economics nuttiness

We are certainly seeing a serious schism in american political life. One might argue that it's time for the country to split into two. Not north versus south, but ultra conservative versus moderate (never mind about ultra liberal, they are a weak force in politics by now). Clearly there is a major fraction of the US population that does not really accept a real role for government - they don't accept the fundamental concept of civitas. They may think that police, fire, education and the arts should all be privately managed, i.e. only available to the well-to-do.

Let's review what actually happened during the past 10 years. After 9-11, the US became hugely militarized, and the the Patriot Act one could say pretty fascistic (when it needed to be, and not against most of the population, but against targeted groups certainly). As usual in time of (effectively) war, the country rallied around its government and its elected political majority party. Unfortunately, the actual military actions were rapidly hijacked by a totally irrelevant agenda, i.e. the conquest of Iraq rather than a focused campaign against Al-Qaeda and its associated groups. Clearly the entire Iraq campaign was unnecessary from a home security perspective (regardless of its possible value to Iraqis under their dictatorship, although it's arguable whether we've actually done the poor Iraqis any good at all). Moreover, it was hugely expensive. The failure to focus sufficiently on Al-Qaeda probably made the subsequent military expansion into Afghanistan necessary.

At the same time that these two wars were prosecuted, marginal tax rates were lowered and financial speculation was wildly over-encouraged, leading to the 2008 fiscal meltdown. The huge deficit incurred by now in the U.S. is a clear outcome of those mostly Republican policies (although plenty of Democrats played the banking deregulation game as well, to their shame). Now hard line Republicans want to finally pay for those wars and financial shenanigans by ultimately eliminating Social Security and Medicare (though most of them won't say as much in as many words). So the true vision of these hardliners is clear: a dog-eat-dog world where nice guys finish last, robber barons run the country, and the justification is that after all maybe I could be one of those robber barons if the rule of law is practically abolished. Sorry guys, but I don't agree with your basic premise. I think it is possible for the country to have sustainable "entitlements", in fact that is not even the right word for them. Social Security and Medicare are basically national savings plans, they are paid by everyone's taxes because everyone will need them some day. The way to prevent them from bankrupting the country is to manage them, which is hard, not to abolish them which seems easy but is in fact vicious and mean.

OK, my two cents today, inveighing against mean spirited fascists.

Rare genetic disorders

this is cribbed from my FB page, but liked it enough that I wanted somewhere more permanent for it. The topic is the genetic analysis of rare single-gene disorders, what are some of the rationales justifying that work.

Our genome has something like 20,000 genes and we need to know what the consequences are of mutations in all of them. In some cases they will be of very general significance, such as mutations causing breast cancer or diabetes or osteoporosis; in such cases even if the genetic disease is rare the genetic pathways identified may provide new drug targets for a much larger number of people who have the same disease due to non-genetic defects in that pathway.

Moreover, even though each of these single gene disorders is individually rare, in aggregate there are thousands of them and together they comprise a significant fraction of pediatric hospital patients. Since each disorder is different, the only way to diagnose and determine optimal patient management is to understand the molecular bases of all of them - so far the human genetics community has characterized about 2500 rare genetic disorders (I personally have been involved in discovering 15 of these). That is still fewer than 20% of all potential single-gene conditions. These include very well known things like Huntington disease, cystic fibrosis, and some forms of breast and colorectal cancers, but also tons of relatively unknown (to the public) things like Marfan syndrome (maybe Lincoln had it), neurofibromatosis (elephant man), achondroplasia (many forms of dwarfism), and metabolic disorders including one that all children born in the modern world are tested for (by enzyme activity, not by DNA test) phenylketonuria. In addition, by studying the genomes of patients with rare disorders, we are learning a lot simply about genetic variation, which is essential for when we move on to trying to understand the genetic component of more complex diseases which have multiple genetic and environmental factors. At the moment we are not really smart enough to tackle that problem (although many scientists are trying), we have to take baby steps. On a purely logistic note, these kinds of discoveries (for rare genetic disorders) cost on the order of thousands of dollars each, sounds like a lot but compared to hundreds of millions that are spent on diabetes, obesity, cancer it's a superb return on investment to the taxpayer

