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Using R for genetic analyses

11/06/2009

As some people know, visit I have been using asreml for genetic analyses for quite a few years and even keep the ASReml Cookbook§. I was quite happy to see the development of asreml-R, ed a package that makes available most of ASReml’s functionality from R. This made my life easier: I still use plain-vanilla ASReml for very big jobs, but I can access a much more comprehensive statistical system for fairly substantial jobs.

One of my main problems with asreml-R is that is not available for OSX (mac). Yes, I can dualboot or use a virtual box, but both options are a bit of a pain. I rather use my computer with its primary operating system and no strange overheads. I have requested several times to have a mac version. It seems that the code can be compiled without problems, but it is the license management software that is not available for the mac.

I then started looking for options to run genetic analyses. nlme was designed around hierarchical models and fitting experimental designs did not feel right. lme4 is looking good and the main issue was around fitting pedigrees, a matter at least partially solved by the pedigreemm package. I then came across the MCMCglmm§ package, which has some nice features: it makes Bayesian analyses accessible, ready support for pedigrees and a syntax not that different from asreml-R.

After playing with the MCMCglmm library, I found that I could not use pedigrees with parents acting both as males and females. I modified the code (line 26 of inverseA.R) to print a warning rather than to stop and the compiled the library again. Voila! it is working (the beauty of having access to the source).


R CMD INSTALL /Users/lap44/Downloads/MCMCglmm --library=/Users/lap44/Library/R/2.9/library

By the way, ASReml is still my primary tool at the moment, but I enjoy having good alternatives.

Filed in genetics, mac, software, statistics 2 Comments

I do run ASReml in a mac

18/01/2007

(Or why do I prefer software where I do have a say)

Recently I was commenting on some software that I use for writing. I think that one of the main reasons non-strictly related to software usefulness is the quality of the community around the software. This has two elements:

  • How open is the developer to feedback from the users and
  • How active is the community at using the software to push the developer(s) to continue moving forward.

As an example, seek I like using Journler to keep track of odd ends in my mac computer. I also like using Writeroom when starting to write, visit because I can focus on my ideas only. Both programs have relatively active groups of users (here and here) and receptive developers, healthful who are looking for feedback. The feeling is of people who care about a product, which in general is a necessary (although not sufficient) condition for good programs. By comparison, I struggle with Copywrite, because there is no public feedback mechanism: I do not know what other users think or what are the projects of the developer for this software. Is he (or she) still developing it or now he is moving to live in Vanuatu to enjoy the rest of his life?

An interesting element is that both Writeroom and Journler are free (sensu gratis)—although the developers ask for donations—while Copywrite costs US$30 or so. There is a psychological element on paying for software; one thinks that the programmers must be working on the product. However, there is no feedback to confirm this assumption in Copywrite. In addition, I expect more activity from smaller companies: they are supossed to be more agile than, say, Microsoft.

Thus, if you are a small company I expect you to show some changes here and there. If you are a small company and charge for your product I better should have a say on what is going on. If you are a large company, most likely I will buy your software only if I need to, because most probably you are developing not very interesting products (there are exceptions1 of course).

1 Wolfram’s Mathematica is an example. Insightful’s Splus is not: R is much more active, there is plenty of feedback and it is free.

  • Movie that I’ve watched the most: Robots. Yes, pills
    it is Orlando’s favourite. How many times? At least a hundred… I wish I were joking.
  • Lesson of the week: the dignity of Amish from Nickel Mines dealing with tragedy. I can only admire their strength and wish them peace.
  • Depressing statistic of the week: I publish more than the whole Department of Silviculture of the university where I studied. This is even worse considering that I do not publish that much. However, the truth is not that bad, in Chile people work in many projects where the only output is a report for the funding agency. The bad part is that many New Zealand forest companies are still delluded into thinking that they are way ahead in international competition. No, they are not; they are resting on past laurels so, wake up!
  • A small sample of Orlando’s words in Spanish: jirafa, cohete, trompeta, axila, harmónica, cocodrilo, refrigerador. Sample in English: ice cream, plane, rainbow, umbrella. Poetic comment: ‘El cohete está haciendo un arco iris’ (The rocket is making a rainbow).
  • Two sites that I have enjoyed reading lately: [dive into mark] and The Tao of Mac.
  • Definition of bric-a-brac: ‘miscellaneous curios’.

