables, and it’s prohibitively expensive to try it in any case. The same team doing 2 different projects in a row isn’t an experiment either.

This is also true for academic productivity. So this leaves me in a conundrum. No matter how much we want to find a theory of productivity and test it empirically, nobody is going to seriously do it because it’s impractical. So we are doomed to have a ream of blogs (yes, like this one) talking about it.

Note that contrary to Steve’s case, where companies cover their failures instead of publishing them, we do have some public log of successful behavior (i.e., scientists do have a track record). We lack the (large?) set of things they tried and failed at to achieve their publication.

Well if you can’t do experiments and you can’t do proofs, there isn’t much science going on. That’s why it’s a slippery problem. It’s why fad diets are still enormously popular. People want fad diets to work, oh boy you bet they do, even I want them to work. And you can point to all these statistically meaningless anecdotes about how Joe lost 35 pounds on this one diet, and all those people who desperately want to be thinner will think "hey, it can’t hurt. I’ll give it a try."

This explains why Steve Pavlina gets so much attention. It aims directly for things that people want to believe work. No matter that testing the claims would be either impossible (falsability is good, remember?) or impractical. This kind of reasoning works for anything that is sold online with a long sales page that cites some spectacular successes and a few ‘testimonials’.

GTD is on that list too, by the way.

Surprised by how good the writing is in Steve Yegge’s posts? I am too, but don’t be. It looks people who have spent quality time on functional languages develop super-human writing skills. (note: I have only two observations here ).

Note: the post gives a lot of detail on how life is inside Google, and how an academic department may not be that far off. Food for thought.

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Recently I attended a scientific writing workshop by Rona Urau and Susannah Goss here at MPI, Berlin.

Plenty of interesting stuff that I’d like to share here. I was under the impression that style doesn’t matter all that much; but the workshop changed my mind. And there is a paper that uses Watson    and Crick’s famous Nature paper as an example of how much style matters. There was a key paper on the same ideas by Avery et al. that was completely eclipsed by the success of Watson    and Crick’s. The key difference? Style and rethoric.

Watson    and Crick  were  extremely  concise;  their paper is only about 900 words long. Avery  et  al.  were  verbose;  their paper  is  about  7,500  words  long. They also were persuasive and used first-person statements (Avery et al. used "the authors"). They stated the importance of their work on the first paragraph, while Avery et al. never made any claims about the importance of their work.

From Urau and Goss’ materials:

And any of you still wondering how attention to stylistic aspects can help get your work published may be interested in the following statistic: "Inadequate writing can slow or prevent publication of scientific research. According to an editor of Evolution for example, poor writing is almost as frequent a reason for rejecting a manuscript as is flawed experimental design or analysis; nearly 50% of rejected papers are so poorly written that reviewers and editors cannot understand the experimental design, analysis, or interpretation (Endler 1992). My informal survey of editors of other biological journals suggests that this percentage is typical." (Moore, R. [1994]. Writing as a tool for learning biology. BioScience 44, 613-617.)

References

Avery, O.T. , C.M. MacLeod, and M. McCarty.  1944.  Studies on the chemical nature of the substance inducing  transformation  of  pneumococcal  types.  Journal  of  Experimental  Medicine  79:  137-158. 

Watson,  J.D.  and  F.H.C.  Crick.    1953.    Molecular  structure  of  nucleic  acids:  a  structure for deoxyribose nucleic
acid.” Nature 171: 737-738.

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Who is Steve?

Steve Pavlina is a top-100 blogger and a personal development guru. He has done several impressive things like majoring in Math and CS in three semesters, trying polyphasic sleep for 6 months, and testing several extremely demanding changes on his habits like eating raw food only. 

In my view, the field of personal development feels scam-ridden. It preys on people who may not have the strongest will. So the title "Personal development for smart people" feels tonge-in-cheek (Oxymoron?). I’m sure many readers, with an empirical bias, may be bothered by all the new-agey chat out there that passes for advice (with no solid evidence backing it up). Now, is Steve different? Is this book better? The answers are no, and ‘maybe, I don’t know what else is out there’.

Problems with his method: Who in the academia should be doing Steve’s job?

One thing that bothers me is that Steve’s book uses no references whatsoever. He claims to have read most self-help books, but does not acknowledge any specific ideas from them. If all the ideas in the book are new and his, then I’m very impressed -I wouldn’t know-, but that seems unlikely. Again, I’m sure self-help books are all like that; making reference to other people’s ideas in a way you can track them down, as sensible as it sounds, remains a signature of the academia.

In the same way, Steve rarely uses links on his blog, unless he is advocating a product or a person.

Which should be a red flag. Still, the guy is tremendously likable because you can see that his intention is to help people, and that he is honest about that.

Someone in the academia should be doing the work that Steve does, but more systematically.

Who is this group? Social psychology? I have no idea. My first reaction is that I’d feel ashamed of being part of that group. Loads of taxpayer money, hordes of grad students, and entire institutions protecting them… and they got their ass kicked by a guy with a blog. Maybe it’s not the academia’s fault.

Another people that should be ashamed is religious organizations, but I won’t sidetrack the discussion in that direction.

Take any of Steve’s topics. For example: does polyphasic sleep produce an overall increase in productivity? If this turns out to be the case, it would make all the sense in the world for policy makers to advise entire nations to encourage people to be polyphasic sleepers. That would remove the social awkwardness of being a polyphasic sleeper (the reason Steve quoted for him to stop!).

