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Saturday, February 23, 2008

Satellite Takedown

Brendan of I Hate Linux, Lady of tdaxp, and I were eating at Pizza Ranch this evening, discussing the US military's shoot-down of the failing spy satellite. With respect to the armed services, we came up with a better method:

  1. Build a giant trebuchet. Giant. So large that low-altitude satellites will need to be diverted to avoid hitting it.

  2. Launch a large boulder from the trebuchet to the Sun. Not directly at the Sun, but close enough so that Star Trek IV-style "slingshot effect time travel method" occurs, sending the boulder back to when the satellite was launched.

  3. Because the trebuchet was built so carefully and aimed so precisely, the boulder hits the rocket that is carrying the satellite during take-off, destroying it on the launch pad.

  4. The engineers in the past, aware that such a direct hit by a boulder from the Sun could only occur because of a time travel into the past in order to prevent a mistake, realize that something is wrong with the satellite. They then rebuild it, but better, avoiding whatever went wrong, as well as eliminating the need for the trebuchet, and, more importantly, the need to waste all the fuel diverting the functioning satellite's out of the trebuchet's path.

The last point is important, because the trebuchet is a carbon offset, eliminating the need for environmentally-unfriendly rockets.

22:28 Posted in Science, Vanity | Permalink | Comments (10) | Tags: satellites, trebuchet

Tuesday, February 12, 2008

More Jews than Whites. What?

Once one of the largest races of man? Or just almost no whites?

From Dienekes and gnxp, part of the conclusion of "Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping" (pdf):

There were small but significant differences in measures of genetic diversity between
AJ [Ashkenazi Jewish] and CEU [Utah whites from the HapMap sample]. Analysis of genome-wide LD structure revealed a greater number of haplotype blocks which tended to be smaller in AJ. There was essentially no difference in global LD decay between AJ and CEU, although there was a tendency for faster decay of nearby SNPs and slower decay of intermediate distance SNPs in the AJ. These data are more consistent with the AJ as an older, larger population than CEU, and would suggest that, depending on regional differences in LD structure, AJ populations may not always provide an advantage for whole-genome association mapping.

I asked:

Re: the population sizes, would a more reasonable non-mathematical rendering be that the smallest AJ bottleneck was larger than the smallest CEU bottleneck, or the average AJ population size was larger than the average CEU population size?

And the Henry Harpending (you may remember him) replied:

Re Dan's question: either answer could be right. Instead of thinking about effective size think of the inverse of effective size, (1/Ne), which is the rate of diversity loss. This inverse can be averaged over time, like any speed. A bottleneck has a much larger effect on the average of (1/Ne) than it does on average Ne.

Will this put an end to the talk about a bottleneck in Ashkenazi history and about Ashkenazi disorders being the result of drift?

This is what is so exciting about widespread genetic testing: not only can we actually get answers for some old questions (are there different genepools within the human race? yes) we can ask questions that never would have occured to us before (what was the last year when Jews outnumbered whites?).

15:41 Posted in Science | Permalink | Comments (6) | Tags: race, jews

Saturday, February 02, 2008

The Genetics of Systems Administration

First, the abstract from Chris Dawes' and Jim Fowler's new article, "Partisanship, Voting, and the Dopamine D2 Recepter Gene" (available as PDF):

Previous studies have found that both political orientations (Alford, Funk & Hibbing 2005 [PDF]) and voting behavior (Fowler, Baker & Dawes 2007, Fowler & Dawes 2007) are significantly heritable. In this article we study genetic variation in another important political behavior: partisan attachment. Using the National Longitudinal Study of Adolescent Health, we show that individuals with the A1 allele of the D2 dopamine receptor gene are significantly less likely to identify as a partisan than those with the A2 allele. Further, we find that this gene's association with partisanship also mediates an indirect association between the A1 allele and voter abstention. These results are the first to identify a specific gene that may be responsible for the tendency to join political groups, and they may help to explain correlation in parent and child partisanship and the persistence of partisan behavior over time.

To emphasize: political orientaiton, voting behavior, and partisanship all are partially determined by genetic heritage.

From a Systems Administration perspective, to the extent that the weight for or against perctain political orientations, voting behaviors, or partisan attachment are different between states, the "baseline" performance of those states will vary

15:02 Posted in Science | Permalink | Comments (2) | Tags: sysadmin, genetics

Thursday, January 17, 2008

Practical Eugenics

Gideon, writing at a public defender, criticizes castration of violent felons because those violent felons may be rehabilitated:

Prof. Berman asks whether chemical castration (if proven to work) should be employed (actually, why shouldn’t it be). As readers might guess, I am uneasy with this proposition. There are several assumptions here: That we know that “high-risk” offenders will re-offend; that all “high-risk” offenders will re-offend. This does dip into some “Minority Report” territory. I’m quite uneasy by the idea that we will assume that all high-risk offenders are going to re-offend and we need to stop that by subduing the sexual urge by reducing levels of testosterone.

Those are some mighty assumptions and I’m uncomfortable with that. There are (have to be) better alternatives to this. What if we have an offender that, despite being “high-risk” is rehabilitated and wishes to live a normal life?

However, to a large extent, speaking about rehabilitation of violent felons misses the point.

Consider: violent crime is heritable:

Estimates of heritability for antisocial behaviour from recent research in quantitative genetics cluster around 0.50. The most reliable estimates come from contemporary studies in the Netherlands, Britain, Norway, Sweden, Australia and the US, because these studies examine large, representative samples using sophisticated quantitative modelling techniques. A complementary meta-analysis of 51 twin and adoption studies yielded an estimate of heritability of 0.41 for the genetic influence on antisocial behaviour. Estimates of heritability below 0.20 tend to emerge from studies with unusual design features; for example, observational measures, small sample sizes, very wide age ranges, small groups of girls, or adults being asked to report childhood symptoms retrospectively. Similarly, some, but not all, studies yielding estimates above 0.70 have non-optimal designs, such as small sample sizes or adults being asked to report their childhood symptoms retrospectively....

The largest estimates of heritability tend to emerge from studies using measures able to array individuals along a continuum from non-antisocial to severely and persistently antisocial. These are studies using other-reported delinquent or aggressive behaviours (such as the Child Behaviour Check List (CBCL) externalizing scale), and self-reported personality traits (such as the MPQ aggression scale). These studies tend to include a very large number of items inquiring about a variety of antisocial attitudes and behaviours. Some of these items, such as robbery, are exhibited rarely by people, but others, such as enjoying violent films, are exhibited commonly. As a result, the instruments are sensitive to population variation in the severity of antisocial behavior. