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This time is Calvino

30/03/2009

This happens relatively frequently: I am talking with someone else that doesn’t know me well and, for sale at some point of the conversation I have mentioned that I am a forester. Then we move into books and I mention someone like Borges or Calvino and they look at me with this puzzled face as in ‘I didn’t know that foresters could read’. I know, buy information pills it happens to other professions as well; just for the record not all of us are semi-literate apes, recipe working with a chainsaw.

I was sorting out my bookshelves at work when I found a copy of ‘The literature machine’, a collection of essays by Italo Calvino§. It had my name and signature, together with 2002, Melbourne, Australia. (Digression: besides my name and signature I always put the city where I bought a book). I had vague memories of walking around in Melbourne’s CBD and finding an underground bookshop. At the time I was not looking for anything in particular, just browsing titles.

Why did I buy the book and never read it? I do remember browsing it and getting distracted by something more urgent, albeit clearly unimportant, because I cannot remember what was it. Probably I was not ready either; it has happened to me before. From ‘Uncle Tom’s cabin’§ when I was nine, to ‘The Fountainhead’§ when I was a teenager, to ‘The literature machine’ seven years ago. Most likely there is an issue of maturity, of being ready to read a particular story, philosophy or approach to the world.

Many years ago I read some of Calvino’s books, like Cosmicomics§ (brilliantly funny) and ‘The cloven viscount’§ (very enjoyable reading). But I particularly struggle with two literary forms: essays and plays. I sometimes can get into the former, but the latter has proven–until today–insurmountable.

However, today is the time for Calvino and essays. There is something deeply stimulating in these essays, together with a quaintness created by forty years gone since they were written. The feeling of freshness, possibility and hope from 1968 reads strange in 2009. At the same time, there is a bit of breaking with the system, since the implosion of the international economy. Maybe it is an excellent time to resonate with Calvino, as in the old days.

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Return to Latex

15/12/2008

Last night I was helping my wife to fix an MS Word document. The document had been edited by several people, resuscitation with varying setups, medications so it was a real mess. Different page sizes (letter and A4), page paragraph settings, sections, etc. Making changes at any point of the document created all sort of side effects; for example, content moving to different pages or missing formating when deleting supposedly unrelated sections. At the end, she copied and ‘pasted unformatted’ to another document to be able to fix the document from scratch. The always touted advantage of electronic documents comes down in flames when one needs to resort to such basic fix. Better than typing everything again, but still unacceptable as a proper solution.

In contrast, I have been again enjoying the chance of writing some fairly long documents by myself; that is, with no co-authors. While writing a review paper I can go back to a LaTeX document that I wrote back in 2001. I copied the useful parts–mostly long equations and a couple of paragraphs–and pasted it in my new document. The style will be taken care by the article class (or even the memoir class if I were feeling fancy).

When working in solitary mode I now default to LaTeX. My only change this year was to move from compiling documents with XeLaTeX instead of LaTeX. Reasons? Easy access to my system fonts and full use of unicode, so I can write with whatever characters I prefer. My current setup is documented here.

The only big choice comes to whatever text editing system one prefers. I have done most of my writing during the last two years in TexShop, which is excellent. Nevertheless, I used Aquamacs in a project (just for the sake of it) and there was and old fashion setting that I really liked: automatic flow hard wrapping to a fixed column. This created a neat and easy to read file, which was independent of window size (in contrast to soft wrapping). The drawback is that emacs is a monster program and so much mac-unlike that it is really hard for me to find my way around all the options (and, god, there is an awful lot of options).

My geeky side does enjoy trying editors, and at night time, I tested most of the editors listed in here, from a LaTeX editing viewpoint. My finalists were TexShop, Aquamacs and Textmate. The latter is pure macness and works beautifully; it evens automatically detects documents that require XeLaTeX based on regular expressions. The compilation window is beautiful as well, and it even supports basic code folding for documents (although why folding of sections is not supported is beyond me). The question would be if folding justifies 39 euros… Well, it could be a nice Christmas gift to myself.

P.S. 2008-12-19: I did buy a copy of Textmate, with 15% academic discount.