For quantitative geneticists and breeders out there: ASReml runs OK in any mac with Intel processor and Parallels. You can find some comments on using it in the ASReml Cookbook.

Incidentally, view
SAS works OK in a mac using Parallels too. However, I am enjoying R a lot more.

Filed in genetics, mac, software No Comments

What’s up in research?

8/07/2006

After playing for a little while, view
I managed to connect my Macbook Pro to the internet using my mobile phone via bluetooth. I have a small Samsung ZV10 and my service provider is Vodafone New Zealand. The steps are quite simple:

  • Click the bluetooth icon in the topbar and select ‘setup bluetooth device…’.
  • Check that the phone is running bluetooth and that is discoverable (Under settings, practitioner
    connectivity).
  • Select mobile phone in the list of available devices.
  • The computer will search and—we hope—find your mobile phone.
  • The computer will generate a numeric passkey that has to be keyed in and accepted in the phone.
  • Select ‘Access the Internet with your phone’s data connection’ in the next menu.
  • The settings to connect to Vodafone in New Zealand are:
    • username: vodafone.
    • password: vodafone.
    • GPRS CID string: *99#
    • Modem script: Vodafone VC701SI

This explanation is based on the excellent—and illustrated—version by Pukupi.

After using the Macbook Pro for a few more weeks, this
I have been settling on my final software selection:

  • Quicksilver: which is a great launcher and keeps learning about my preferences. Additional plugins installed: del.icio.us, help dictionary, firefox and iphoto.
  • Office: well, I do exchange a lot of documents with colleagues and friends that use the Windows version. In general works quite well, although compatibility is not perfect. My main issues have been spreadsheets containing lots of VBA or embedded Activex controls and compressed graphics in PowerPoint, which show that puzzling ‘QuickTime and a TIFF/JPEG decompressor are required to view this picture’ message. In addition, Microsoft has not released a Universal binary for Office, and will not do it until they have the next version available, whenever that is.
  • Thunderbird: after trying Mail.app and Entourage, my experience was disappointment with how unreliable Mail.app was (missing emails and crappy IMAP support) and found Entourage too big and clunky.
  • Firefox and Camino: Firefox is a great browser, but it feels a bit un-Macintosh. Camino uses the same engine, but with a nicer interface. I like the ability of closing the tabs just next to their names (a la Safari). However, it does not have (yet) incremental search, which is something that I love in Firefox (PS 2006-06-29. It is possible to have a close button in the tabs of Firefox through the use of the Tab X add-on. PS 2006-06-30. Bob Cantoni points out ‘to close Firefox tabs, just middle-click on the tab to close it; i.e., click the scroll wheel’).
  • R: a great cross-platform (and free) statistical software. I do most exploratory analysis using it, and only go to SAS, using Parallels (see below), when strictly necessary for working with other people.
  • Parallels: allows running windows and I currently use it only to run SAS. It still feels a bit slow, but for writing and prototyping SAS code is good enough. I bought the pre-release copy at US$50.
  • Copywrite: I normally become very easily distracted when using a word processor to write. All the options, fonts and formats become a real nightmare. Enter Copywrite, which is a simple writer’s editor. It allows only basic formatting, so it is very good for the first couple of drafts.
  • Devonthink: after reading Merlin Mann’s comment on 43 folders, I decided to give it a try. I am quite tempted to use it in a continuous basis. It is a good brain dump, where I can put all odds and ends that I normally loose. The current version still has some bugs and missing features, like that the full screen editor works only for plain text and that changing the colours of text may have effects on other parts of the program. Anyway, searching and connecting notes seems to work quite well. I still think that Copywrite’s full screen editor is much better and less distractive. PS 2006-06-30: I have decided to wait until the next version before buying Devonthink: still too buggy for my taste.
  • Writeroom: I just started testing this great full screen writing system. Just write there, no need to save. If I want something a bit more complex, I can type using Markdown and convert it to HTML using Humane.Text service. PS 2006-06-30. Jers Novel Writer is another writing program that supports full screen mode and that deserves a try.
  • TeXShop a highly polished LaTeX distribution, that I am using for writing lectures notes for STAT220 (Biometry I).

