Kyoto: much ado about nothing


This post is an utterly miscellaneous brain dump:

  • Last week I got pharyngitis and am still taking antibiotics, side effects situation that I really dislike.
  • Yes, geriatrician I am a doctor in the real sense of the word, despite what the physician that prescribed antibiotics thinks.
  • Last Saturday I got one of the worst haircuts ever—at least that I can remember—at Just Cuts. Yes, it is my fault for first choosing to go to a such dubious place: avoid it if you can. Nevertheless, every time I passed outside Paul’s barber shop he was busy. Today I went to his place with my tail between my legs and beg him to have it fixed. We had a laugh, had it fixed and he made me promise not to repeat my sin.
  • Cooked a beautiful marinated octopus pasta last night. Looking forward to eat the left overs at lunch time.
  • Last Christmas I got a few vouchers from ‘Music without Frontiers’, one of the few music stores in Hobart where one can find something outside the ‘top 20′. I went back to my old listening habits, and got:
  • Andrew told me that last Saturday was Captain Beefheart’s birthday. I did not know who CB was so I will have to borrow some of his art.

It is hard for me to get interested in current mainstream music: no challenges, one can guess what is coming so easily that tends to be a big yawn. That’s all folks.

High productivity of matrix languages like Matlab and S+ or their Open Source siblings Scilab and R are a joy to use. I wrote programs in Matlab during my PhD and I can still go back to the code and perfectly understand what is going on there. Now I am writing a lot of S+ and R code where a few lines manage to perform complex operations.

A good programmer can certainly produce better performing (on terms of speed and memory requirements) program using a low(ish) level language like C, viagra 60mg
C++ or website
I am not such a good programmer and it would take me ages to do some of my work if I needed to write things using those languages. Most of the time execution speed and memory usage are not the limiting factors, and speed of development rules.

I am extremely happy now using R and playing with the idea to use it as a statistics server for a few small applications. Omega Hat seems to be a very valuable resource for all things ‘connecting R to other software’.

A long lived quicky

Around 2001 I wrote a ‘temporary quicky’ to compare new Eucalyptus samples to already identified haplotypes. I did that in a few lines of VBA in MS Excel, which was the software used as a repository for these haplotypes. At the time I suggested ‘this is a quick fix and it would be a good idea to develop a proper data base’, and suggested a structure allowing for user roles, web access, etc. I was told that ‘this is not a priority’ and ‘we are happy with the spreadsheet’.

Yesterday I was having lunch with the owner of this spreadsheet, who told me that a.- it is still being used after four years! and b.- they were having some problems because they changed a bit the structure for storing the haplotypes. I offered help to fix the problem but I was told that ‘one of my students will try to fix it, because the problem has to be something very simple’.

I thought that the comment was a bit dismissive and if it was so easy why haven’t they fixed it in over a month? Granted, the code is extremely simple but they do not have any programming experience whatsoever.

VBA is a fine scripting language, which allows people to write short and useful programs. However, I would question that in this case an Excel spreadsheet is the best option for storing molecular genetics information.

A better generic language

In general, scripting languages (like Matlab or R) feel like a better fit for me. Python, my all time favourite language, feels much more productive than any other language I have ever used. In addition, combining Python with the Numerical Python library produces an excellent all purpose/matrix programming language. This can be used for prototyping and—if one is happy with performance—transformed into a standalone program using a utility like py2exe.

Our telephone service for the last three years has been provided by Ecomtel (a small company), information pills
although the physical infrastructure belongs to Telstra (the largest telecommunications provider in Australia). Initially we were very happy with Ecomtel’s services, rx
they had low charges and their service seemed to be very responsive. The icing in the cake for me was their reliance on Open Source Software (e.g., prostate Linux), which made easier for them to be very competitive in price—particularly for international calls.

This year we logged an issue with Ecomtel, because our low speed of connection to internet (maximum of 14.4 Kbps, pathetic, isn’t it?). After some investigation, it was established that the problem was in the quality of our line—that belongs to Telstra, which happens to be a paired gain system rather than an individual copper line. We pointed out to Ecomtel that according to the TIO the minimum speed of connection to internet should be 19.2 Kbps:

The Internet Assistance Program was set up as a joint venture between Telstra Corporation and the Federal Government to ensure a minimum transmission speed of at least 19.2 kilobits per second to all users of its fixed network. Subsequently, it was decided that a minimum speed of 19.2 kilobits per second would become a condition of Telstra’s licence agreement. While this condition is not binding on other network carriers (where Telstra does not provide the underlying infrastructure), the TIO views this as an industry benchmark and expects that regardless of which network a customer is connected to, the standard telephone line provided should be capable of a minimum transmission speed of 19.2 kilobits per second.