I have not checked the literature on polyphasic sleep. I’m sure there’s work on this. But I’m also sure nobody has made the same impact as Steve converting people to polyphasic sleep.

Also, nutritionists should take note on how a single person can switch the food habits of a large group of people by blogging.

This may sound terribly negative, as if we academics were playing some zero sum game with bloggers and other influentials (in fact, Steve advices against this mentality, and encourages thinking in terms of abundance). But isn’t it sad when academics spend entire lives working pretty much every hour they are awake, and nobody cares? For an academic, chances of changing society at a scale Steve does are slim. Very slim.

I may sound like an ‘academic absolutist’, who believes that nothing out of the academia has any value. Far from it; if you have followed this blog, you know we are critical of the academia and are disgusted by several common practices in it.

But wouldn’t it be good if more non-academics actually cited where their ideas come from? Note: this doesn’t imply all good ideas come from academics, and I’m trying to fish citations for them. If anything it’d make the reader’s life easier if he decided to master the topic he is reading. With more people writing content for others (that never gets revised or filtered properly, thanks to the wonders of self-publishing and the Internet), I’d love to see more use of citation. It doesn’t have to be compliant with any of the standards (APA, Chicago, etc): just tell me where you got your idea from so I can investigate more if I want to.

The basic question that keep popping in my mind and the book fails to address: "How do you know what you know?"

Take any claim. For example : "Many people set goals and then assume the path to reach them will require suffering and sacrifice. This is a recipe for failure." Why? If we know something about expertise is that it is acquired through deliberate practice and that is not a pleasant thing to do. Playing scales on a piano, training a repetitive move that is key for your sport, memorizing chess openings etc are all key for success on those activity. And they are ’suffering and sacrifice’.

If I can find a counter argument in a few seconds, the claim is not backed by any kind of evidence, and there’s no reference I can look for to satisfy my curiosity, my bullshit detector buzzes. Sorry.

Not that citation is the panacea, either. Most people I know agree that 90% of the published papers they read are horrible. Peer review (the traditional variety) is crushing innovation and make science look like a political game. But still… why are most bestselling books missing the most basic form of referencing where their ideas come from?

And one could count the millions of readers that Steve has as evidence that his stuff is good. But can it be that there are millions of people whose bullshit detectors are not in the same category as ours?

Should we aim to educate people so they look for better indicators of authority? And what are those indicators of authority? This is the question we’ll address in a future post.

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In this post, I want to review the basic tools for storing key indexed data and the pros and cons of each technology. Being productive is largely about using the right tools for the job and the numbered folders problem is no different. So below I’ll review what I see as the four basic options and how they can be used generally and for the numbered folders technique.

1. Plain text
   This is the mother of all data formats. Plain text files are portable (they work on any operating system, as long as you’re careful about end-of-line characters), open (i.e. non-proprietary), and therefore you can format and hack them any way you like. For these reasons and more, the experts at 43folders have discussed the appeal of plain text for productivity tasks at length.

   To make this work with the numbered folders approach, you might go for a simple comma-separated schema like the following:
   
id,title,start,status
1,My first paper,17/10/2007,Published
2,My second paper,17/10/2008,Concept

   You can then use almost any programming tool you can think of (including standard spreadsheet software) to manipulate this data and generate useful reports. For more sophisticated projects, plain text can also mean using XML, which uses strictly formatted text validated against a schema or document type definition. This is more than you need for numbered folders but hopefully it gives you an idea of the scope for plain-text data storage. Anything’s possible really.

2. Spreadsheet
   Most people use spreadsheets as the default option when playing with data and in many cases, this is a good way to go. I tend to think of spreadsheets as a sketchpad: it’s easy to enter information, do some quick calculations, and maybe make a few graphs. They often have built-in scripting tools as well (e.g. VBA for Excel) but in my opinion, these are dirty hacks and shouldn’t be used for any serious analysis.

   There are at least three problems with spreadsheets. First, they store their data in proprietary formats such as Excel’s .xls. This means is you want to edit the file, you need to have access to the software that will open it. If you’re using OpenOffice, the data format is open and so as long as you know how it stores data, you can still access your information any way you like. But it doesn’t entirely avoid the second point, that you’re meant to keep your data in the host application. By adding graphs and pivot tables and other features, you basically have to manipulate your data from within these applications which may or may not be acceptable to you. And the final point is that you are often restricted in how much data you can store in one file. More than 256 columns or 65536 rows in Excel 2003? Tough. (Things have improved in Excel 2007 but size limits are still a problem.)

   For the numbered folders technique, these issues aren’t really an obstacle. Your index spreadsheet is likely to be small and you can easily export the information to a plain text format if you really need to. But bear in mind that for any serious data application, you should not use a spreadsheet. In fact, if you even think your application might get big, start with a database.

3. Portable database
   Databases are completely different beasts from spreadsheets and while they may have a bit of a learning curve, they are ultimately the most scalable and powerful data storage applications. There are different types of database and by a “portable” database, I mean one where the data is contained in a single file that can easily moved from one computer to another. Microsoft Access is the prime example.