Sharing printers in a mixed network

I can not remember another time when I have been using so many computers in such a regular basis. My main work machine is Mastropiero1 (Macbook Pro 15”), although there is an exception for simulation work, where I use Nutcracker (a.k.a. Black Box, a generic 3GHz, Windows XP machine, which just happens not to be beige). In addition, at home I also use Happy Meal2, a Power PC Mac Mini that acts as back up and has the printer connected. Last—and certainly least—I keep Beige Box (a generic 1GHz Windows XP machine) still functional at home, just in case we need some extra simulation capability when time is not an issue.

Last weekend, we bought another cheap windows laptop for Plus Tree, our consulting arm. It is a Compaq Presario V2000, temporarily named Lucrezia Borgia3.

Given that the printer is attached to Happy Meal and that we some times need to access it from either Mastropiero or Lucrezia Borgia using wi-fi, we:

  • Shared the printer (using System Preferences, Sharing), which works for any Mac computer in the network, including Mastropiero.
  • Allowed access from Windows machines—like Lucrezia Borgia—installing Bonjour for Windows, which has a handy ‘Bonjour Printer Wizard’. Use the Wizard and the printer is now available to Windows too. Piece of cake!

Incidentally, after using the Compaq laptop for a while, I can say that it feels as warm as the Macbook Pro on the top surface. The exception is the part above the function keys in the MBP, which is bloody hot.

P.S. 2006-06-30. Welcome to 43 folders’ readers. Five hundred visits in two days; not bad for a small sidebar link.

1 Homage to the (in)famous composer so many times presented by Les Luthiers (and English article in Wikipedia).

2 Its volume is actually a bit smaller than a MacDonald’s Happy Meal box.

3 Obvious reference to this Renaissance woman.

It has been a log time without writing about research. New country, click new city, unhealthy new job. In addition, thumb
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…

Filed in genetics, research No Comments

Back from conference

25/04/2006

I some times visit Techcrunch, unhealthy a site that profiles new web 2.0 companies. Most of them share the use of tags (some ridiculous name for the good old keywords), doctor
allow sharing content with other users and will go bankrupt. I may try some of them but most of the time they have no incidence at all in my workflow and just forget about them.

Google mail has changed my workflow, at least for personal email. No more folders, just keywords and archiving. Some people may have privacy concerns but, hey, do you encrypt your email? I didn’t think so, so stop complaining because anybody can read it. I would love to encrypt mine, but none of my correspondents actually uses encryption, so it is an uphill battle.

All the other Google services (Froggle, Maps, Chat, RSS syndication, news)? Have not made a dent on my workflow, so from a practical point of view, they are pretty useless to me. One exception in the horizon is Google Calendar (CL2). The fact that it is an internet calendar is not surprising or innovative at all (they are dime a dozen at the moment), but integration with my Google mail (which I find really nice) it is.

There are services from which it is very easy to move away; for example, web search. I may be used to Google, but if there is a new service which provides more relevant results, I will start using it without hesitation. That is what I did when moving from Altavista to Google in 1998. Yahoo is now looking more relevant to many searches I am doing, so I may switch to them.

Apart from that, what would I like to have?

  • My desktop everywhere, like YouOS (a java script based web operating system) but that actually works for me. Having a crummy editor and spreadsheet does not qualify as useful, because I often use the more obscure features of software. However, the idea of runnning a desktop that I can easily access from anywhere is compelling.
  • A well integrated wiki+blog. I use PmWiki and Textpattern, but I would rather prefer to use a single system with complete linking across themes and posts. Infogami looks like going in the right direction, but still needs a fair amount of work. If it is a hosted solution I want to have a escape route, so I can save my data externally in a meaningful format.
  • A remote disk to keep my things synchronised across computers, something that I can mount from my PC, Mac or whatever I am using at the moment. It needs to have a decent amount space and no, 1GB is not enough (think of pictures, please)!