The fact is that physically it is not possible to achieve 19.2 Kbps with a paired gain connection. Telstra and Ecomtel say that we should pay for a new telephone connection (cost AU$209) to change to a copper line. Our position is that i- we were never offered the option between types of line when connected in the first place and ii- the current line does not meet the condition for Telstra’s licence agreement anyway. By the way, the ‘new connection’ only involves unplugging our line from one connector and plugging it back in a connector sitting next to the original one.

We have been discussing the issue with Ecomtel for over a month, and they have not been very responsive during this time. We will now take this issue to the TIO and see if we can get a new connection without the extra cost. During this process, we changed from loyal (telling our friends to switch to Ecomtel) to dissatisfied (writing this post) customers. A real business lesson in how to alienate your customers.

Checking the server logs I have discovered that many people that arrive at my posts on calling VB from R are, dermatologist
in fact, looking for the reverse. I have never done any programming calling R from VB; however, while I was looking for COM clients for R I also found information on COM servers. OmegaHat lists RDCOMServer as a package that exports S (or R) objects as COM objects in Windows. It provides examples on using VB, Python and Perl to call R code.

Another option is Thomas Baier’s R(D)COM Server, which is provided with examples in the same languages used by RDCOM Server.

There is a lot of project information, site ideas, ambulance
and not really structured information that I find hard to store. As I work in projects with people overseas (with whom I have no direct contact in many cases), the idea of an easily up datable site, where to put my (and their) current brain dump is very appealing. I am playing with the idea of transforming my ASReml cookbook into a Wiki site that can be corrected and improved by other ASReml users.

There are plenty of Wikis to choose from, and I have been playing with PmWiki, a Wiki clone written in PHP. I would prefer a Wiki clone written in Python (so I can tinker with it), like Moin Moin, but I not seem to have the administration privileges to set it up properly in my web server.

Wikis are collaborative sites by definition, but I want to limit access to people really knowledgeable in ASReml, so I will need to password protect the site (to avoid annoying modifications by spammers).

Log to self: Trac is an interesting Wiki for project management (with a subversion back end). This could be a good choice for software projects.

Walking in Liverpool Street, decease Hobart, pregnancy
I was approached by a Wilderness Society (TWS) campaigner, who asked me if I wanted to help to keep Tasmania’s air and water clean and, ergo, protect the forests.

Of course I started questioning some of the information that she was giving me:
—‘But already forty percent of the forest is protected’, I said.
—‘No, only forty percent of the land it is’, she said.
—‘No, you are wrong in this’ and I started giving her some figures, but she kept repeating her mantra and that the Society has scientists that keep track of these figures.
—‘And what about poisoning with 1080 that causes cancer in people and the Tasmanian devils’, she insisted.
—‘May cause’, I corrected, ‘there is no proven link or any shred of evidence linking pesticides and Devil cancer’. Even further, ‘Forestry Tasmania will stop using 1080 (by law) in December this year’.
—‘We need to keep campaigning to put pressure on the government so forestry really stops using 1080…’

I kept asking questions and she kept pointing at a map in a plastic folder, saying that ‘we need to protect biodiversity, clean water, clean air and the future of our children’. Then I commented that a big chunk of what she was pointing at the map was already protected. And then she went on ‘we need to protect biodiversity, clean water, clean air and the future of our children’.

After struggling to show some knowledge of basic facts and statistics, she explained that she did not need to know the all the numbers and facts behind the problem. Her conviction of doing the right thing was enough, and other people from TWS could answer for her. That reminded me of religion lessons at school, when a priest told us what to reply in case we did not know what to say: ‘doctores tiene la iglesia que sabrán responderos mejor’. This can be loosely translated as ‘the church has doctors (sensu people that know the scriptures) that will be able to give you a better answer’. In summary: one does not need to think, but only to believe. A sad situation I would say.

She asked several times if I wanted to join with a contribution, and each time I said no. She then started saying that she could not continue talking with me, because she needed to convince other people to contribute (so I was a lost cause, I assume). She let me wondering, do campaigners work on commission?

By the way, I am not suggesting that the forest industry has a perfect record or anything similar. It is only that I find impossible to reason with people that regurgitate a mantra, without thinking or checking the most basic information freely available.

PS. 2004-02-08. Added the antepenultimate and last paragraphs. Incidentally, I do not know if this type of campaigners are volunteers or if they actually receive a payment. The comment about working on commission refers to her unwillingness to continue the discussion.