   There are two main reasons for using a database. One is when you have lots of data, i.e. millions of records, and a spreadsheet won’t cut it. The second is when you have structured data relationships. In these cases, you can apply the concepts of data normalization to split independent aspects of your data set. Let’s see what this means for the numbered folders approach.

   Suppose you have a data table to track your folders like the following:
   
id,title,date,status
1,My title,1/1/08,Concept

   Looks great but what if you want to add a status update? Your choices are either a) overwrite your current data:
   
id,title,date,status
1,My title,1/2/08,Drafting

   Or b) add another row:
   
id,title,date,status
1,My title,1/1/08,Concept
1,My title,1/2/08,Drafting

   Fine but suppose you typed the title wrong in the second row? Now you can’t sort by title and get the right paper!

   I personally use a database structure like the following to keep track of my numbered folders.

   

   Note that each type of data is confined to a unique table. This means I can then declare the links between the tables using the unique ids and not have to worry about data duplication and errors. Then it’s simply a matter of joining the tables and pulling out the data I need. As an example, the following query gives me the titles of all papers with the status of CONCEPT, targeted at the journal Energy Policy, sorted by descending date.
   
SELECT p.title FROM papers p
INNER JOIN journals j ON p.jid = j.id
INNER JOIN status s ON p.sid = s.id
WHERE s.name='CONCEPT' AND j.name='ENERGY POLICY'
ORDER BY p.duedate DESC;

   Getting the hang of writing queries and so on does take time. But once you’re used to thinking in the database way, there’s no going back really – it’s just too powerful.

4. Database server
   Last but certainly not least, the most powerful option is the database server. Here your data is stored on a computer and can be accessed from wherever that server is accessible, whether that’s keeping it only on your local computer, over an intranet or the entire internet. MySQL, for example, is a powerful open-source database platform which runs many of the web’s largest websites, containing many gigabytes (even terabytes of data). Portable databases, like Access, struggle at these sizes and with thousands of simultaneous requests for data.

   The two big advantages of database servers, besides the size thing, is that they are good at handling multiple users with complex permission schemes and they can support a wide range of software applications. So if you want your colleagues to read what projects you’re working on but not change any of the underlying data, you can easily control this. And this information can be presented via a php script generating an online report of your papers, analysed in detail using R or manipulated with a Java interface. Pretty much whatever you can think of, a database server will support it.

   A database server is overkill for the numbered folders approach, unless you need your information to be accessible from different locations. It also has a larger learning curve, as database servers typically lack the graphic user interface tools found for the other platforms discussed here. But with a database server, you can get your data from anywhere, access it using almost any modern programming language, and you’ll rarely have capacity problems.

Conclusion

I’ve covered a lot of material here but hopefully the message is clear: use the right tool for the job. If you’re generating gigabytes of highly structured data and sharing it with colleagues all over the world, then a database server like MySQL is the only practical option. However if you are simply trying to manage a few local projects, a tool like Access with its accessible interface and reports can be very helpful. A spreadsheet works fine too as long as there isn’t too much data and complicated relationships between the data. The table below summarizes the main features of each technique.

So getting back to the readers’ original questions about the numbered folders technique, I would say you’re probably fine using a spreadsheet. If you like maximum control, a text file is a good choice and shouldn’t get too unwieldy unless you’re really a prodigious writer. If you want to learn a bit about databases, then managing your folders is a perfect excuse to try out a portable database like Access. Just choose what works best for you and your needs.

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Thomson […] claims that Zotero is causing its commercial business "irr eparable harm" and is wilfully and intentionally destroying Thomson’s customer base. In particular, Thomson is demanding that GMU stop distributing the newer beta-version of Zotero that allegedly allows EndNote’s proprietary data format for storing journal citation styles to be converted into an open-standard format readable by Zotero and other software. Thomson claims that Zotero "reverse engineered or decompiled" not only the format, but also the EndNote software itself.

So, if a proprietary software gets an open source competitor that does beat it in many aspects, the best solution is suing it.

I’m an endNote user, mainly because I have already lots of text with endNote references. But endNote bothers me with new upgrades that are expensive, but add little. If you are a zotero user, I do hope you can help its authors to keep doing what they do: create outstanding software.

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In my last post, I looked at how intended learning outcomes (ILOs) can help focus your work and improve your productivity. Specifically, we saw how ILOs can be written to mesh with longer term goals, clarifying your immediate priorities and guiding interim assessments. This post will consider the last point: how ILOs can contribute to evaluations of your productivity.

The first tip is a pretty basic one. If you have a regularly scheduled performance evaluation, write ILOs that coincide with this time frame. The advantage of this is that you can clearly demonstrate your progress to your supervisor and together you can agree a specific workplan for the coming year. However before meeting with your line manager, you will need to do some serious preparation and this is where a technique called reflective learning can come in handy.

In the context of an academic environment, reflective learning is used largely as an informal assessment technique. Some of the feedback we receive can be formal: peer-review comments on our papers, feedback forms from our students, or performance reviews with our supervisors. But since academic research is such a self-directed activity, it is important that we use feedback from whatever sources we can find. Reflective learning is ideally suited to this type of self-evaluation.

The concepts of the reflective learning come from the Kolb cycle of experiential learning (see below). It basically says that we can learn from our past experiences, provided that we think carefully about the experience and apply these lessons to new situations. Therefore by reflective learning, I mean the process of actively reviewing your experiences and thinking about how you can improve things next time.

