The genome is neither a blueprint or a map, it's more like a set of Ikea instructions.

1. Make lots of cells by mitosis.
2. Now there are a lot of cells. If you are a cell on the surface of the ball of cells, turn on gene 125. If you are inside the ball of cells, turn on gene 452.
etc etc
4,567. If you are a cell next to some other cells that are next to some other cells that have gene 452 turned on, turn off gene 452 and turn on gene 681.
etc etc.

In other words, there is no way to easily "decode" the primary DNA sequence of a genome and "guess" what the organism would look like. Genes get turned on and off, proteins and other biomolecules get made, they assemble together (or not) and physically modify each other by phosphorylation, glycosylation, etc (or not), and cells end up having certain shapes, which in turn cause organs to end up having certain shapes, which end up making the whole organism have a certain shape. Some of this is encoded in the basic laws of physical chemistry, which even for a single protein cannot easily be applied. So it's no surprise that we are still absolute infants in our understanding of genomes. I consider this to be a project of centuries at least, hardly years or decades. That doesn't mean we can't answer some reasonable questions, like are there specific genes which if mutated cause someone to have high cholesterol (yes), or get lung cancer with high probability (I don't know). But these are just the tip of the real genomic information iceberg.

I have just finished reading The Price of Inequality, by Joseph Stiglitz (Nobel price in economics 2001). Despite the author being a "pundit" and someone who has advised to governments, hence could be accused of being part of "the problem", I found this book a compelling analysis of the failures of the new right wing economic theorists. Though not shying away from more technical analyses, the book also makes some points with utter clarity, while not overgeneralizing: "Taxing bad things (like pollution) is intrinsically more efficient than taxing good things (like work)" (my paraphrase). "Rents (things like government subsidies or tax breaks to particular industries) are inefficient and at the same time contrary to the principles of free-market capitalism itself" (again, my paraphrase). Clearly he sees the prevalence of rents (things like regressive taxes, military spending, unlimited campaign contributions, being motivated by power politics, and not defensible even if one accepts de-regulation -which he does not accept anyway.

The book is repetitive in places. On the other hand, there are many examples where the author explains with lucent and simple prose why bad ideas are bad and are hurting the economy, that it's beautiful, although at the same time very frustrating - isn't anyone in power reading this stuff?? For myself, I can only conclude that there is indeed a class war going on, on the part of the rich to shut everyone else out. It is well understood that owners benefit from high unemployment in the short term, giving them leverage to lower wages or other forms of compensation without losing productivity. In the long term of course this leads to societal breakdown if not outright revolution. But who takes the long term any more? Stiglitz may not be an outright socialist, but he makes it clear that he considers the purpose of the economy as being to benefit the greatest number of people, not to create the greatest amount of total wealth regardless of how that wealth is distributed.

One point that does bother me, as with other economists the author downplays or ignores the role of cheap energy as a driver of wealth production in the post-WWII world. When the US hit peak oil in the 1970s, world oil prices went up almost immediately as OPEC now had the economic leverage to raise those prices without the US keeping prices low with its own supply. Although higher oil prices raise profits, they also raise costs for just about everything we buy including food, clothing, housing etc. I have yet to see a hard-core economist explain how we can expand "wealth" distribution to the entire population, even with fairer tax codes, etc, in the face of higher intrinsic costs of production of all goods. The economists who do in fact address rising oil prices and coming oil shortages, seem to think on the whole that endless growth is impossible. If the human population keeps growing, but total wealth does not, then obviously people overall will get poorer, even if some ("capitalists" say) get richer.

Sensory mnemonics

OK I realized something tonight. We have a nice mnemonic for the colors of the rainbow (ROY G BIV) and also for the notes of the standard musical measure (EGBDF and FACE). We need some new mnemonics for the other senses. So here goes (hoping this goes viral): The tactile spectrum, FOR B. GUS: Furry, Oily, Rough, Bristly, Gooey, Uneven, Smooth The odor spectrum, BOB VILA: Basil, Orange, Beefy, Violets, Iodine, Licorice, Ammonia.      Make up your own!

Pure, unregulated capitalism leads to endless series of boom and bust cycles; this seems documented beyond doubt through detailed historical analyses. The bust cycles always cause serious economic hardship, which is bound to fall on the poorer members of society more harshly - if rich folks lose a greater percentage of their wealth, they can usually afford it as long as they have reserved a proportion to cover their basic needs. The obvious corollary is that ONLY governments can mitigate such hardship. The issue therefore is whether one believes in such mitigation or not, not whether "states" or the "private sector" can step in - demonstrably the private sector cannot. The republican agenda is that governments simply should ignore the suffering of the citizens. This is economic elitism at its most ugly and mean. I am not saying that endless government spending is the solution to everything. It is also clear that public debt has to be managed; at some point too much debt also causes hardship. The weakness of the republican platform is to decry current levels of US debt. Levels are high, but not as high as many other countries'. Furthermore, given that the dollar is still the international currency of last resort, there is no evidence that high debt is causing any immediate fiscal weakness. It has serious impact, because the financing costs of the debt still come out of the federal budget, leaving less money for other things. What I am saying is that the extreme reaction against federal government should be viewed clearly - it is a desire to return to a "simpler" life, which has a BIG downside notwithstanding the romantic idealism it seems to induce.

