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

Is the US heading for President Reagan 5 (or Clinton 3)?

Via Naked capitalism.

Dean Baker: The high priests of the bubble economy. Some snippets

Those following the meeting of Barack Obama's economic advisory committee could not have been very reassured by the presence of Robert Rubin and Larry Summers, both former Treasury secretaries in the Clinton administration. Along with former Federal Reserve Board chairman Alan Greenspan, Rubin and Summers compose the high priesthood of the bubble economy. Their policy of one-sided financial deregulation is responsible for the current economic catastrophe.

...

While the Bush administration must take responsibility for the current crisis (they have been in power the last eight years), the stage was set during the Clinton years. The Clinton team set the economy on the path of one-sided financial deregulation and bubble driven growth that brought us where we are today. (The deregulation was one-sided, because they did not take away the "too big to fail" security blanket of the Wall Street big boys.)

For this reason, it was very discouraging to see top Clinton administration officials standing centre stage at Obama's meeting on the economy. This is not change, and certainly not policies that we can believe in.

Worth reading...

Some of the resident EuroTribers might know Sudden Debt, a blog on the state of US (and world) economy. Although the quantity of posts (and in part the quality) has decreased in the last weeks, this was the probably one of the first places where the current situation was forecast and with unbelievable accuracy. If you spend some time reading past posts you will notice how the author, "Hellasious" (Hell as IOUs) really was able to see what was coming. Heck, just the name of the blog shows some prescience.

One of the things that always seemed strange on Hell's analysis was the forecast of deflation. Today he has put up a post where he insists on the issue and seems to be at odds with what he calls a Keynesian approach.

Some food for thought from someone that was always "right on the money" (silly pun intended).

It is quite easy to detect formal limitations to freedom of expression. Say in dictatorships freedom of expression is either formally limited by the law or it is dead obvious that you cannot say something without the state interfering with your freedom to do so. Much has been said about those.

There are other ways of limiting freedom of expression which are recognized by all and essentially accepted as "reasonable" in western societies: Freedom of expression at work is curbed a lot. In fact modern workplaces are mostly hierarchical dictatorships. This is known, discussed.

One thing that concerns me a lot is informal but pervasive ways of curbing freedom of expression.

Imagine going to a typical religious (probably creationist) group and defending a evolutionist position? You will probably be labeled as a frickin' nut. Of course you could opt not to go there, but if all your friends, if most of your social life is there, is that really an option? Are you going to leave your community just because of that? Most probably you won't. So you will adapt, adapt by not avoid saying that "sacrilege".

Of course one can abstract the reasoning and replace "religious group" by any other group. Let's say "European Tribune". Is is possible to have a healthy discussion on issues like "race", immigration, science? Can one easily defend here that that, say, immigration is "bad"?

[Don't see this has a criticism to ET (probably one of the few places that I know where this issue is less noticeable), this was just an attempt to have an example that is near (as opposed to impute this behavior just to others)]

Obviously, non-conforming points (to any group) will make the system respond back, that is normal. The problem is that, some responses make people be afraid of genuinely speak their hearts out: You might be fired, or be ignored or not "invited to the party" (social pressure is a mighty deterrent).

This has consequences: first, and sometimes very consciously, you avoid speaking from your heart, but you might still think it. So you might have that "strange" idea about X, but you don't utter it but probably practice it (think catholics and condoms/abortions). Another, probably more damning consequence is that you end up training yourself to think only inside the box. Some thoughts are dangerous if uttered by mistake... The limit becomes "hard-wired": there is no need for formal control of freedom, it is inside you.

This is to be seen in many lefty groups where some ideas are cast in stone: race, environment, emigration, ... . These issues are sometimes called "principles" (a word sometimes used for issues that is not to be discussed - dogmas).

Not only there is the whole principle of freedom of expression and the fundamental ability to be spiritually free, but it is probably also a pragmatic issue, e.g., if there had been space for a candid discussion on immigration in some countries in Europe, there would probably have been less space for the emergence of certain far-right parties. But the truth is, that it is very hard to have a non multiculturalist view on the left without being branded by some with some very bad epithets. This is an example among many.

Living in the UK (and I comment on the UK because it is one of the few examples that I do based on my real experience), I sometimes think that the local politeness/friendliness ends up having precisely the same effect: There is a framework where it becomes very difficult to voice your "strange" opinions (voicing disagreement is very difficult to do without being branded "rude").

Aloha,

I am converting a suggestion from metatone on the Monday opening thread to a full diary in order to see if the idea goes forward...

What about a North (West?) England ET meetup?