Google Maps continues to include some higher resolution images (if not maps) for some parts of the planet. I was able to find the cure
-70.640792&spn=0.002986, viagra approved
0.005831&t=k” title=”link to Barrio Bellavista in Google Maps”>place where I used to live in Santiago at the level of buildings and houses. And here is ampoule
-70.631586&spn=0.002856,0.005831″ title=”link to Antumapu in Google Maps”>where I used to study Just have a look at the centre of the pictures.

Distances between Christchurch places where I have lived at some point of my life (obtained using Geobyte’s city distance tool):

  • Hobart, Australia: 2442 km.
  • Palmerston North, New Zealand: 431 km.
  • Valdivia, Chile: 8647 km.
  • Mendoza, Argentina: 9487 km.
  • Valera, Venezuela: 12876 km.
  • Los Teques, Venezuela: 13255 km.
  • Santiago, Chile: 9351 km.
  • Concepcion, Chile: 8930 km.

It should be relatively easy to tag the images with every conceivable story that one is blogging about, although a bit time consuming. However, for most places I write about, imagery resolution is too broad for anything useful. I am sure it is just a matter of waiting a couple of years to sort out this issue.

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, stuff
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 insufferable mumbling? Anyway, viagra 100mg
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).

Filed in genetics No Comments

Current obsessions

21/03/2006

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

  • Optimisation of breeding programs, diagnosis 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 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.

Filed in gardening, genetics, miscellanea, photos, research, statistics No Comments

Content management using Drupal

3/12/2005

This post is about people “saving time” doing the wrong things. The whole ‘life hacks’ area has become much more visible since the presentation by Danny O’Brien on 11 February 2004, visit this
who presented results of interviews with highly productive hackers (notes of the presentation taken by Cory Doctorow). There was a second presentation (notes by Cory again). This has spawned a number of sites treating more or less seriously; for example, Sildenafil
43 folders and Life Hacker.

Originally, the idea was very simple. These ‘high achievers’ all use mainly one application (and one file to keep EVERYTHING). This can be a combination of text file + editor, a private blog or wiki, etc. There are a few scripts using data from that file (if text) or RSS feed (if blog or wiki) to keep things synchronised. Now, how come that this concept has been expanded to cover such a diverse array of approaches?

First, different things work for different people—fair enough. However, the main problem seems to be that people have been developing all sorts of hacks for the wrong reasons. An example of the first approach is the Hipster PDA. Why bother with big electronic files if there is a simpler, low-tech approach (more about this later). Another example would be this article on dealing with email overload. The second approach, however, implies just a simple waste of time. Some examples:

  • Why do you need to worry about how to organise thousands of RSS feeds? That is clearly too much information, unless your job description is ‘to summarise thousands of feeds per day’.
  • The last few weeks there have been plenty of people worried about watching too much TV, so there are ‘life hacks’ to reduce time seating watching TV, movies, Tivo, etc. Just turn off the bloody box! Easy. There are some people clearly using too much disposable income for getting more ways to be distracted.
  • And anything iPod (in its many incarnations) related.

Let’s go back to simple and important problems and drop the fluff. Talking about fluff, I put in that category most online approaches to keep your life sane (e.g., Backpack). They imply constant connection to internet, which at least for now it is not possible, unless you are a completely urban-being with your rear permanently glued to a chair in front of a computer.

After a false start, health system
I am again putting some of my bookmarks in del.icio.us. I will probably add the tags (newish term for old-fashion keywords) to blog posts too.

Playing with cream

Paul Ford’s comments on Amish computing certainly hit a soft spot on me. I do miss Wordperfect 5.1! It was back to simpler times when using computers was certainly much more productive for me. Multitasking is a nice feature to have when strictly necessary, for sale but not all the time.