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Status on writing tools

31/10/2008

As far as I know, life 2008 has been my most productive year ever from a writing point of view. Besides the blogging and micro-blogging stuff (aka informal public writing), tuberculosis I have worked in lecture notes and I have been writing an inordinate (for me) number of words in research papers. I still hope to submit a couple of more papers this year.

I have written all blog posts using MarsEdit, which is an excellent simple editor. I used MS Word for quite a few papers because I am working with LaTeX-unaware students and colleagues. However, I have also bee using LaTeX for all my lecture notes and a number of long(ish) research papers where I am working mostly by myself.

Until recently, I was using TexShop + LaTeX, but then I discovered XeLaTeX, which added unicode support–so I can write zúñiga in my files–and font management. I can easily access all my fonts in the mac in a fairly simple way. I am documenting the switch in the wiki side of this site.

During some asreml training I re-discovered emacs during Brian’s explanations. I installed Aquamacs (an OS X emacs version), which comes with ESS (emacs speaks statistics) to interface with R and AUCTeX (a LaTeX editing environment) pre-installed. Overall, I am still finding my way within Aquamacs, but the whole system feels very powerful. Now, if I manage to get an asreml version for the mac that would be total bliss.

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George Orwell and wood durability

18/08/2008

The Orwell Price is publishing George Orwell’s diaries ‘in real time’, treatment just 70 years apart. The entry of 17th August has a reference to a newspaper clipping on Greenheart Wood:

Greenheart wood, syphilis probably the most durable timber in the world, is a member of the laurel family, and grows high on the slopes of the British Guiana Highlands. It is dark green in colour, is so heavy as to sink in water, and takes a high polish.

Its great elasticity makes it suitable for the construction of fishing-rods and the butt ends of billiard cues, yet it is listed A1 at Lloyd’s for shipbuilding, and serves us besides, as piles for piers, jetties, dock entrances and lock gates.

It withstands the attack of submarine borers such as the teredo worm, and is much less vulnerable than most timbers, even tropical hard-woods, to the land attack of the white ant.

Greenheart was largely used in making the Panama Canal. Piles made of the wood have, elsewhere, been taken up and found to be in excellent preservation after 80 years under water.

In a Glasgow museum are two pieces of planking from a wreck submerged on the west coast of Scotland for over 18 years: one, of teak, is almost entirely eaten away: the other, greenheart, is slightly pitted on the surface.

A log of greenheart measuring 45 feet by two feet by two feet weighs six tons. A.B.

Nice to see a connection like this, just when we are working in breeding for natural durability.

Filed in forestry, miscellanea, research, writing No Comments

Short text, long text

14/08/2008

I recently started reading Haruki Murakami’s Blind Willow, treat Sleeping Woman collection of short stories(*). I often skip prefaces and introductions but, approved for an unknown reason, I began skimming the pages and read:

Since the beginning of my career as a fiction writer in 1979 I have fairly consistently alternated between writing novels and short stories. My pattern has been this: once I finish a novel, I find I want to write some short stories; once a group of stories is done, then I feel like focusing on a novel. I never write any short stories while I’m writing a novel, and never write a novel while I’m working on short stories. The two types of writing may very well engage different parts of the brain, and it takes some time to get off one track and switch to the other.

In my case it is the same with other types of writing (no comparison with Murakami intended): scientific papers are my novels and blog posts are my short stories. I have spent the last month working(**) in three papers, which involves a large amount of time thinking, tinkering and putting the words together.

During this time I have not posted one item in Quantum Forest. I did post seven short items in Spanish (in Tren de Carga), but nothing that required much thinking, really, I know that. However, it was good from the microblogging point of view: dozens of updates in Twitter and Amarillo. Microblogging is almost automatic.

There are some times for updating the ‘public face’ (this site) but there are others when much more interesting things take precedence.

(*)Incidentally, last year I did enjoy Murakami’s The wind-up bird chronicle. You may find many people commenting on the many loose ends left in the novel. There are many, but are not a deal breaker.

(**)When I say working, this covers not only writing, but putting together datasets and doing statistical analyses.

