Today [Saturday] a cold front came -- and with it, the first, meagre snow. In the park on the shore of the Danube, the wind blew it straight into my eyes.

Update [2008-11-23 6:51:2 by DoDo]: The snow remained this morning, and another blizzard came when I visited a new rail bridge -- so five more photos and some Bridge Blogging below the fold.

European Tribune invites « progressives » and presents an ideology as described in `About' and the FAQ.

Those who claim they don't have an ideology still live in this material world and will have some in the form of ideals, value systems, personal or absolute truths, beliefs, etc.

`Ideological' people will try to identify others as they belong or don't to their own ideology.

Sometimes it is difficult to accept ideological concepts and classification because someone doesn't clearly identify with one or the other because he/she has been inspired to develop a very different ideology that doesn't fit into the polarity of just two ideologies at hand - plus those situated between the two poles.

CASE IN POINT - myself

Rather than assigning a political colour to people according to where their words and ideas seem to position them, we might rather need to learn, and acknowledge that one does not always speak from an ideological viewpoint, but based on and looking at a real-life situation.
This seems to be the new way in politics: rather than governing from the centre, raising above it to face the reality directly, without the bias of a predetermined political position, without the skewed 3D glasses of a particular ideology.

The Electoral College, when it is noticed at all, is usually dismissed as an anachronism at best and a foe of democracy at worst.  But some of our current problems might be more manageable if we made more use of it, not less.

For more on pruning back executive power see Pruning Shears.

With two senior Obama aides leaking the news (reported at Huffington Post) that President-elect Obama plans to name Sen. Hillary Rodham Clinton (D-N.Y.) as his secretary of State shortly after Thanksgiving, speculations about the effect of this appointment on the prospects for Middle East peace become increasingly relevant.

An article from Lawrence of Cyberia as well as one from FireDogLake are strangely positive about an early peace deal between the Israeli and Palestinians, which could be seen as the linchpin of Obama's foreign policy toward the entire Muslim and Arab worlds: a reversal of the Islamophobic Neocon disasters the Bush administration subjected the country to in the name of fighting terrorism.

In spite of the Clinton legacy that left much to be desired in the 90s, both authors believe that peace between Israelis and Palestinians "will again be center-stage in U.S. foreign policy," and quickly.

Is NATO dying, as a piece excerpted by nanne in this morning's Salon alleges?

After describing all the problems that plagues the organization and suggesting that euthanasia would be the best way to deal with it, the author, Nick Witney, ruefully concedes that NATO is here to stay for some time more at least, due to Europe's snail-like progress in developing the necessary alternative structures on which to rest the transatlantic security relationship.

Meanwhile, according to one Cathy Young, NATO's supposedly threatening existence towards Russia is actually quite useful for Russia's leadership, which uses it as a convenient "external enemy" to divert the Russian public from their mounting frustrations with their country's stature and living standards.  If so, according to Young's logic, any intiative by Obama to defuse the NATO "threat" towards Russia will, paradoxically, not be welcomed by Moscow, who would then be forced to deal with the true causes of Russia's "inferiority complex toward the West and, in particular, the United States".

Geoengineering describes a project of rapid, large-scale intervention at some points to alter the earth's surface temperature. It's been discussed in-depth in these two diaries on the European Tribune:

Cooling the Earth: CO2, SO2, and The Sunscreen Fix by technopolitical (Oct. 2006)
Geoengineering: basic principles, some thoughts, some questions by asiegel (Mar. 2008)

There may be large differences in how we think about geoengineering. In my opinion, it should be seen as both an extreme and transitional measure. But at least we seemed to agree that there is a need to research it and to set priorities. What I proposed was the following:

Planting trees and mechanical air capture of carbon are better than injecting SO2 into the stratosphere, which again is better than seeding the oceans with iron dust. In my opinion...

There are more interesting options beyond those, which you can find in asiegel's diary.

Now we have a bit more to go by, as some of the more common ideas about geoengineering have been studied and ranked in a Nature Geoscience paper by New Zealander Philip Boyd.

Promoted by afew

I have said many times on ET that I don't trust most computer simulations of reality. I never supported this claim with any argument. Considering that this is the area where I work, I think I can give some ideas on the topic based on personal experience. My plan, in the future is to write a robust and extensive argument on this issue. For now, I will start with a simple example, using mostly naive arguments. Feedback is highly encouraged (especially antagonistic viewpoints that are rationally fundamented).

