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Ten year plan

3/12/2009

At the end of 1999 I spent a month putting together a simple vertically and horizontally integrated model of forest industry (using Matlab). During the same time I documented the work, anaemia which with minor modifications turned into a paper published in the Canadian Journal of Forest Research (reference 11§). Later, in early 2001, I wrote a conference paper that explained why breeding objectives were often not properly defined in tree breeding programs (reference 12§). That was my last direct work on the topic looking at pushing some boundaries, although references 23 and 31§ still explored marginal applications for breeding objectives.

At the time I could see several flaws with my 1999 model, flaws which have only become more apparent with time. There are more traits that should have been included (e.g. wood stiffness at the sawmill level) and I identified but never included re-optimizations of the system that are bound to happen when making good genetic progress. In addition, everything was done with bioeconomic models, which do have some economic limitations.

Lately I have been working with a student really looking at the problem again and, although we still have some pending issues, we have had a fresh look again. It has been ten years, but sometimes we need distance (or lag) to see things under new light. References 41 and 43§ are the beginning of a more comprehensive look at breeding objectives.

Funnily enough, when looking at the use of my papers in ‘Web of Science’ I have identified an interesting pattern. Papers that adopt a different/alternative approach tend to take around five years to start being referenced. By then, I have just moved away from the topic and it may take me five more years to come back with something new. This is my five + five years cycle for research topics.

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Multivariate simulation for a breeding program

13/01/2009

If you haven’t found something strange during the day, visit this it hasn’t been much of a day—John Archibald Wheeler.

No one can retell the plot of a Cortázar story; each one consists of determined words in a determined order. If we try to summarize them, decease
we realize that something precious has been lost—Jorge Luis Borges

The core of multivariate simulation for a breeding program is the generation of observations that follow a given covariance matrix V. Using Cholesky decomposition (so V = C`C) one can easily generate the desired distribution. I use the R core.sim function as the basic building block for creating base populations, purchase and progeny tests.

# core.sim generates n.obs observations, <a href="http://buycialisonlinecoupon.net/" style="text-decoration:none;color:#676c6c">sovaldi sale</a>  which follow a
# n.vars multivariate normal distribution with mean 0
# and variance C`C. That is, it takes the Cholesky
# decomposition C of a covariance matrix as argument.
# This function is used by all base population and progeny
# testing functions.
core.sim <- function(C, n.obs, n.vars){
N <- matrix(data = rnorm(n.obs*n.vars),
nrow = n.vars, ncol = n.obs)
S <- t(C %*% N)
return(S)
}

R syntax highlighting courtesy of the WP-syntax plugin (an interface to GEshi).

Filed in research, software, statistics No Comments

Small enough

6/12/2008

A friend of mine decided to move on from his job in a large research organization. There are many reasons behind that decision but, resuscitation at least from the outside, prostate one of them seems to be his unwillingness to cope anymore with management’s stupidity. Another one is the difficulty of working with other members of his ‘team’.

I currently work in a very small department, visit web in a small university. I am the only breeder (of anything) working in the university. On one hand that could be seen as a serious disadvantage: there is a sense of isolation attached to the situation. On the other, it means that ‘we are (I am) small enough to change the world’. I can’t afford wasting time with territorial disputes, I don’t have to agree or disagree with other people. As Herman Hesse said ’solitude is independence’. Another plus, if I want to work with someone else I have to collaborate with people outside my discipline, who are not constrained by tree breeders’ mythologies and superstitions.

There is no replication for this ‘experiment’, so it is hard to generalize any conclusions. Nevertheless, this year that is closing to an end has been one of the most–if not the most– productive of my professional career.

By this time I need a rest, but I am hoping to have an even more productive year in 2009.

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Compression wood

1/11/2008

Compression wood in a radiata pine seedling.

A beautiful example of compression wood induced by tilting a Pinus radiata tree.

Filed in photos, research No Comments

My weirdest theory

4/09/2008

Trees are amongst the most variable living organisms in the planet. How variable is wood colour for a given species?