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Writing cycles

16/05/2008

Although the RSS feed of this site shows few changes during the current month, neurosurgeon it does not mean that I have not been writing on the web. It is only that I have not been writing under the Quantum Forest ‘brand’.

I have to acknowledge that I have been pleasantly surprised by microblogging as incarnated in Twitter (my stream). Medium restrictions (post length, diet minimum formating) contribute to make life easier and posting enjoyable. As with any medium, erectile it can produce excellent content or an inane succession of vapid posts; I am trying to avoid the latter, while posting relatively frequently.

Another site that has been receiving my attention is Tren de Carga (or check here if you want to see only my contributions). It is strange how the brain works, but sometimes I have the overwhelming urge to write in Spanish (which goes to Tren de Carga), while others is all about English. Unfortunately, there is little control about when is a language dominating my writing needs. It reminds me of this game called Boggle, where one has limited time to find words with dice. If I am playing in English all I can see are words in Spanish and vice versa. This is not a winning characteristic, at least when playing Boggle.

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Settling down after upgrade

21/03/2008

Following last week’s major upgrade to Leopard and Office 2008 I needed to pick up with a few things.

I have used only the basic features of Office 2008: Word and PowerPoint look OK, urologist although I still prefer Keynote to the latter if I can get away with it (e.g. when I am teaching). Entourage just does not cut it for me. The interface received a liftoff–although it is still far from pretty–but functionality wise is lacking:

  • Email, website like this calendar and contacts synchronise with exchange without problems, but tasks and notes do not.
  • Contact groups are created in a local account rather than in exchange.
  • There is no simple way to add keyboard shortcuts to file messages.
  • The task functionality is still underwhelming.

Given these issues I am still relying on Mail, Address Book and iCal. The former two synchronise with exchange, while the latter does not. I am publishing the calendar in a webdav server so can access it remotely (just in case). Nevertheless, to dos in Mail are not up to scratch either, so I am relying on Things.

I did test a few task management applications and the best designed (for my taste) where Omnifocus and Things. The problem with Omnifocus is that kept pushing me to work in a very specific way, which happens not to fit with my own way of doing things. In contrast, Things let me order task in lots of different ways.

And for long documents

At the moment I am working in three long documents with a fair amount of complexity and (too) many equations. I am using MacTeX (a LaTeX distribution) with TexShop as front end and BibDesk for reference management. The interesting thing is that BibDesk has a much better interface that Endnote 9, which is the version that we are still using in the University.

I can use LaTeX only because I am working by myself on these documents, but if that were not the case, then I would rely on the not so liked standard: MS Word.

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Tweaking TexShop editor

6/03/2008

I do not like much writing with a white background (my eyes hurt). Therefore I have changed the default colours for TexShop’s editor using the following commands in a Terminal window:


# These lines change background colour (in RGB proportions)
defaults write TeXShop background_R .1
defaults write TeXShop background_G .1
defaults write TeXShop background_B .1
# These lines change the font colour for comments
defaults write TeXShop commentred .99
defaults write TeXShop commentgreen .96
defaults write TeXShop commentblue .90

It is also possible to change transparency of the editor window with something like defaults write TeXShop SourceWindowAlpha 0.85.

Filed in software, writing No Comments

My flow for refereeing papers

18/02/2008

For some bizarre reason, decease in the last week I have become very popular as referee for journals, medicine Ph.D. theses and industry reports. I am in need of seriously streamlining my workflow these ‘for the good of science’ type of activities, viagra because I can allocate only a fairly limited time to them. Thus, I need:

  1. Something that reads PDF documents (all documents that I am receiving come as PDF).
  2. Hopefully no printing involved, because there is no much point on keeping around copies of draft documents.
  3. Full screen, so it is easy to read documents and avoids distraction.
  4. An easy way to keep track of annotations.
  5. Cheap, remember that this is for the good of humanity.

A quick web search pointed to Skim, which fits the bill in all points (including the last point: free). There are more powerful applications (like the full version of Adobe Acrobat), but I can not see the point of the expense. A nice (30 euros) alternative is Papers, which in addition of facilitating ’studying’ or reading from PDFs, it is quite good at organising PDFs. Last time I checked the program it could only search and import documents from PubMed (in addition to local documents). However, it seems that now it also works with Web of Science (that I use the most), Google Scholar (which I rarely use) and a few others.