The Kolb Learning Cycle (reproduced from the Encyclopaedia of Informal Education)

Reflective learning assessments are most effective when done by sitting down with a paper and pen and carefully breaking the learning experience down into its constituent parts. Although there’s no fixed way of doing it, I find the following headings useful:

• Describe the learning situation. Start by giving as much relevant detail as you can about the learning situation (e.g. who/what/when/where/why). So if the assessment is to cover the last year’s progress, you might wish to highlight the main projects you’ve worked on, who you have worked with, the actual work environment (see these notes on the importance of situated learning) and so on. Try to be descriptive and avoid making any judgements at this stage about the influence of each factor. It’s a good idea to do this as a free-writing exercise, i.e. with no editing, as even little details can prove important later on.
• The outcome of the learning. Having described what you did, now describe what actually happened. This is where you will want to make explicit comparisons with your original ILOs. If you believe there were mitigating circumstances for not achieving a goal, make note of this but again, we’re interested primarily in description, not judgement, so stick to the facts.
• What worked well and what didn’t. Now that you’ve described what you set out to do and its outcome, use your critical judgement to assess what worked well and what didn’t. This stage, like the others here, can be done as a bulleted list if convenient.
• What will you do differently next time. The Kolb cycle demonstrates how the product of our reflections must be fed back into practice if it’s to be useful. Write down those specific changes in practice that will help you work more effectively. These items can then be worked into your ILOs for the coming year.

I mentioned earlier that you might like to use reflective learning in the context of preparing for an annual assessment. But as you’ve probably guessed, doing an assessment for a whole year’s work can be quite cumbersome. How do you identify the contributions of a single bad day to a whole year’s work? Therefore my final tip is to reflect often. Perfect opportunities for this are:

• After submitting a paper. How did the research and writing processes go? What would you change next time?
• After giving a presentation/lecture. Did the talk go well? Were there too many slides? Could you do more to stimulate interest in the audience?
• After an annual assessment. How did your preparations go well? Did you find that using ILOs helped track your progress? How might the meeting’s outcome change your ILOs for next year?

These shorter assessments are much easier as they don’t take long to do and consequently, they can easily become habitual. Keep the notes (e.g. in a research journal) and by the end of the year you’ll have a whole series of reflections and hopefully, demonstrated improvements. You can then use these to assess your own progress against your ILO goals, to demonstrate this progress to others, and to plan your future productivity goals.

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"Well, it's round, apple-y and …"

I want to introduce the idea of intended learning outcomes (ILOs) as a template for planning your productivity. Planning is a key part of the Getting Things Done (GTD) system but it’s perhaps an overlooked one. I think part of this problem is that it can be difficult to coordinate plans over the various recommended time horizons: career, 5 years, this year, this week, etc. ILOs help overcome this obstacle by clearly defining what you hope to learn and over what period.

An intended learning outcome is therefore simply a normative statement of your intended learning over a specific period. They are typically used in the design of courses, modules and learning sessions by helping students and teachers understand the scope of a particular lesson and how it fits with other content. For example, in a teaching situation, a set of ILOs might be:

By the end of this lecture, students should be able to:

• list three key features of apples
• compare apples and oranges
• assess whether an unknown fruit is an apple

This simple example shows the main features of a well-written ILO:

• they contain a clear timeframe.
• they should be SMART; that is, specific, measurable, achievable, relevant, and time-bound. Note for example that the first LO states exactly how many apple features students should be able to list.
• they should be phrased using an infinitive verb, chosen to represent an appropriate range of cognitive learning classes. Table 1 of this helpful ILO guide lists the various levels and some sample verbs. For example, to test surface-style knowledge-based learning you may wish to use verbs such as “list” or “recall”. However to test deeper understanding of a concept, higher level verbs like “evaluate” or “argue” can be used. (See here for more on surface versus deep learning styles).
• they should transparently support assessment. That is, as a teacher, you could easily design a test to assess how well you had taught the appley-lesson and similarly students would know exactly what was expected of them.
• Although not explicitly shown here, ILOs should also fit in with other objectives. They may for example be guided by overall course objectives.

Adopting ILOs for personal productivity requires very little modification. From the points above:

• Time frame: You still need to be clear about the time frame of your intended activities. In a later post, I’ll talk a bit about assessing your progress against ILOs but the early tip is to try and align the time frame of your ILOs to existing performance evaluations, such as your annual performance review.
• SMART-ness: They should still be SMART goals.
• Verbs and cognitive learning: This one may require some modification. Chances are you won’t find it very useful to list three new facts in a year’s time. However you may wish to divide your goals into similar easily assessed things, like “Publish two papers” along with more abstract things. Remember though you want to be specific: try and avoid statements like “Understand post-modernist geography” (bit of a losing battle that…) and go for something like “Write a two-page summary of major themes in post-modern geography” instead.
• Assessment: Again we’ll tackle this in a later post but try to keep your annual performance review in mind while writing your ILOs.
• Dove-tailing with other objectives: This is a key one. GTD advocates planning your goals over a series of different time horizons. If you write ILOs or other productivity statements for, say a five-year horizon, you should be able to use these to guide the creation and assessment of your “next-year” learning objectives.

In the next post, I’ll look at how to make the most of intended learning outcomes.