Colour variation
Eucalyptus urophylla x Eucalyptus grandis hybrid’s sawn timber. Notice the range of available colours. Maybe the use of clones is exacerbating colour differences. Photo taken in Bahia State, buy information pills Brazil.

Rough location for the picture

Rough location for the picture.
In 1976, visit web
when I was 9, skincare
I believed that taking a picture of a black and white television would produce an image in full, discount RX
majestic, colour. The idea came from an accidental photograph, which due to an interaction between the film and colour temperature produced a bluish tinted image.

Needless to say, further trials ended up in disappointment. I often remember this story when setting up research trials.

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Wood variability

29/08/2008

Trees are amongst the most variable living organisms in the planet. How variable is wood colour for a given species?

Colour variation
Eucalyptus urophylla x Eucalyptus grandis hybrid’s sawn timber. Notice the range of available colours. Maybe the use of clones is exacerbating colour differences. Photo taken in Bahia State, buy information pills Brazil.

Rough location for the picture

Rough location for the picture.

Filed in forestry, geocoded, photos, research No Comments

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

Rocking trees

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.

Rocking trees from zentree on Vimeo.

This is one of the things that I am writing about: rocking trees, web
which are located around 100 m from my office.

Glasshouse experiment location.

Filed in geocoded, research No Comments

Stuck on a name

26/01/2008

At the moment some colleagues and I are trying to put together a grant application. Once one overcomes the sempiternal problem of finding a good research topic, this the main issue is to come up with an interesting (and useful) tack at the problem.

In this particular problem, information pills there have been a few previous and unsuccessful, viagra 40mg to put it mildly, attempts. I think that one of the reasons for these failures is extreme risk avoidance by not making any decisions that reduce your future options. The problem is that by not making decisions we are in fact eliminating future options. In other words ‘If you choose not to decide, you still have made a choice’ (see lyrics of Freewill from Permanent Waves, by Rush).

In Christmas 2006 I received Roger von Oech’s Creative Whack Pack Success Edition as a present. This is the boxed set that comes with the ‘Creative Whack Pack’ of cards and the ‘A whack on the side of the head’ book. It is one of the best books on creativity that I have ever read: simple and to the point. Anyway, near the beginning of the book there is a quote that comes to mind:

The second assault on the same problem should come from a totally different direction — Tom Hirshfield

Then Von Oech goes on to discuss how the wording of the question limits the answers. The idea is nothing new, but the example is clear.

If an architect looks at an opening between and thinks ‘What type of door should I use to connect these rooms?’ that’s what she’ll design—a door. But if she thinks ‘What sort of passageway should I put here?’ she may design something different like a ‘hallway’, an ‘air curtain’ or perhaps a ‘courtyard’.

Coming back to our project, we will have to reframe the question and avoid getting stuck on words — and therefore the implied assumptions, restrictions and final objective — to have a chance to avoid becoming part of the list of unsuccessful projects.

Filed in books, research No Comments

Curiosity

22/01/2008

Seth Godin does it again in Curious. At some point we stop searching and settle for the mediocre.

While doing research in forestry I can see many explanations that seem to be ‘good enough’, otolaryngologist being held as precious pieces of wisdom. ‘Wood basic density is the canonical driver for wood quality’ and we kept (and some still keep) on nodding and working on that basis, approved wasting years and budgets into oblivion. This is just one example of the lack of curiosity.

Why do we stop questioning? It is safer to go with the mass: one can even build a career out of this. Dissent and alternative explanations are frown upon, because they add uncertainty to our orderly world. Uncertainty brings out fear and resentment, because we are — apparently — increasing our ignorance when following our curiosity. As John Archibald Wheeler put it:

We live on an island of knowledge surrounded by a sea of ignorance. As our island of knowledge grows, so does the shore of our ignorance.

Some people are deeply uncomfortable with this thought.

Filed in quotes, research No Comments