Quantum Forest

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?

• Profitable shorter rotations. What are the limiting factors (hint: crappy wood quality, small size pieces and scale of the operations) to make this happen?.
• Very early selection of adequate trees. Notice emphasis: selection does not to be perfect to be useful. Adequate selections at age two is much better than good selections at age ten years.
• Why do trees grow the way they do in wood properties? Why do trees choose different strategies that have such dramatic differences in wood quality?
• Rapid turn-over breeding strategies. Are we still taking fifteen years for a breeding cycle? It is 2006! Can’t we do any better?

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:

• Simulation of breeding strategies. I have a project working on this topic starting in October this year.
• Mate allocation and population structure. Trying to show that we can get rid of sublines and other artificial groupings when using sensible mating policies.
• Large scale genetic evaluation: how simple is simple enough? My way to help having frequent genetic evaluations.

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…

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

• Optimisation of breeding programs, for which I am learning to use AMPL, with Fritz’s help. I will need to create and format some data to include in some simulations analysed by AMPL and I think I will use Python to prototype them. If I run in to speed bottlenecks I will reimplement numerically intensive processes in either C++ or Fortran 95.
• Genetics of wood properties. After some early forages on wood properties—which finished when Carolyn changed jobs—I am back at it. John has been very welcoming and we are trying to put a couple of projects together. We should have some early results by mid next year.

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’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.

I finally completed (and submitted to Silvae Genetica) the manuscript for ‘Genetic variation of physical and chemical wood properties of Eucalyptus globulus‘. This is not my first or last paper (it is publication 25), but it took such a long time that it deserves a special mention. The project was plagued with problems and delays that, although did not affect the final quality of the data, made data analysis and writing the manuscript a real pain in the back.

By the way, Silvae Genetica looks like a very old fashioned 1800s journal. I always associate the image of a very old German worker printing the journal in a damp basement. Nevertheless, it is almost compulsory reading for tree breeders and the publisher seems now keen to give it a facelift.

When writing papers I use either a combination of MS Word and Endnote (a reference manager) or LaTeX in its MiKTeX incarnation with TexnicCenter as a text editor. I use the latter combination for large documents, like convoluted course notes. This time I chose Word but did not have a ‘Silvae Genetica style’ for Endnote, which is necessary to format the citations in the text. I created a style that works for journal articles, books, book chapters and conference proceedings, which you can download from here.

I do not expect to see the manuscript for around three months. By then I should receive comments (I hope positive) from the referees.

This week I spent three days in Melbourne, attending a meeting of the Research Working Group on Forest Modelling and Information Systems (RWG2). It was my first experience in this group, having participated in meetings of RWG1 and RWG7 in the past. One of the nice things of working in a new area is that there is no sense of respect for the ‘big names’. There is no ‘they were my lecturers’ or ‘I have read their papers’, so meetings and relationships are much freer and relaxed.

People were very nice and welcoming, and I was able to put faces to names like Cris Brack (Australian National University), Ian Ferguson (University of Melbourne), Chris Goulding (New Zealand Forest Research), Valerie LeMay (University of British Columbia) and Jerry Vanclay (Southern Cross University). There were many other ’small names’ (including mine) and we have quite a bit of fun and exchanged lots of ideas. Thanks guys!

I always have lots of fun presenting and this time was no exception, talking about spatial models for modelling mammal browsing in plantations. This is one of my current pet topics (pun intended), I mean spatial models, not only for browsing, and I hope to have something in publishable form soon.

Scamander, Tasmania

I spent a few days based in Scamander, North Eastern Tasmania. The drive up North with Rebecca and Andrew was quite pleasant; only three hours and we reached the first stopover. Note: this was written last Tuesday, but there was no way to connect to internet from the hotel.

In the last couple of months I came across two papers about the analysis of progeny trials that require some comment: one on diallels and one on clonal data. Both of them expand on the tricks and contortions required to run those analysis using SAS, specifically using proc mixed and proc iml.

I was quite surprised about the transformation of computational limitations of a specific piece of software (namely SAS) into research papers. Both problems can be tackled in one line of model specification in ASReml. Potentially, one could write a macro in MSWord for BLUP analyses, but is it worth doing it? So what is going on? It seems that being provincial and sticking to old school models pays on terms of boosting publication records. Please guys, just visit the ASReml cookbook and get a life!

Several years ago, I think it was 1996, I was given a copy of A Ph.D. is not enough: a guide to survival in science (link to Amazon), which is an easy to read and entertaining book. Not that the information contained in it is groundbreaking (it should be of most use to some extreme nerds), but there are a few things that I still remember. For example, a fundamental principle, in preparing a talk, is never overestimate your audience and the concept of publon, the minimum publishable unit.

Publication is a funny game, because in most academic institutions is one of the basic components of the survival system (by the way, this is not my case). Because of this, the publon (quantum of publication) is dominant in scientific literature. A set of publons, a series of short papers, looks much better in your curriculum than the odd juicy paper. Unfortunately, that puts a lot of stress in the publication system, with thousands of journals trying to cope with the influx of tens of thousands of papers each year.

Journals take quite a long time to review the manuscripts, and we end up with not so interesting papers that take a long time to be published. Biometrics has an interesting document entitled Review times in statistical journals: Tilting at windmills? (PDF file) by Raymond J. Carroll, discussing strategies for Associate Editors and Referees with the aim to reduce publication time. In summary, editors should reject some papers without any additional review, while reviewers should focus in content rather than in correcting spelling or suggesting useless changes to the manuscript. Using this approach in forestry journals would make my life easier: I wouldn’t waste time reading manuscripts that will never be published and publication would be much more expeditious.

In summary, pushing for fewer and juicier papers, and streamlining the publication process would certainly benefit researchers.