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You’re writing an email to invite a friend to meet at a local San Francisco restaurant that neither of you has been to.  You’d like to include a map. Today, this involves the disjointed tasks of message composition on a web-mail service, mapping the address on a map site, searching for reviews on the restaurant on a search engine, and finally copying all links into the message being composed.  This familiar sequence is an awful lot of clicking, typing, searching, copying, and pasting in order to do a very simple task.  And you haven’t even really sent a map or useful  reviews only links to them.

What I find impressive is the clarity of thought that could detect this as boring, repetitive and build a tool that obviates it. I’m not using Ubiquity (nor Firefox as my main browser) but this makes me consider switching.

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In an impressive display on coherence, Merlin Mann (43Folders) declares moral bankruptcy of the ‘productivity Pr0n’ cult. This is something I have discussed before on ap.com (post: rethinking life hacks).

Merlin has declared he wants a new direction for 43Folders; it was harming people more than helping, since the time readers spent on the blog was taking them dangerously away from their goals. I like his new motto:

Ask yourself: Why am I here right now instead of making something cool on my own? What’s the barrier to me starting that right now?

Will Merlin succeed? Or will he be captured by the gravitational field of cheap self-help advice? We will have to wait until the next episode of 43Folders: the saga.

>

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A reader writes:

“Dear Academic Productivity,

After having finished a phd project, I am starting a new research project together with a colleague. As a collaborative project requires, well, collaboration and coordination, I wonder if you or perhaps your readers happen to have any good advice, both on best practices and concrete suggestions for web-based collaboration tools.
Some examples of our needs:
* As we’re studying public policy change, the bulk of our empirical material consists of various sorts of text documents (official reports,  government bills, parliamentary minutes, media reports, interview transcripts etc.), some of which are available online. I figure we need a searchable database just to keep track of it all; ideally, it should allow us to archive and annotate full-text documents.
* …or even more ideally: a web-based CAQDAS package. Are there any?
* Reference management: Awaiting an online collaboration version of Zotero, what’s the best way of managing references?
* …and/or sharing reading notes and lit reviews? Now we’re just pouring our reading notes into a blog, which is not an optimal solution.
I’m aware of the basic options available (blogs, wikis, project management software etc), but as they are all aimed for other purposes than research, I’m curious to know what tools and practices other researchers actually use.”

For those not in the know (i.e. myself we recevied this email), CAQDAS is an acronym for “Computer Assisted Qualitative Data Analysis Software,” which can be used to search, organize, categorise, and annotate textual and visual data.

I have asked others the same question as Mr A. Reader, and as of yet I have not found a single tool that captures the needs of academic research groups. I also haven’t encountered any academic research groups that make comprehensive use of  online tools, so I would be interested to hear from our readers in the comments.  

One tool that might fit the bill is wikindx. It allows shared references and annotations and uploading of documents, though you would need to host your own server for its database. New kid on the block is Mendeley, which we should be reviewing soon. It creates a searchable index of your PDF documents, extracts references from them, and has an online shareable reference management system as well. In the above case, if you converted all your supporting documents to PDF it might fit part of the bill.

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Google is going to release in the coming hours what looks like a revolutionary new entry in the browser arena: Google Chrome. The GUI design and engineering effort behind Google Chrome looks impressive. What is more, Chrome is going to be released under an open source license.

In spite of the sugary rhetoric (“it’s in our interest to make the internet better”– yeah, thanks Google), is this going to be the ultimate Firefox killer? And how will this affect the landscape of open source development altogether?

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Precisely two years ago, Shane posted our first mission statement. Simple and ambitious as it was, that post pretty much sums up why we are still here.

There’s been a lot of work behind the curtains, lots of lessons learned (“we shouldn’t just mention sex in the titles whenever possible. We should also try to mention alcohol”) and a few, intense epiphanies (“A mincer in 3d perspective. On top of everything, half-way into the mincer, a brain: it must be very recognizable”). After 2 years, we are a 2.5k subscribers strong community and it’s time to celebrate and finally get more productive drunk.

A big thank you to all our readers, guest contributors and imperturbable partners for making this blog happen.

[CC-licensed geekcake courtesy of freakgirl]

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But what do you do if you use LaTeX not Word to write your papers? Traditionally BibTeX comes to rescue. It uses a formatted plain-text file to store references and with the custom-bib and natbib packages, creating citations and bibliographies is fairly painless. You can even use a graphical editor like JabRef to help manage your BibTeX database.

However there can be problems when collaborating with people who use Word. How do you share your BibTeX references with EndNote users or vice versa?

My approach is to use EndNote as the master database for managing references. This lets you easily integrate with Word if necessary and you can still take advantage of the connection functions to retrieve references from your university’s library or other indexing services. However to share references between EndNote and LaTeX, you’ll need to follow these steps:

1. Set EndNote to use Unicode. Go to Edit > Preferences… > Display Fonts and set both display fonts to a Unicode font, like Arial Unicode. EndNote already uses Unicode internally; this just makes sure that what you see is what you get.
2. Label all your references with a unique identifier. You must use the “Label” field of each reference for this. I tend to use something like “Smith2000″ as these labels should be intuitive for later citation within LaTeX.
3. Export the references using the BibTeX Export style.
   1. Activate the export style. Edit > Output Styles > Open Style Manager…. Then tick the BibTeX export style. Close the style manager.
   2. Select the BibTeX export style from the style drop-down at the top of the main window.
   3. Select all references in your library. Right-click on the reference and select Show All References if available. Click on any reference and press CTRL+A to select all references.
   4. Export the references by selecting File > Export… and choosing a destination. This should be the same directory as your LaTeX source file. By convention BibTeX files have a .bib extension so you might like to call your file something like refs.bib
4. Tell LaTeX to use Unicode. Do this by adding \usepackage[utf8]{inputenc} to the preamble of your LaTeX document. This will tell LaTeX to process any accented characters in your main file and reference list correctly. Incidentally if you need to edit your exported *.bib file at any time, make sure you use a Unicode compliant editor like Notepad2. Otherwise any accented characters in your references might get messed up when saving the changes. Within the main LaTeX document you can still use LaTeX code such as \"{u} for ü or, if using a Unicode compliant editor (i.e. NOT the otherwise excellent TeXnicCentre), just enter the character directly.
5. Use natbib and cite your papers as normal. Follow the instructions for using the natbib package and cite your references using the labels added above, e.g. \citep{Smith2000}, and something like

   \bibliographystyle{plain}
\bibliography{refs}

   to generate the bibliography (where refs refers to the refs.bib file saved in the LaTeX source directory as noted earlier and plain is a BibTeX style file – see this page for more info.

6. Compile as normal. i.e. run LaTeX, BibTeX, LaTeX, LaTeX. See the previous link for details.

If you have a lot of references already in EndNote, it can take some time to set up the labels properly. However once you start using the system, it’s easy to maintain; you can add references, label them and export to a new BibTeX library in seconds. I should also add that this is mainly a Windows-specific fix; perhaps someone else can shed some light on what to do for a Mac. (If you and your collaborators write exclusively on Linux, then lucky you. No Word to worry about!)

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By the way, Nielsen knows what he is talking about; he wrote the standard text on quantum computation the most highly cited physics publication of the last 25 years according to Google Scholar.

The first example he uses is Nature’s open peer review system:

Inspired by the success of amazon.com and similar sites, several organizations have created comment sites where scientists can share their opinions of scientific papers. Perhaps the best-known was Nature’s 2006 trial of open commentary on papers undergoing peer review at Nature. The trial was not a success. Nature’s final report terminating the trial explained: There was a significant level of expressed interest in open peer review… A small majority of those authors who did participate received comments, but typically very few, despite significant web traffic. Most comments were not technically substantive. Feedback suggests that there is a marked reluctance among researchers to offer open comments.

His second example is the usual suspect: wikipedia.

Seigenthaler has described Wikipedia as "a flawed and irresponsible research tool".

Nielsen marvels as scientists missing the point of wikipedia:

[...] You’ve bought into the current game, and take it for granted that science is only about publishing in specialized scientific journals. But if you take a broader view, you believe science is about discovering how the world works, and sharing that understanding with the rest of humanity.

I’m thinking lately that Thompson research (Web of science, -WoS- endNote) have a monopoly on academic journal access, and are making millions.

They have partnerships with journal publishers; those charge universities, and for the general public it’s ‘please insert coin to continue’ ($20-25 per article!). These are articles we write, and we don’t get paid a dime. Plus, we actually benefit if the general public has access to them.

Even though most blogs are so-so, give an amateur access to the same journals we use, and lots of motivation, and he may come up with original research rivaling the one we do at the ‘walled garden’ of the universities.

Enter Google scholar and zotero. Not that far from Web-of-Science/endnote. Open. Accessible to anyone. Sometimes better. For example, Zotero does things that endnote cannot do, most importantly capturing references from all kinds of websites such as amazon. Google scholar offers citation counts that may be more accurate than the ones in WoS; they do not agree (at all) with the ones that WoS produces, since for Google scholar, an article published online is still one citation, whereas WoS looks at published journals only (the establishment).

What if all articles were accessible to everyone? (have you read ‘the right to read’ by Stallman?):

For Dan Halbert, the road to Tycho began in college—when Lissa Lenz asked to borrow his computer. Hers had broken down, and unless she could borrow another, she would fail her midterm project. There was no one she dared ask, except Dan.

This put Dan in a dilemma. He had to help her—but if he lent her his computer, she might read his books. Aside from the fact that you could go to prison for many years for letting someone else read your books, the very idea shocked him at first. Like everyone, he had been taught since elementary school that sharing books was nasty and wrong—something that only pirates would do.

I just came back from the library here at Max Planck. All the good books are taken and since there’s no deadline to return them, I"ll have to bother my peers to get the book from their office. I asked if we could have an electronic version of these books, and the answer was that the publishing companies didn’t provide that. I wonder why. And of course they must be investing enough money on lawyers to fight google’s book project to feed a few small countries for years.

What is happening is that more often than not, when something is not accessible with a click or two, I just don’t bother reading it. And I love the feeling of a paper book; but I know that getting it is more trouble than it’s worth most of the time. And I’m on a good institution. With lots of money to have an up-to-date library. What happens to the laymen out there in the real world? Well, they seem to be doing the same systematic biased reading, but at a larger scale. If something is not online, they won’t read it. That includes the ‘insert coin to continue’ papers published in traditional journals; when you are not within the walls of a fortress (education institution), you just don’t read it. I’m really curious about how many of our papers publishers sell at that special price of about 25$ a pop.