Next year I need to spend a fair amount of time writing lectures and I am certainly tempted to ‘going back to basics’. Most of the text that I need to prepare is not highly complex, generic
so I am thinking of writing at least the first drafts in text files with a simple markup. The most humanly readable markup is probably Markdown. Once the text is in Markdown it can be easily converted into html (e.g. using the Markdown dingus, and adding the ‘html’ and ‘body’ tags to get a complete page) and from there to other formats like LaTeX or MSWord. If I decide to go for a longer document probably LaTeX would be the way to go.

I have been playing with Cream, the VIM mode for dumb users like me (another distraction). I hope to slowly learn a few tricks at a time to become a more proficient VIM user, but that is not a real priority. It is a really nice editor mode!

I installed the vim-latex suite, which seems to add pretty good latex support to VIM/Cream, but it seems to override some of the Cream configurations (e.g., F9 is not code folfing/unfolding anymore). It seems to be a matter of getting used to that though. Anyway, I will not need it for the first version of the documents.

Making more changes to Tim’s site

We have had a few problems to have the PDF file of Tim’s book indexed by search engines. My theory is that engines aren’t very happy with Textpattern’s internal links (of type http://mysite.com/file_downloads/2) for a PDF file. Today we changed it to something more explicit like http://mysite.com/bookfiles/file.pdf. Actually, the story was not as simple as that. When first trying to use the new code we ran into a ‘missing page’ problem, which I traced back to a problem with the .htaccess file. I dropped a <IfModule mod_rewrite.c> condition from the file, leaving it like below and it just works.


RewriteEngine On
RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^(.+) - [PT,L]
RewriteRule ^(.*) index.php

A few years ago I obtained my Australian citizenship and simultaneously—at least in theory—I lost my Chilean one. Last September the Chilean congress approved law No 20050 (PDF version in Spanish) reforming 54 aspects of the constitution including:

  • Recovery of citizenship and accepting the principle of ‘ius sanguinis’ (acquisition of citizenship through descent—textually, bronchitis
    by right of blood). This would give my son access to Chilean citizenship.
  • Elimination of designated (non-elected) and lifetime senators.
  • Reduction of the presidential period from six to four years.
  • The president can now remove commanders in chief of the military and security forces, approved
    without requiring the consent of any external authorities.
  • The National Security Council (Consejo de Seguridad Nacional) has its role greatly reduced, Myocarditis
    minimising its interference in public affairs.

Finally, after fifteen years of recovering democracy (year and a half after a famous plebiscite), there are substantial changes to the political system eliminating several of the vestiges (but not all) of a dictatorial system.

I got you! This post is not about the end of forestry activity in Tasmania, viagra 60mg
but about the end of the Forestry in Tasmania web pages. After two years compiling materials and hand formatting HTML I have decided to stop updating the sub domain. The fact that I am leaving Tasmania at the end of the year—so I will not have time to keep up to date with what is going on—is just the straw that broke… you know.

I still need to decide what to do with the site; either I will leave it unchanged for posterity’s sake or pull the plug and delete the whole thing. Over these last two years I have received a fair amount of abuse and a few examples of praise for keeping the site and trying to present a ‘fair view’ of environmental discussion in Tasmania. However, ailment whatever tries to pass as debate is so low quality that it is easy to get disheartened with what one reads in the media.

Will I start a ‘forestry in New Zealand’ page? I doubt it; my role will be completely different and forestry activity over there is much less contentious. I rather spend some time learning Maori—I am quite keen about this—and practicing the haka with Orlando.

This post started as a question to myself: Why did it take me so long to start caring about economics? Only last year, resuscitator
at age 37, sales I felt the urge to start reading about economics and its relationship with society. Before that, anaemia
I used to have this primordial (to use H.P. Lovecraft’s language) reaction towards economics, particularly its free market variants.

I think that one of the major ‘whack on the head’ moments was realising that claiming an admirable objective is completely different from achieving it. That, in addition to the realisation that many good intentioned policies actually achieved opposite effects was enough to decide start reading about economics and ‘classical liberal’ approaches. The last part of my excuse is that I was first exposed to free market principles under Augusto Pinochet’s dictatorship.