Suggestions for place: Liverpool and Manchester were given, but I would say anyplace accessible with public transport (preferably train) would be a candidate.

Date: Any suggestions can be placed here. I am traveling from the 6th to the 27th of September, so if possible outside those dates would be appreciated (but feel free to consider that time interval also, as your diarist is normally traveling and probably won't be able to attend anyway) . The sooner the better as the number of hours of sun per day is fading quite rapidly ;)

Everybody is invited (especially people from North Wales, as it is so close ;) )

This is a private diary entry (stop if you are not interested in private diaries - although if you know a lot about North America your help would be appreciated), although it has a political background.

The political background is simple: Since half a dozen years I have become convinced that we are facing oil scarcity. This year I have the opportunity to return to the US (and Canada) based on my work. And considering that I believe that traveling (especially intercontinental) will become more expensive, I just accepted the temporary work related visits during this Summer in North America.

Here starts the private part...

I am going to Las Vegas (7 days), Toronto (3 days), New England (flexible: PA, to MA, all goes in between - 5 days), Missoula (MT) (15 days), California (SF and LA - 9 days). This is from mid July to mid August...

I would like, among other things, to meet new people (especially of the progressive kind).

In this light would you recommend any places to this "old left" social-democratic European who as a very soft spot for the US in his heart? I know of the places in the touristic guides, I was thinking in something recommended by people who know the local places (and with a liberal bias)...

I am stealing this from The Oil Drum. Maybe as a remainder that "Anglo" disease is not something structurally Anglo, but just the triumph of Reagan and Thatcher.

It can happen anywhere... it can also be avoided.  

"We will find neither national purpose nor personal satisfaction in a mere continuation of economic progress, in an endless amassing of worldly goods. We cannot measure national spirit by the Dow Jones Average, nor national achievement by the Gross National Product. For the Gross National Product includes air pollution, and ambulances to clear our highways from carnage. It counts special locks for our doors and jails for the people who break them. The Gross National Product includes the destruction of the redwoods and the death of Lake Superior. It grows with the production of napalm and missles and nuclear warheads.... It includes... the broadcasting of television programs which glorify violence to sell goods to our children. "And if the Gross National Product includes all this, there is much that it does not comprehend. It does not allow for the health of our families, the quality of their education, or the joy of their play. It is indifferent to the decency of our factories and the safety of our streets alike. It does not include the beauty of our poetry, or the strength of our marriages, the intelligence of our public debate or the integrity of our public officials... the Gross National Product measures neither our wit nor our courage, neither our wisdom nor our learning, neither our compassion nor our devotion to our country. It measures everything, in short, except that which makes life worthwhile, and it can tell us everything about America -- except whether we are proud to be Americans." - Robert F. Kennedy

Bill Moyers. America at its best.

Anglo health. (from DailyKos)

One of the problems of the current left-wing discourse is the scorn of all that is "family" and "security" oriented. Only conservatives and authoritarians talk about those issues, so they say...

The "ignorant" people care about these "reactionary" issues.

Can I propose a different view of the world: Family and Security are fundamental values in a sane society. It has been a failure of the left to ignore them.

Security brings about the image of fascistic/stalinistic/authoritarian states. But the bottom line is, the right to access both public and private space without being harassed is a fundamental right: like education or health. Actually it is quite difficult to even exercise the other fundamental rights if streets are not safe. Violence and insecurity also breed in mistrust for "others". And of course, if streets are insecure, more affluent people will be able to buy out security (by self segregating in secure places), making a basic human right only available to a select few. This is not an endorsement of police brutality or anything like that, it is just a simple statement that a more secure and non-violent society should be a "left" priority and we should not be afraid to embrace it. How? That is another (much more complex) topic, I am just making a philosophical stance here: The "left" should embrace the idea that all people should be entitled to a non-violent environment (and "non-violent" could and should, of course, also encompass the right to health/housing without which existence is a violent experience).

Family...

Yes, yes, family used to mean a close group of macho controlled, female submissive, heterosexual based relationships, which, after started could not be abandoned and had to be endured "until death separates us apart". But we can go past that can't we? We are now in a position to redefine family as a voluntary association based on various types love and equality. I am fully aware that things are not perfect but, instead of fighting the notion of family, the discourse could shift in both protecting families and continuously redefining family (and community) in a more democratic way. Family and local community are the most direct places to practice solidarity and community involvement. I would say, that when the left abandoned the concepts of family (for good/comprehensible reasons) towards a more "cosmopolitan" view of human relationships is also helped to shape a cultural environment which favours atomization/mobility and ultimately disconnection from strong, long lasting human relationships which are the fabric of a more emphatic society...

Yep, just Sunday rumblings...