thoughts on health care in america

In the immediate aftermath of yesterday's controversial court decision, saying that the health care plan requires unconstitutional control over private citizens' pocketbooks, there seems a very widespread sense that the single payer plan would have circumvented this legal problem. However that alternative falls afoul of the reactionary impulse toward smaller government at all costs. It seems to me that this is less a case of the white house and congress kowtowing to industry, but another in a series of poor but necessary compromises with a strong right wing. This is part of the larger breakdown in american political life between what I would call modernists and antiquarians. It is simply not feasible or realistic to have a 'small' federal government in a huge highly industrialized country. Our system of checks and balances is still the best way to control the excesses of power, even when it works poorly or slowly. The alternatives, too much central power or too little, lead separately to police states or to gross economic inequity. I suspect that hundreds of years from now when historians consider the 21st century, that is the major conflict that they will see.

GM foods

A friend of mine asked me what I thought of a particular author's argument against genetically engineered foods, in particular GM corn expressing high levels of bacillus thuringiensis toxin to target particular pests. Here's my response (some points may not make sense without reading the original, but you'll get the picture):

Unfortunately, my motto these days is trust nobody. I don't automatically trust any company. There are plenty of people in companies (including most of their scientists) who are honorable and do their best to make a useful safe product. There are also obviously completely amoral people in companies who don't care about anything whatsoever except money. I also don't trust anti-corporate luddites because they typically indulge in shoddy thinking (as indeed you note multiple instances in this guy's rant against BT). On the other hand, I don't like the idea of eating corn containing large amounts of any bacterial protein as a result of overexpression in the corn cells themselves. I also don't like the idea of eating corn sprayed with neurotoxins, or corn covered in fungus containing neurotoxin because it was not sprayed or engineered. As long as we grow food on huge farms, some kind of technology will be used to keep pests off, and it's all at least somewhat dangerous. The alternative is to watch a big chunk of the world starve to death. As long as human beings are trapped in their genetically evolved "Have to make exponentially more copies of myself" mindset, these things are inevitable.

2012 not

Wow, I really did not blog at all in 2009, what's wrong with me? Anyway, having just seen 2012 I am inspired to point out a few of the more obvious scientific either blunders or at least tremendous unlikelihoods. First and foremost, I can't imagine any way that alignments of the planets would have an effect on the sun's activity. The planets have negligible mass compared to the sun's, so I don't think general relativity would predict any variation in solar output based on position of planets. Secondarily, I'm not aware of any obvious alignments in the planets coming up any time soon. This is more speculative, but I'm not sure whether the mayans actually knew of the planets, in the sense of recognizing that they move differently than other "lights in the sky" and predicting their patterns mathematically moreover.

The exact nature of the solar event is not specified in the movie (lucky for them! I can't pick it apart) but the claim is that it generated a lot of neutrinos. The sun already generates a lot of neutrinos, almost all of which go right through the earth, us, and all regular matter without effect. One thing that does generate bursts of neutrinos is supernova explosions - neutrino detectors place around the earth all saw the burst that preceded the visible appearance of supernova 1987a in a nearby galaxy. By the by, this was a wonderful validation of solar physics theory. I think we would have noticed if the sun had gone supernova. But in the movie these were not ordinary neutrinos, they "mutated" into some other kind of particle that could heat up the earth's core. Well, anything is possible, but I would expect something that could heat the earth's core to fry pretty much everything on the surface first. The core is mostly iron and nickel we think, so maybe these mutated particles just heat up metals. But we have a fair amount of iron in our bodies (all those red blood cells and hemoglobin, for example, plus lots of muscle myoglobin) so we should have heated up too.

Some new kind of solar wind that could do that to the earth's entire core would certainly have fried all communications systems. But tv and cell phones were working in the movie all the way through, as were cars, planes and other metallic engines and motors using electromagnetic induction fields.