I still believe that imposing economic change without political freedom is wrong, and costed me years of rejecting open economies. The problem is this: an unelected government (a dictatorship to be honest) pushes for economic reform. Because I disagree in principle with a dictatorship and the lack of freedom, I will tend to oppose most policies, even reasonable ones. At some point this includes supporting the opposite of economic freedom, well, sort of. Chile represents a funny free market, an economic system that for many years lacked transparency.

An interesting feature of this dicothomy between ‘market freedom’ and ‘political freedom’ is the attitude towards democracy in Latin America. The Economist published the results of The Latinobarómetro poll, and even in countries like Chile—that has had major economic growth—around 50% of people are still ‘not very satisfied’ or ‘not at all satisfied’ with the way democracy works (see Figure 3 in the linked document). So, why are people still struggling to come to terms with a freer system? I would venture that there are at least two important reasons:

  • The extreme level of inequality1 still present in society. By the way, I do not believe that one of the reasons for this is the presence of a capitalist system but that the system is not truly capitalist2 yet. The major issues would be: the existence of a small number of people restricting a proper access to a market economy for the rest of the population, and lack of property rights, with a substantial proportion of transactions in an informal economy3; namely Hernando de Soto’s dead capital argument.
  • The feeling that there is a ‘restricted version’ of democracy, where there are still groups of people (e.g., higher ranks of the military, very rich people) who are beyond the reach of the legal system. That is, a feeling of lack of justice and unfairness, which I think is being corrected, albeit very slowly.

Is a future of free market and democracy possible for developing countries? I believe so, particularly if we are talking about ‘real capitalism’, with more responsible politicians and business people, as well as a preoccupation for the unintended consequences of electoral promises. May be there are too many ‘ifs’ in the previous sentence, but the experience of countries like Venezuela4—devastated by demagogy and government/business inbreeding—may be a good reminder for personal and social responsibility.

Footnotes

1 I do not think that the mere existence of inequality is in itself an issue (I do not mind about the existence of multimillionaires). The problem is when there is still a large proportion of people that has little hope for the future, as is still the case in many Latin American countries.

2 This is well put by Johan Norberg in his In defence of global capitalism book. By capitalism he means (PDF 112KB):

…the liberal market economy, with its free competition based on the right of using one’s property, the freedom to negotiate, to conclude agreements and to start up business activities. What I am defending, then, is individual liberty in the economy. Capitalists are dangerous when, instead of capitalist ownership, they join forces with the government. If the state is a dictatorship the enterprises can actually be a party to human rights violations, as for example in the case of a number of western oil companies in African states. By the same token, capitalists frequenting the corridors of political power in search of benefits and privileges are not capitalists either. On the contrary, they are a threat to the free market and as such must be criticised and counteracted. It often happens that businessmen want to play politics and politicians want to play at being businessmen. This is not a market economy, it is a mixed economy in which entrepreneurs and politicians have confused their roles. Free capitalism exists when politicians pursue liberal policies and entrepreneurs do business.

3 This problem is also linked to environmental degradation.

4 I am not ‘just picking’ on Venezuela. I lived five years in the country and have very good memories of its people and landscape.

P.S. 2005-11-10: Johan Norberg emailed me saying that ‘I’m sure I would also have shared your attitude had I experienced that’.

I was writing a Python prototype of DogSim, discount
an inheritance (sense Mendel) mode simulator, tadalafil happily coding and brushing up my Python coding. I usually listen to energetic music while coding, dentist
and this time was the Red Hot Chili Peppers turn. First was Blood, Sugar, Sex, Magik, then ‘Californication’ and then ‘By the way’ (my least favourite album). But no, wait a minute: ‘By the way’ would not play at all in my laptop. Tried again, and the disk was not recognised. What was going on? Quick Google search and then discovered that the Australian released CD had ‘copy protection’ that would not allow it to be played in a computer.

I understand that artists may not like someone making a million copies of their CDs and selling them for a profit. But from there to denying a legal user the possibility to play a CD in a computer… that is way over the top. Over ninety percent of my listening is in my computer while working, the other ten percent is listening children’s music in the car. So, what happens when I am faced with that situation? Well, I just have to circumvent the protection, so I can make a copy of the CD that plays in my computer to listen to the bloody thing, so I can justify spending the money in an overpriced piece of plastic.

My web search found a reference to IsoBuster, a data recovery software that mounts the CD and ‘shows you all the tracks and sessions located on the media, combined with all file-systems that are present’. So it gets around the typical double table of contents problem that renders CDs unplayable in a computer. Then one can copy the music contents to the hard drive and then back to another CD. The funny thing is that I did not manage to mount ‘By the way’ in my crammy Matshita UJ-820S CD drive—so I need to try in my desktop computer—but I managed to get a copy of the enhanced version of Portishead’s Live: Roseland NYC. The latter has given me grief for many years, always trying to use its special player to play in the computer, not letting me do any other thing.

What is the point of the whole exercise? Commercial piracy will not be deterred by some lame form of protection, but end users will be really annoyed. May be music companies should read Cory Doctorow’s presentation on digital rights management.

P.S. By the way, a lot of this copy protection issues are completely side stepped in my mac.

Last week I had my fourth trip to New Zealand in less than a year. Apart from almost being fined NZD200 for forgetting to declare a pair of boots in my luggage (I got away with a warning about the dangers of soil attached to boots) and missing my domestic connection the trip was OK. Air New Zealand is upgrading its planes in the Melbourne-Auckland route, visit web
and this time I flew in a Boeing 777-200 with an ‘on-demand’ entertainment system. It is nice to be able to pause the movie (any of the 40 ones available) if one wants to go to the loo.

And the perils of presentations

Every time one goes to meetings PowerPoint makes its appearance, troche
and one gets endless bullet points, people reading slides (the teleprompter approach), chart junk and obvious recycling of old presentations. It really annoys me when someone is going over dozens of slides skipping the ones that are not useful for the current presentation.

I do enjoy presenting and most of the time spent quite a bit of time thinking and preparing:

  • Who are the members of the audience and what do they know about the topic?
  • What is my core message and the best way to deliver it?
  • Then I write a little ‘script’—which is also the basis for the handout—and then I create some slides. By the way, when I say handout is not that ‘cute’ printout of your slides, but text actually written to support the presentation. This time was 9 slides for a half an hour presentation.
  • I always remember something that I read in A Ph.D. is not enough by Peter Feibelman: ‘never overestimate your audience’ (page 28). I read that as always provide some context so even people that have little idea about the topic can get something of my presentation.
  • I do not use a specific style for all slides (like, for example, the Takahashi Method of few large words, or the Kawasaki method, although I use few slides), but I combine them. I use as little text as possible, almost never in bullet point form, tend to use good quality pictures (taken by myself, from istockphoto or, if lucky, I get a freebie from stock.xchn). I do use simple diagrams and sometimes one or two slides with just one number or word.

A good resource for presentations—not necessarily PowerPoint— is Presentation Zen.

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, dermatologist
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.

Filed in genetics, software, web 1 Comment

Strategies in Noosa

1/09/2005

Part of my two weeks away included a meeting with old friends in Noosa, sickness 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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Kick-starting plus tree

6/04/2005

This post represents the first official reference to Plus Tree, dermatologist the site that will support most of my genetics and breeding work. I know, drugs the site is not yet ready for prime time, mind but I think it has reached a state of ‘potential usefulness’ for people interested in the topic.

I will try to post short essays around once a month, but there are no guarantees. A friend of mine asked ‘Why are you giving away that stuff for free?’ The simple answer is because most posts do not represent ground breaking ideas; however, the fact is that they are rarely implemented in breeding programs — particularly in a single program. In addition, imagine what you would get if you actually pay me to do some work!

In the not so distant future I will make available a couple of features that I am still testing for the site, including access to open projects — or at least the basic ideas behind them — as well as (probably) a Wiki system.

Some people know that I have been looking from the sidelines of genetics for a while. Let’s say that now I am starting to play again: slowly but steadily.

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Done with the bloody paper!