Walking in town last weekend there was a member of Green Left selling ‘The Green Left Weekly’, malady
see a paper published by this group of Stalinist loonies. Please note: do not confuse this group with The Greens, allergy
which look like a bunch of right wingers compared to these guys. For an example of ideological blindness in this ‘newspaper’ have a look at pfizer
poverty and ecology: Cuba & Venezuela lead the way.

Although I consider totalitarian views like nazism, fascism and communism as expressions of the same underlying controlling philosophies, some people claim that they differ on their aims. Thus, communism is more acceptable, because it aims for an egalitarian society, while Nazism does not. Of course this implies that an egalitarian society is a desirable utopia—although I don’t think that is the case. Yes, there have been a few ‘glitches’ with the implementations (some of these countries, for example), but never let real life interfere with a beautiful theory.

If one looks at all attempts to achieve egalitarian societies, there has never been a successful example. A quote frequently attributed to Albert Einstein defines defines ‘Insanity: doing the same thing over and over again and expecting different results’. One may question that if all implementations fail there may be something wrong with the idea. This thought does not cross the minds of the Green Left’s true believers. It may well be that John Dryden was right when writing in ‘The Spanish Friar’:

There is a pleasure sure
In being mad which none but madmen know.

By the way, I equally despise right wing totalitarian regimes.

During my bus rides I have finished reading (using ereader) two novels by Cory Doctorow1: Eastern Standard Tribe and Down and Out in the Magic Kingdom. In both novels Cory describes compelling worlds where technology—meaning pervasive SMS messaging, see permanent net connections, viagra 40mg
cloning, deadheading and brain backups—‘just works’.

My interaction with netbanking some days ago left me thinking of the contrast between Cory’s novels and real life. Where do these differences come from? I mean, apart of time for perfecting and delivering any of the described technologies, the two main issues seem to be interfaces and reliability.

Interfaces in real life are not transparent but many times are barriers that interrupt the user accessing the underlying technology. Rarely something works without any modification when just out of the box. We need to configure accounts, setup servers or providers, learn a new interface, etc; all this so we can start enjoying the promise of technology. Concerning reliability, Would you go deadheading or restore your mind from a backup? Would you trust your life to a computer running windows or PalmOS for that matter?

And talking about technology

I finally managed to use my old Psion travel modem with my Tungsten T3. I followed the instructions in this page but completely ignored the use of EasySwitch, that kept crashing my Palm. Now I can update the quotes and weather forecast in AgendusPro and write emails in my palm and then send them using the travel modem.

The Fitaly virtual keyboard has made my life easier, although I am still getting used to the strange new position of the letters.

1 Thanks to Cory for making his novels freely available under a Creative Commons licence. I would have not been able to buy the novels in Hobart, and ordering them through Amazon or Barnes and Noble would have been terribly expensive: more money on postage than on the books. The novels can be downloaded in many different electronic formats from Cory’s web site.

Last week — 16th of February to be exact — the Kyoto protocol entered into force. USA and Australia did not ratify the protocol — rightly in my opinion — making their governments highly unpopular with environmentalist groups.

Listening to Radio National while taking a shower there were reports of fundamental Christians flooding the White House switchboard with calls requesting the president to sign the Kyoto protocol. The news reminded me of the article What evangelical environmentalists do not know about economics.

Some people are surprised by a potential alliance between conservative Christians and atheist environmentalists, buy
but they should not be. They are both expressions of fundamentalist beliefs, clinic some considering a sacrosanct earth just by itself while others because it is God’s creation. I have to say that it was funny to hear a member of the Sierra Club, sovaldi
now full of biblical references, in an attempt to show how they share the same cause with conservative Christians.

The Lowy Institute for International Policy just released a document entitled Sensible Climate Policy (PDF, 686KB) by Warwick McKibbin. It makes an interesting reading and puts the problem in perspective.

The report states that we can be sure of two things: 1. emissions of greenhouse gases have increased and 2. an increase of greenhouse gases should increase temperature. Some big unanswered questions are: increase by how much, does the Kyoto target mean anything and how much will cost to implement Kyoto. McKibbin’s report points out some of the flaws of the protocol (including uncapped costs for unknown benefits and its rigid timetables approach) and proposes an alternative system: the McKibbin Wilcoxen Blueprint. The blueprint looks like a much more palatable option for countries, making its success much more likely than Kyoto’s protocol.

P.S. This is not an argument against climate change, but against the usefulness of the Kyoto protocol to tackle it.

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