Are normal people outside the garden walls of academia missing what’s inside? Not fully. Today you can teach yourself anything. I have a friend that designed and built his own house without hiring an architect; everything he needed was available online. He learnt enough about structures, security, materials etc online, reading sites and asking around in forums. Even the hands-on work can be learned by asking construction workers, or just looking at them.

But I do think that full-access to academic publications by anyone may have a huge impact. For a start, it may increase the average quality of blog posts, something I’d really welcome :)! It would also have an effect on how we write papers. If we knew that the general public (not only those hard-core into our filed) could potentially read our paper, I’m sure our writing styles would be a lot more palatable. And with time, some brilliant scientific contribution could come ‘out of a garage’ (instead of a well-known academic institution. The garage phenomenon happens everday with startups; why not in science? Of course, if you need tools out of the ordinary, like a particle accelerator, to do your work, forget it; but there are lots of expensive things people buy in their garages to foster their hobbies (Hi-fi equipment, parts for a sailing boat, etc). I wouldn’t be impossible to conceive someone buying scientific materials for their hobbies, like lab rats or stereotaxic instruments if you are into neurosciences ). For example, one of the top participants on the Netflix contest is in fact a psychology afficionado that doesn’t work under the dome of any university.

Because, let’s be honest, sometimes the university environment is not the most condutive to great work. If we could create an ideal intellectual environment in a living room or a garage, bypassing paperwork, teaching load, and other obstacles, it could be a lot of fun. And productive. In fact, it has happened. The legendary example is the Institute of Advanced Study (IAS). The IAS, where von Neumann’s machine was built, was basically a dorm near Princeton, but not officially affiliated with Princeton, started by some philanthropists who wanted scientists to stay there, have their lodging and food paid for, and get their science on.  Big time. Einstein was one of the first residents, as were von Neumann, Kurt Godel, and J. Oppenheimer.

Free access to publications and, what is more important, a stigma-free scientific society that accepts data and contributions from people working out of a garage, could make this possible.

Why the open science ideal is not happening

Here’s Nielsen’s main hypothesis: the old system of paper journals and snail-mail letters to reviews worked to incentivize sharing. However, in modern times the effect it has is just the opposite:

This is ironic, for the value of cultural openness was understood centuries ago by many of the founders of modern science; indeed, the journal system is perhaps the most open system for the transmission of knowledge that could be built with 17th century media. The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.

Some barriers are social; of course those in the establishment (i.e., journal editors and publishers) would be reticent to change. And economists would argue that no matter how easy it is - from the point of view of technology-  to disseminate information, people still pay for it gladly so there’s no point of giving it away for free. In fact, you should offer something in exchange for those people who are now getting paid for their efforts if you want them to support the ‘extreme open science’ movement. But here’s the catch: the authors are not really paid, so they would be all for it. The intermediaries (book and journal publishers, database creators, etc) are the ones who could have an interest in blocking an open science movement; but not the authors. In fact, in terms of money we get nothing for journal articles and next to nothing for books (With textbooks being the exception).

How the ideal world of open science looks like

Nielsen presents a few examples of working tools. Since 1991 physicists have been uploading their papers to the arXiv, often at about the same time as they submit to a journal. The papers are made available within hours for anyone to read.

Some fields work very well under a fully open paradigm already. The example he uses is programming. Some people would expect the level of shared code to be so-so, but this is not the case. A walkthrough the forums will show that top programming minds are sharing their ideas and having a kick out of it (it buids ’street cred’).

Making all information not just human readable but also machine readable; there are people wanting this left and right; some don’t even know they want it, but will once they see it at work. I’ll post more about this as my ideas develop. Working on semantic web issues makes for a good amount of thinking on this line.

Nielsen proposes friendFeed as an interesting place where barriers of entry are low, although he warns that most scientists won’t have the time for microblogging. He follows about 200 people he ‘knows’, and some collaboration could easily come out of friendFeed. For example:

Suppose that for a particular problem, Alice estimates that it would take her 4-5 weeks to acquire the required expertise and solve the problem. That’s a long time, and so the problem is on the backburner. Unbeknownst to Alice, though, there is another scientist in another part of the world, Bob, who has just the skills to solve the problem in less than a day. This is not at all uncommon. Quite the contrary; my experience is that this is the usual situation. Consider the example of Grossmann, who saved Einstein what might otherwise have been years of extra work.

This is the power of open science: social networking on steroids! It’s really true that in my experience at least, we park a problem because one of the steps is not trivial to do… only to learn, maybe years later, that this step is a solved issue in a neighboring discipline that we ignored. Better communication and networking (like in the fictional Alice example) would definitely fill this hole.

Another of Nielsen’s crucial points is in the line of our previous ‘attention economy’ posts: "Expert attention, the ultimate scarce resource in science, is very inefficiently allocated under existing practices for collaboration." This is a great topic for another blog post. If anyone wants to take it and run with it, please do (behold the wonders of a blog!).

A general reminder: Ap.com is an open blog. If you have something you want to discuss with the ap.com readership, feel free to make a post. It doesn’t have to be earth-shattering (as you see, I post both long and short things) to be interesting.

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By the way, is any of you keeping any kind of log of where your time goes? Or running any application like rescueTime?