More realistically, solar physicist expect the sun to expand into a red giant in a couple (5-10) of billion years. That is a real problem, the sun will grow probably to larger than the earth's orbit, and the earth (plus venus and mercury) will either melt or vaporize. We'll have to do something by then - leave the earth, move the earth, or learn how to control the sun. None is even remotely in our reach today, but a billion years is a long time. The average survival of any species on earth has been about a million years, and we humans aren't even halfway there yet. I myself doubt we'll make it that long, but maybe we will smarten up sometime.

personality type

I'm an ENFJ. That's a particular kind of personality type based on the Myers-Briggs classification scheme (check out Wikipedia for more on the scheme). First question, how reliable is the classification itself. The test involves lots of questions and redundancy, and seeing the outcome I'm reasonably comfortable with this typing.

E means extraverted. I do think a lot about other people though, how they might react to me, what they may be thinking about. If someone describes having a problem I tend to jump in with ideas or suggestions - which can be helpful but obviously not always. I sometimes jump in pre-emptively, to say that I know someone else who knows something or can help with whatever the person I'm talking with is talking about. Networking comes automatically to me.

N is for intuitive. This is a very particular sense of the word according to MB. It refers to the kind of information that is gathered and relied on, whether it's more sensory or more abstract and related to other similar information. I have a strong tendency to make connections between ideas, so that they validate each other. As a scientist (or even as a person) there always has to be validation by real observation, so it's not a matter of ignoring sensory input. But pure observation is overwhelming, I use patterns and schemes to organize it, and these come from internal reflection (as in intuition) but also as I said by cross-checking with other information. Ideally the different kinds of information are orthogonal, that is, based on really independent sources, so less likely to be purely coincidental.

F meens feeling, versus thinking (T). This too has to be understood within the language of the scheme, these aren't the common uses of the words. These have to do with paradigms of decision making. F tends to make decisions from within a situation, rather than from the outside. I'm not too clear about this one, for me to be an F seems a little bit contrary to also being an N. But for the afficianados of MB, there it is.

Finally, J means judging rather than perceiving. This seems to have to do with how one is perceived by others, as logical or more emotional and empathetic. My being a J here makes sense - although I think of myself as quite logical, I'm probably not really perceived that way by others (but feel free to comment!).

In any case, ENFJ types come with fairly specific description in the system. They are sensitive to others, they react to the general tone of a situation, and they are often organizers. In the Keirsey system, which is related to the MB system but focuses more on the practical implications, ENFJs are described as idealists, with a strong bent to being teachers. For sure I have a strong pedagogic streak, I love explaining things. That can be quite tedious if overdone or in the wrong social context. But when I give lectures I spend lots of time on the materials, and try to think about the information that I'm conveying as I want it to be perceived by my listeners.

It gets more interesting when you see how you match up with your partner. There are 16 MB types, so 256 different pairings of course. I don't think MB has something to say about each of these, but it's fun to make the comparisons ourselves.

That's all I have to say about that!

account management

How many accounts do you have? In my case, let's see, just at home I have my main email address, my previous email adddress which is still working even though we changed providers and don't have that service any more, my facebook account, my linkedin account, and my blog. These are just the personal ones, that doesn't include all the various banks and other financial and "home management" ones. At work - don't get me started. And if you're like me, many of them require regular changes of password for "security", but not on the same schedule of course. No one could remember all those changing passwords, so of course we all use shortcuts, common formulas, or even (heaven forbid) postit notes on our desks. My laptop tries valiantly to keep up, but it seems to be rather poor at it, since it tends to auto-fill in the wrong password for many sites I log on to, so I have to repeat it manually anyway. And then of course once you clean up your internet activities by deleting your temporary files, page history, and cookies, it's all gone the next time you fire up the browser. It's not that I prefer a world without computers, it's just that they do eat a fair amount of time for things that were supposedly easy, and also create new frustrations that require new coping mechanisms (besides throwing the mouse against the wall, that is).

I was going to write a nice blog about summer and the flowers in my garden, but it took 15 minutes to remember how to log onto this account since it appears to be irrevocably attached to my previous, not my current email address. This is not obvious because my current email address is there in my profile, but that's not the same as the one the account is formally linked to - and there seems no mechanism to update that, I think I would have to stop this blog and start another one. Arggh. Well, the flowers are very nice but more details will have to wait...