10/11/2004

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), melanoma but it took such a long time that it deserves a special mention. The project was plagued with problems and delays that, stomach 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.

Filed in forestry, genetics, research, software, writing 2 Comments

From the sidelines

11/07/2004

Any time management book worth its salt will tell you that you must make the most of commuting time. Well, sovaldi at least that is the theory if you spend a reasonable amount of time moving from point A to point B. Living in Hobart and spending between 12 (no traffic) to 20 (lots of traffic) minutes going from home to work there is no much that one can do with commutes (particularly if I am not travelling alone). However, viagra there is radio. I do not mean FM-greatest-hits stations but old fashioned AM Radio National. (Digression: I am quite geeky about gadgets and things like that, but concerning media I like AM mono radio. I believe this is a vestige of driving my Ford Cortina 1972 — that I sold in 2002 — which only had AM radio.)

Yesterday the program was an interview to Chilean writer Isabel Allende, of ‘The house of the spirits’ fame. Actually, I think that most of her books are rehashing ‘The house of the spirits’, but that has nothing to do with this comment. She was talking about feeling at home in a culture, and how she never felt that in the USA. However, despite of living many years outside Chile, she feels culturally at home every time she visits the country. She would understand every reference, body language, expression, etc. This did not mean that she felt like returning home for good; she didn’t. It was just the relaxation that comes with familiarity.

Isabel Allende’s explanation got me thinking. Yes, going back to my country of birth presented the familiarity (although I grew up in three Latin American countries). However, it was only familiarity with the old aspects of the culture. I would miss many references to newer events and TV programs, and TV really permeates any modern culture! Familiarity did not translate into ‘I want to stay here’, though. It was more like ‘I know this, but I want to go back home’. In Australia I feel familiarity with the newer aspects of culture, but when people talk about the ‘Whitlam era’ is like they were talking about ancient Egypt (in Egyptian). I have only lived under Howard’s era; yes, it sounds pathetic, but I didn’t choose him as Prime Minister.

It might well be that, having grown up in many different places and then moved to other countries as an adult, I am destined to have only partial familiarity with many cultures. It is a strange, sometimes difficult, sometimes really enjoyable destiny.

It has been fifteen months since I stopped working full time in genetics. I was feeling tired — some may even say burned out — of the topic. After ten years there was nothing really exciting. I think that I was trapped by the routine, about it
dealing with small problems and loosing track of the big picture. I did not completely stopped working on genetics, no rx
but I have been spending less than ten percent of my time on it.

Two weeks ago I started thinking again on tree breeding, but mostly about big picture items. For example, how to integrate different parts of breeding programs rather than how to obtain an infinitesimally small covariance component. I realised that I still enjoy very much this area of genetics and breeding.

This experience got me thinking about the rise and demise of research groups. During the 1970s the tree breeding group in the New Zealand Forest Research Institute (now Forest Research) was one of the most exciting places to be in, putting forward new breeding strategies, using selection index and type B correlations. Later, during the late 1980s and early 1990s, the School of Forest Resources and Conservation from the University of Florida was a very interesting place, and they were busy applying BLP (basically selection index) to every possible dataset. Starting in the mid 1990s, the School of Plant Science and the Forestry Cooperative Research Centres based at the University of Tasmania thrived evangelising forest geneticists about BLUP and breeding objectives. All those research groups are still active, but in general they are not at the forefront of tree breeding anymore. Some researchers will apply the same techniques to 300 datasets in one go rather than to a single one, but that is not exciting or very rewarding either from a research or an industrial viewpoint… It may be that researchers got tired after a wild ride.

Another interesting point is that many of these groups developed a reputation applying techniques developed in the animal breeding world (e.g., selection index-BLP, BLUP, breeding objectives). It is not that people in forestry are not very creative, but we do lack critical mass when compared to animal breeders. It may be that the new exciting topics will come again from animal breeding. It may also come from other areas or even be developed from the inside. I am just happy to have recovered the “love for the trade” again, and am looking forward to dedicate part of my time to work in “big picture” items, wherever they come from.

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