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I was recently involved in a project where I needed to examine some research literature on learning and memory. In particular, I was investigating the spaced learning effect on memory. Memory research has been central to psychology for as long as  psychology has existed as an academic discipline, and the spacing effect (also known as distributed practice) has been studied for well over an hundred years. Studies of the spacing effect have shown that when you space learning over separate learning intervals, long term retention is normally much higher compared with the equivalent amount of training from a single or “massed” session. This effect is robust across different time scales, different kinds of learning, and is even true across different species. Another effect, not quite as well studied, is the testing effect. Repeated testing over time is also beneficial for learning, mainly because testing involves effortful memory retrieval, which is advantageous for the formation of long term memories.

Spaced learning (and testing) is to be recommended for the autodictact, but the purpose of this post is not to espouse the virtues of this method of learning, Instead, my main aim here is to have a moan about the non application of this method in education. Most textbooks make use of the repeated testing technique, by the use of quiz sections at the end of each chapter. But it is still relatively rare to make use of spaced testing, where material from previous chapters is also included in an end of chapter test. In higher education institutions (though I speak mainly from experience of the British system), the typical format for teaching is for students to be taught in a single semester, where each week a new topic is introduced, and the course is assessed by a single essay or exam at the end of the course. This design encourages the cramming technique, beloved of procrastinators, where vast chunks of the course syllabus are memorised in a mammoth session the night (and morning) before an exam. This is a valid strategy for investing the minimum amount of time to reap the maximum reward in marks attained, but is a poor technique to maximise long term retention. Of course, conscientious students can use spaced learning techniques. And by their very nature, some disciplines more than others require a form of spaced learning and recall. For example, higher maths involves recall and use of basic maths, whereas the recall of Shakespearean plays is typically not essential in the study of Dickens.

Though there are an many exceptions, it seems that an important part of the design of educational systems is that of convenience. The business of education, is increasingly, a business. The easiest way of administering courses is by the single semester, single assessment model. It means less marking, and less time spent running a course. This makes it popular with academics, and with most students too. Students can learn the material for a course, get the grade, and then forget about it, knowing they will not be tested again. However, if one were serious about taking the spacing effect seriously, then one might design courses that spanned several years, with testing throughout those years. However, I can’t palm off all the blame onto educationalists and academics taking the easy route. Part of the problem lies in the difficulty in applying cognitive psychology to education. Cognitive psychological research typically has not provided the kind of robust evidence for benefits that allows educationalists to take such principles as spaced learning for fact, and worth the effort to implement. In the instance of spaced learning, a research group led by Hal Pashler have undertaken research that straddles the theoretical and applied research border, and are pushing for adoption for the application of spaced learning in pedagogical contexts. A short summary of their work can be found here, which provides further information and some references.

,

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This part is particularly moving:

Perhaps the tragic life of the French mathematician Evariste Galois (1811–1832) best illustrates my argument (Singh, 1997, pp. 210–228). Despite the fact that he died at age 20, Galois made a large number of significant contributions to mathematics. (His work was integral to Andrew Wiles’ celebrated proof of Fermat’s Last Theorem in 1994.) Galois was involved in an affair, and the woman’s fiance challenged him to a duel. The night before the duel, Galois stayed up all night and wrote down all of his mathematical ideas on paper. (It is due to these notes, written on the last night of his life, that many of Galois’ ideas survived to the posterity.) From  other comments written on the paper, next to a series of mathematical notations, however, it is clear that Galois spent the night, intensely thinking about the woman over whom he was to have a duel the next morning. Something compelled this young man of 20 to produce so many brilliant mathematical ideas in one night and then go to a duel the next morning, ready to kill or be killed over a woman. It is my contention that the same psychological mechanism was responsible for both.

So _IF_ Kanazawa is right, other than staying single and surrounded by desirable partners, what can one do? Well, maybe sports are a good way to pump some testosterone in. It makes sense: many people I know, myself included, feel more productive after exercising. More so if it involves any kind of controlled risk or competitive activities.

Another good thing for testosterone levels: dancing (with a partner).

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remember that solitude has always been, in all the history of mental achievement, a requisite for great work. (…) The great poems written in lonely garrets—the masterpiece paintings conceived by the artist amid the fields—the divine harmonies first heard by the musician communing with the stars—the sublime oration which first stirred the soul of the orator as he tramped in the forest—all attest that the best comes to man when he is alone.

This is interesting. I always found that some people complained I spent too much time in front of the computer… maybe that is what it means to be lonely. The funny thing is that nowadays it is a lot harder to be alone. Maybe alone is just a romantic surrogate for ‘uninterrupted’ I don’t think the mood implications of lonely help in any way, unless you are producing poetry, music or plastic arts… but certainly not papers.

So, do you feel lonely? Do you seek time apart from ‘the world’? It’s true that most academics’ social lives suck (not mine ). But what is the right causal path here? Do we kill our social lives so we can get ‘in the state’ more often and be productive? Or is it the other way around: we are ‘in the state’ so often that social relationships just die off?

One thing is true: having an internet connection provides constant, second-class (in the sense that it’s not as rich as real-life interaction) social stimulation; being in front of the computer is not a certain way to achieve ‘the state’ (lonely or not). But maybe a good solution is to concentrate a lot (no surrogate activities, like me writing this blog post while I should finishing up my paper), and then get a lot of first-class, ‘live person’ social action.

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