Caveat: I exclude computational chemistry and physics from all this (a preamble where I explain why, is due in the future). For computational chemistry and physics I mean only what theoretical chemists call ab-initio and semi-empirical methods.
Caveat: I will trade rigor for clarity (especially the word gene will be abused).

Short bio:
Undergrad in computer science (with lots of experience in software development)
MSc in bioinformatics (area: population genetics, conservation genetics)
PhD is tropical medicine (ongoing - theoretical study of the spread of drug resistant malaria)

For obvious reasons it is quite difficult for me to talk about the PhD work. I will just say that I have even more reasons to believe in what I believe.

Population genetics and simulated reality:

In many research studies involving population genetics empirical data is compared to simulated data (by a computer). Conclusions about the real world data are made according to the relationship between that data and deviations from the computed data.

An example
Imagine trying to find in a certain population which genes are under selection - Imagine, say, that a certain population of fish are able to adapt to very cold waters while others aren't, you might be wanting to know which genes are responsible for that (assuming there is a genetic basis). The procedure is more or less like this: You go to the field, collect samples (something that has DNA from individuals) from several populations. Then, in the lab, several possible candidate genes are genotyped from each individual. Each individual will have 2 copies of a gene, different versions of the same gene may exist (different alleles). You are looking for genes that seem to be "different" for the majority. The underlying hypothesis is that "normal" genes are neutral while "different" genes are under selection (hopefully are related to thermal-regulation, what you are looking for).
Imagine that you sample 2 populations (one in normal waters, another in cold waters), 10 individuals on each population and (only) 3 different genes. Imagine that you have the following distributions (I will call alleles for first gene a and A, for the second gene b and B and for the 3rd c, C).

Population a   A |  b  B |  c  C

Normal     10 10 |  0 20 | 10 10

Cold       10 10 | 20  0 | 10 10

It would seem the the first and third genes have the same distribution in both populations and the second gene is quite "different".
This is, of course, a simple and highly skewed example, for explanation purposes.
Reality is normally much more complex, involves more genes, more populations, and possibly more alleles per gene.
So what do researchers might do? They simulate a bunch of neutral("normal") genes on a computer, calculate some confidence intervals for some statistics on that simulation and then compare each gene (or the statistics derived from those real genes) against the computer simulation results. Genes that fall outside the confidence intervals from the simulation are deemed candidates for being "under selection".

So, real data is compared against simulated data to derive conclusions.

So what about the realism of that simulated data? In population genetics, most simulations (not only my selection detection example) are based on Coalescent theory. I am not going to explain the coalescent here, or this would become huge. I will present some of the common assumptions done on coalescent simulations (note that some simulators might do different).

1. Random mating among individuals. The meaning of this is obvious. Or maybe not.

 

 
1. Some simulators don't have the notion of gender. So random mating might mean really random mating of genes.

 
2. Random mating is not very good in many situations. We all know of many species where mating is not random at all. But it is said that random mating is a good approximation for humans (especially because we don't see one male for all female behavior - Though Irish might complain here (search for Niall), or Genghis Kan descendents, by the way). So we have random mating used for species which don't mate randomly at all; and for humans, where it is seen as an acceptable approximation. I will not even go into politically dangerous terrain about random mating among humans, I will just say this: If you do some trivial math, random mating produces lots of half-siblings (where one of the parents is shared but the other is not) and almost no full siblings (where both parents are shared). Do you think this is a reasonble approximation of the reality that you know? Especially think in terms of genetic diversity (which is what we are discussing here).

 
3. Random mating is actually an extreme in the sense that it maximizes the transmission of genetic diversity. For instance if in the real scenario only one male is responsible for the next generation gene pool (this is quite typical in, say, domesticated animals), you loose the genetic diversity that all the other males might give. A random mating approach looses very little in comparison.

 


2. Meta-Population structure. Let me give an example with humans. Humans are normally studied theoretically as three populations (Africans, Asians and Europeans - forget about Native Americans to start with). These 3 populations are, you guessed it, in random mating and individuals migrate among populations (equal rates of migration among populations). So according to this model, a Portuguese like me (think about this simulation modeling ages before planes or cars existed) had a much bigger probability of mating with a Finish than with a Moroccan (as a funny aside, people from Lisbon and south, like me, are called by northern Portuguese as Moors).


