Quantum Forest logs are written by Luis A. Apiolaza in Christchurch, New Zealand and powered by TextPattern.

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What's up in research?
Published Saturday July 8, 2006 · Permalink

It has been a log time without writing about research. New country, new city, new job. In addition, consulting and professional service. Last but not least, family and friends come first: the end result is very little time to blog and even less for writing about research.

So, what am I doing at the moment? Simple, trying to figure out areas where I am not hitting diminishing returns too quickly. For example, estimating two hundred variance components is too rich, if we can do the job with ten. The practical return from all the additional works tends to zero: we are not making much of a difference. So, what’s the point? Yes, I can publish that, but who cares?

From a practical point of view, the real issue for me is on what is affecting competitiveness in a big way. Forestry is a long term endeavour, and the longer the rotation the higher the risk. From that point of view, extending rotation because radiata pine wood quality is not good enough borders on the stupid. Doh, of course is crappy wood; answers:

  1. Use something else or is there life beyond radiata pine?
  2. Select and breed for trees that have decent (I do not mean good) quality.

So, what are my current obsessions?

There is an obvious quantitative void in my obsessions, I know. But I am going back to attempting to understand some basic processes before I embark in more number cruncing. Despite of this, I am also interested (but not obsessed) in the following problems:

What else? I am involved in a couple of three projects with students, dealing with wood quality, breeding or both. I have a new Ph.D. student starting in August on the interaction of economics and breeding. Ah, I almost forgot: there is a large number of lectures coming my way, better look busy…

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Back from conference
Published Tuesday April 25, 2006 · Permalink

Last week I attended to the 13th Australasian Plant Breeding Conference. This conference was somewhat tangential to my interests—which are much closer to tree and animal breeding—but it still had enough appeal to give it a go.

As in many conferences, most of the presentations where appallingly boring and/or badly done. What is with scientists and presentations that manage to turn an interesting topic in unsufferable mumbling? Anyway, there were also a few good presentations and I was thinking what did they have in common? It was not the slideware, or the choice of fonts or even the number of slides. The most important part, I think, it is to have a good story. The story provides enough background to be of interest to anybody, the story is coherent and one can see how the pieces fit with each other.

For example, I have no idea about rice breeding or tomato breeding. Until last week I did not use to care about them; not at all. However, when you start a presentation saying that 3 billion people (yes, half of this planet’s population) get most of their calories from rice you really get my attention. So maybe Swapan Datta’s presentation on golden rice (see the wikipedia article too) was not flawless, but I could feel the sense of urgency and importance of this work. Susan McCouch’s presentation on understanding and using the variability of rice populations was very entertaining. Steve Tanksley had a great story on breeding tomatoes using molecular genetics tools, going back to wild relatives and skipping phenotyping for a few generations1. So there are some scientists that are good speakers and can communicate a good story.

Note to organisers: having a lectern with a fixed microphone and the screen behind the presenter does not help to give good presentations. Some people like to move around, some people want to point things in slides so they turn, but when they speak the microphone does not pick up any sound.

1 This reminded me of a presentation on tomato paste ideotype breeding with molecular markers, by Jeanne Romero-Severson in the Genetics of Radiata pine conference (Rotorua, 1997).

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Current obsessions
Published Tuesday March 21, 2006 · Permalink

I have slightly changed the focus of my attention during the last month or so. My current obsessions are:

There are a few bits and pieces that do not fall in these two broad areas, but they will converge pretty soon.

Family-wise

Working with Marcela and Orlando in the veggie patch. I have never had much of a green thumb, but I am really trying. We sowed coriander, parsley and chervil, and planted bok choi, onions, dill, lemon balm and capsicum. Apart from the capsicum seedlings that are struggling (a drainage problem is my guess) everything is doing fine.

Marcela and Orlando checking worm farm

Marcela’s worm farm is the old-new addition. We used to have a worm farm in Australia, but due to quarantine issues, we decided to leave it there. So we needed to get a new one plus order the first batch of worms by mail.

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Content management using Drupal
Published Saturday December 3, 2005 · Permalink

This has been a long hiatus without posting in the blog. My excuse? I was evaluating a number of CMS to provide members of the IUFRO unit 2.04.02 (Breeding theory and progeny testing) with a way of communicating, including web page, newsletter, forum, calendar of events, etc. As the coordinator of the group, I am really keen on having people interacting, but the IUFRO site is, to put it mildly, close to useless.

I tested Drupal, E107, Mambo / Joomla and Plone. The first four are written in PHP and require PHP+MySQL, while the latter is written in Python. Although I prefer Python as a language, the idea of getting special hosting for Plone, because of especific server requirements is a bit of a turn off. I first had a quick drive test of lots of CMS at the Open Source CMS site, which is a great resource. After that I installed and configured Drupal, E107 and Mambo in my test system, where they are still working together without any conflicts. CMS Matrix provides a fairly detailed comparison between all the systems.

In principle the simplest interface seemed to be Mambo’s (plenty of eye candy), followed by E107. Initially I struggled with Drupal’s interface, but after a while I got the hang of it. On terms of functionality, all systems seem to provide most of the features I need: basic user management, forum, event coordination and easy posting. However, after a while I found that Mambo/Joomla are a bit of an overkill, bringing too many things by default. Putting together a magazine-like interface in E107 implied creating folders by hand (one per issue) and posting in those folders (a bit too primitive for my taste). Going back to Drupal, I started exploring all the contributed modules and I think I can get everything that I need from there.

I am now slowly putting together the IUFRO Breeding theory and progeny testing site, which should be operational by January 2006. The configuration of Drupal will be explained in my next post.

del.icio.us tags: cms drupal forestry iufro.

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Strategies in Noosa
Published Friday September 2, 2005 · Permalink

Part of my two weeks away included a meeting with old friends in Noosa, Queensland. Noosa is a very civilised place where to discuss breeding strategies: warm even in winter time, with a lay back, holiday atmosphere. After each day of discussions there were plenty of chances for having long walks followed by dinner. We stayed at the Noosa Lakes Resort for the third time (location map).

breeders in Noosa

The picture shows Mark Dieters, Colin Matheson, Heidi Dungey, myself, Tim White, Jeremy Browner, Fred Burger and Mike Carson. In addition to people in the picture, we had Paul Jefferson, Michael Henson and Steve Verryn (next to me in the picture below) in the meeting. Colin—our resident wine buff—made some interesting choices so we tried a wide range of whites and reds.

Dining out in Noosa (picture by Colin)

It was great to see Tim again, after all these years. I met him for the first time in 1993, when I thought ‘this is a very clever guy’: pretty good at navigating the politics of meetings. He did not disappoint me and this time he was even better, helping us to come up with a good strategy.

I am looking forward to participate in other strategy meetings. With some luck Steve may be able to organise a conference in South Africa (country that I have never visited) and we could have a go there.

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