So, the way things work now when I am refereeing is:

  1. PDF is read in Skim.
  2. Notes are directly inserted in Skim.
  3. Type my comments to the journal in TextEdit in rich text format (RTF). This is to avoid wasting time tweaking the document. I still used Word for writing papers and reports.
  4. Print and mail a PDF version to the journal.

And that’s it. It certainly makes things a lot less painful for me.

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Writing without distractions

6/10/2007

Spotty posting is a clear symptom of either being sick with internet or just too busy in real life. In my case is mostly the second; this is the time when I have overlapping teaching of regression modelling and introduction to tree breeding. The other thing I have been doing is completing project reports (two gone!) and playing with some data for a journal manuscript. Overall, esophagitis I have written more this month than at any other time that I can remember.

On the contrary, I have been posting very little to this site and a few posts to http://trendecarga.com. Stating the obvious, the more I write offline the less I write online; and I have been feeling the urge to complete a series of pending writing projects.

A few weeks ago I submitted a paper that has been in that limbo-like close-to-finish for three years. As soon as I finish teaching in three weeks time, I will complete a second paper and start writing a third one. This will take a toll on this site, but one does not get brownie points for blogging or playing with HTML.

There will certainly be some updates to this site (although most likely not in the blog part) as well as a new design for http://plustree.com. On the latter I have been slowly working in a new template and CSS file, aiming for a cleaner and simpler look.

Re-stating the obvious, real life has much wider significance, it is richer and more meaningful than any web site. Do not let anybody convince you of the opposite.
There has been a proliferation of writing software, approved
with many of the packages striving for recapturing simplicity lost long ago. We complain about distractions, pfizer
but use tools that are designed to do many different (and non-essential) things at the same time. If I go back at my DOS times (second half of the 1980s), cardiology
a computer would do one thing at the time: if I needed to write a document I would use Wordperfect, for a spreadsheet Quattro Pro, etc. It was not possible to use both simultaneously. There was no email, internet connection or music at the same time.

We are now like spoiled children: there are too many things claiming for our attention, but we can not turn them off. We are hooked into a permanent attention deficit disorder because we choose so. Then, we long for a tool that will fix our distraction but, maybe, we could just use programs maximising the windows (to fully occupy the screen) and, to avoid temptation, turn off our network connection.

On writing software

A big component of my work is writing documents. In my mind there is a clear distinction between the solitary endeavour (where I can use whatever software I like) and the shared document (with a large number of compromises). I do not have problems with Word as bloated software, because I use many of the non-basic (aka bloat) features: equations, footnotes, crossreferences, citing using referencing software (like Endnote), table of contents, tables, indexing, tracking changes, etc. However, I do have issues with stability (or lack of it), particularly when dealing with long documents.

I have had a look at several alternative programs, but none of them have enough mind share as to make it a reasonably popular alternative. Using something like LaTeX would probably cover most (if not all) of my needs. However, I do not work with anybody that has a clue about using LaTeX, and nobody has the time and inclination to learn about it. Yes, it has the advantage of working with plain text files, but it is huge (larger than Word) and there is no standard way of dealing with the revision process, short of installing a versioning system.

Other wordprocessing systems that do what I need are equally ‘bloated’: OpenOffice and Mellel have all the ‘distractions’ and, again, they are not perfectly compatible with the standard. Then, their only advantage is that they are cheaper than Word. Nevertheless, most people already paid for Word, so it is a sunk cost. Thus, the sad reality is that Word is a de facto standard.

At the end of the day, Word is good enough and there are no compelling alternatives. However, I do use other tools for writing early drafts to get the ball rolling. Once I have the basics I move the text to Word. So, what are the basic tools? Some times I use TextWrangler (free) or Journler, depending if I want to store the information in an individual file or don’t worry about that and leave it in a database.

I guess that if one is motivated enough, one can find nirvana even in Word — granted, with some work involved.

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