3. Hierarchical population. Continuing and detailing the example above, each population is normally in random mating. It is known that genetic diversity varies quite a lot in Europe (the Finish are normally presented as an example of an highly-inbreed nation - more than the Icelandic). But most models have no account for this internal population structure. There is normally, in most models no notion of hierarchy (i.e., the are 3 human populations are not internally subdivided).


4. Independent generations. According to most existing models we can only mate with people of the same generation. No Charles Chaplin for you (or Niall, or Gengis Kan ;) ). Actually I think this is a bigger problem with some non-human species.


5. In a completely different front are field and lab errors: Repeated sampling of the same individual? Might happen especially with elusive species. Errors in the lab? There is ample evidence that researchers do lots of errors in interpreting results from sequencers. How does a certain method cope with average error rates?

Now that I think of, most of the assumptions discussed above (the last being a more ambiguous case) tend bias for the increase genetic diversity...

Notice also that I am discussing approximations that are easy to dismount. In many cases much of the history of populations (especially non-human) mostly is unknown: population size, population structure, mating habits, genomic structure. So you invent.

Now, people are aware of this and the counter-argument is: "most methods are robust to changing assumptions". The immediate question then becomes: "Show me proof that your method is robust" (this can be done by doing theoretical studies where you change a certain assumption and compare the results)? Normally the answer becomes: "If have tested for a certain specific change" (normally from a certain demographic model to another). "What about for this other n differences which are also important (like, say, mating)?" The answer is invariably: "You can do it yourself, that would be nice to see".

I am consciously avoiding a discussion of the economics and sociological part of this, or to explain why people don't test for all these conditions. There are reasons why people avoid doing this, but that is not the point of this exercise (though a discussion about the sociology of science would be cool).

The only thing that I want to do, is to place some seeds of doubt on the current use of computational simulations as a proof/forecast mechanism in science, and doing that by explaining, roughly, the underlying science of it.

By the way, I also think that in many cases we are really not talking about science as many of these methods are falsifiable, but people seem to prefer to ignore that ("this method can still be used in many realistic scenarios", "This method is valid if the (unrealistic) assumptions are, if you have different assumptions that it is your responsibility").

This text was, I have to admit, half-baked. Please accept my apologies for that. It is my intention to develop the argument over time, but I think I owed some explanation on why I doubt so much of using computer models for making predictions. Please allow for some language abuse, I just want to pass the rough idea for now. Comments are very welcome

Update [2008-11-21 5:31:58 by Ted Welch]: What did you Puritans ever do for us, Oliver?

... On the eve of a new drama about Cromwell and the English Revolution, its writer Peter Flannery tells Lucy Powell we've got the Roundheads all wrong

What did the Puritans ever do for us? They banned Christmas, closed the theatres, and made "tippling" illegal. So, if I ask you to picture a Puritan, the image, inevitably, is not appealing.

...as a new four-part series on Channel 4 is set to illustrate, the Puritans of revolutionary 17th-century England were not entirely the black-clad killjoys history remembers...

Here, Flannery explains why the Puritan revolution merits such a vastly ambitious overhaul, the legacy it left us, and why those plain-clothed, no-nonsense men are sexier than you might think...

The amazing people at la laquadrature.net are ramping up their campaign against Sarkozy's antidemocratic and liberticide plan.

In spite of 88% of MEP voting in favor of amendment 138 which would preemptively bar the adoption of three strike laws in the EU, our right wing government is lobbying through back channel to try to kill it.

Note that it is customary for EU member state to refrain from legislating on an issue that's still being debated in the European Parliament. Yet naboléon felt that pleasing his buddies in the mass entertainment industries was more important than respecting our european partners.

Recent efforts by conservatives in the US have reopened (again!) the issue of the purpose of education. In keeping with the tilt toward authoritarianism and conservatism over the past 40 years the push has been towards more structured education. This is a sharp change from the development of "liberal" education started by John Dewey at the beginning of the 20th Century. I examine both schools of thought below.

There are two views as to the function of education. Let's call them "knowledge" vs "process".

Introducing "Irving" (our second adopted stray) to ET.