life changes

My mother passed away last week. I was with her for about three weeks immediately before that, during which time she grew increasingly weak. I was present and holding her hand when she went. I want to keep a record of various thoughts and memories, nothing that shouldn't be read by others but not necessarily of particular interest to anyone else. Caveat lector! Food for the body: As a result of her illness (multiple myeloma) in the last few months mom lost most of her appetite as well as a lot of weight. She revived a bit when my wife and I and then my brother and his girlfriend showed up. One evening she treated us at a nearby Portuguese restaurant. She had asked my brother if he liked lobster and when he said he did she presumed that that was what he actually wanted and tried to order it for him, which he had to forestall to get what he actually happened to want. There was half a lobster in my paella though which was excellent, so mom ended the evening satisfied. On one afternoon mom announced that she felt like calves' liver with onions and a vanilla shake. We guess that her system was demanding iron, but anyway it was another success, though only partial as the liver was overdone after I had to go get and then re-heat it. The next day I searched the kitchen and found her blender, and several times over the next week made her coffee milk shakes which she enjoyed even when she stopped eating solid food. One day when she still had energy to go out, my wife and I took her for mexican. Mom had tacos, a great favorite, and shared a margarita with me. She was already on pretty strong pain meds, but she and I agreed, "why not?" on the margarita. Mom wanted to take us to her local sushi bar. Unfortunately, time ran out and we never made it. A few days after the funeral my brother and I went there to honor her memory. No sake though as it was byos. Food for the mind: For years mom participated in and sometimes ran a book club for local residents and friends. This was a major activity for her. Going through her books, there were a number stuffed with half a dozen or more 5x7 index cards lovingly written out longhand with notes about the author, the plot, points of interest in the book, etc. She often told me about these in phone conversations, as she was deciding which books to review. I wonder how the club will continue now that she is gone. She said that people did not always read the book, but just came to hear the reviewer (not always her) talk about it. Mom was for many years a serious player of duplicate bridge. For those who do not know what this is, the cards are pre-dealt at each table and the same hands are played by different teams. Thus one's team of two is not playing against the other two at that table, but against other teams who had had the same cards, so the challenge is to do the best one can given the deal. This takes most of the randomness out of the game. Mom played in tournaments and on cruises, and had accumulated a large number of "Master points". Oddly, for a highly sophisticated reader, physics teacher and self-avowed intellectual, mom also loved tawdry bodice-rippers. I have now donated whole shelves of them to the local library, where they can start a KSamuels Memorial Romance wing. She was having a lot of trouble concentrating towards the end, and was trying to get through one of these books. She complained that it was going way too slow, she was a third through and no one had gotten laid yet. I think she finally tossed that one. We watched a lot of the summer Olympics together in the last weeks. More on that another time, but in the present context it should be noted that mom had fun discussing with my wife the physiques of the male divers. Things got rather explicit, and I ran from the room in embarassment, prompting her to note that I had always been prudish. Food for the soul: A few days before she died, but was still sometimes alert, I asked mom what she thought came after. She said pretty flatly that there was nothing, when the body went the mind was just gone. I said that I tended to agree, but that if we were both wrong we would meet again. Death is somehow the ultimate adventure. As a scientist, despite my personal opinion and despite having no particular desire to hurry things along, I admit to a certain curiosity to find out whether I'm wrong. We all get to find that out eventually I guess.

conservative politics

In the aftermath of the Nevada republican primary yesterday, the activities of Mr. Adelson have come to the fore. He is a wealthy Jewish casino owner, who has supported Gingrich and now promises to support Romney as well, with the single-minded objective of "defending Israel". This whole thing falls well within the historical support for Israel that has long been a part of Republican party platforms, although both parties have been equally helpful to Israel in practical ways. In this case, and given current evens in the middle east, I feel compelled to comment. Adelson does not "speak for" american jews. It appears to me that his concept of what is "good for" Israel is extremely short-sighted. That country could probably no longer survive a concentrated all-out conventional war of the 1948 and 1967 types. Only its nuclear threat keeps the situation stable. However its neighbors, both arabic and persian, have every right to be concerned about such a one-sided situation, and I think a nuclear middle east is ultimately inevitable. In my personal opinion, only close economic and cultural ties among all the countries of the region can hope to maintain peace in the event of the extremely difficult to avoid coming nuclear standoff. This requires very long-term thinking and society-building, not bluster and aggressive threats. I speak as the descendant of Holocaust survivors.

energy

I've recently become aware of a couple of facts, or more specifically connections among facts. Supposedly income inequality in the US started to rise significantly during the 1970s. US internal oil production peaked in the early 1970s. World oil production reached a plateau in 2005 - it is unclear whether we are actually at 'peak oil' as defined by available reserves, but from a practical perspective it doesn't matter since if reserves are too costly in money and energy to recover, they don't really do any good. A couple of economic sites suggest that rising oil prices from 2005 were at least partly responsible for the timing of the 2008 recession - it was a doomed bubble in any case, but as energy costs rise, then all material costs rise as well, and at some point that simply has to effect the general economy.

So, if these are not just coincidences, they suggest that world economies will never fully 'recover' in some sense. Unemployment may go down, per capita growth measured in dollars may go up. Oil or other fossil fuels will never truly be used up. But the entire united states population, much less the rest of the world, will hardly be able to return to the profligate post-WWII era when one could buy anything on credit, and drive or fly anywhere with little regard to the effects on household budgets. And having won the 'war' on marxism, and added over a billion chinese and russian workers accepting very low salaries (compared to american workers) to the world's competitive free-market doesn't help.

On the plus side, assuming that at some point total world production of everything will contract, measured at least in terms of fossil fuels burned up, then at some point we will in fact stop exacerbating global climate change. The only issue is how bad things will be at that point. The prudent thing to do would be to plan ahead for such a world, and start conserving oil and water now, and finding an alternative economic model to material production-based growth measurements. The typical human thing would be to put head in sand, ignore facts, and starve to death or engage in endless border wars with neighbors over oil or water 50 years from now. I won't say which future I personally think is more likely, that would be too depressing (hint!)