                               

Mme. LEP and estHer want to call "Irving" "Boby" after Boby Lapointe because Irving has a broken tail which stands straight up, thus La pointe. I think you have to be French to get it. But I'm refusing to call him "Boby;" to me he's always "Irving"- because he's such a schlub. When he sits down on the table the whole house shakes. To me thats an "Irving."

Today, its "Photos as usual" again along with "ask the expert."

Happy Posting :-)

    Last week I was talking with the edit beast about some strategic marketing stuff and he says "You know, we need someone with a big name to take an interest in this stuff ... like Bill McKibben." It wasn't a day later that I notice gmoke's diary on stuff happening at Harvard and MIT and there's Bill McKibben listed in one of the panels.

    I went charging off to see the event, but things were a little more challenging than normal ...

I certainly used too, but the more I learn about it the more I worry the theory might be completely wrong.

November 13, 2008

The Jewish Telegraphic Agency (JTA) reported this story a few days ago, which apparently never made it to the US mainstream media: how a right wing supporter of Israel, Alan Dershowitz, the famous Harvard lawyer, convinced Barak Obama to shun Jimmy Carter at the DNC convention, presumably due to Carter advocacy for the Palestinian people through his book, Palestine: Peace Not Apartheid, and his statements about the siege of Gaza, which he called a "human rights abomination." We all witnessed Jimmy Carter's brief humble trek across the stage to applause, then disappear, never to be seen again.

Dershowitz claims he is a liberal Democrat but if a liberal Democrat can support the inhumane treatment and suffering of any people, what is he, really? About Carter, there are no doubts that he is a statesman and humanitarian, who won the Nobel Peace Prize for his worldly efforts to bring peace and democracy to foreign peoples. Dershowitz, by contrast, deserves not to be mentioned in the same sentence with Jimmy Carter.

Government set to decide on second Lisbon vote - The Irish Times - Sun, Nov 16, 2008

The Government will make a decision on holding a second Lisbon Treaty referendum before a meeting of EU ministers next month, the Minister for Foreign Affairs said today.

Micheál Martin said the Government will table proposals at a European Council meeting next month to deal with the impasse following the Irish electorate's rejection of the treaty in a referendum last June.
--------snip

"We want to be at the heart of European decision making," he said. "That would enable us to have some impact on decisions into the future and that would strengthen our hand in negotiations on agriculture and budgets and so forth."

Mr Martin said the Government has yet to make a decision on holding a second referendum. "The Government will make that decision in advance of the December meeting," he said.

-------snip

Earlier this week, Mr Martin dismissed speculation about forcing Ireland from the European Union if voters reject the treaty a second time.

The so-called "Norwegian option" of reducing Ireland to associate member status has been floated by senior German foreign ministry officials as a means of clearing the way for the ratification of the treaty.

--------snip.

"We are at a turning point in our relationship with Europe and, as a Government, we will offer advice that future generations are better at the heart of Europe than at the margins," said Mr Martin.

"But the Germans are very committed to Lisbon, they are not leaving us in any doubt about that."

The Norwegian suggestion was, he said, "not in any room of consequence".

So take that, you nasty "senior German foreign ministry officials"!

Promoted by DoDo

On unlikely filtering of news: the largest employer and largest industrial base in the US is on a collision course with economic and political reality.

While it has the cards to set off an energy revolution.

We've all heard it this week, the skillfully leaked report that Senator Hillary Clinton was being considered for Secretary of State in President-elect Obama's administration. Then, details emerged about the Senator's quiet trip to Chicago to confer with Obama, and neither Obama's press office nor Clinton's staff issuing a public correction of the basic premise that she's been offered the post. So it is probable (provided she and Bill pass the vetting process) that she will be nominated, and if so, then she will likely be confirmed as the next Secretary of State.

Democrats' aversion for Nader's spoiler role in past presidential elections might compel ignorance of his advise, especially when it was directed at the president elect, Barak Obama, only one day before the election on November 3rd. This open letter to Obama is focused on the Middle East and how Obama has made himself a obsequious darling of AIPAC, the now hard right wing handmaiden of the Likud party of Israel.

Thanks to Mark Elf of Jews sans frontieres for the heads up on this missed advise from a persona non gratis, who should probably be listened to more often.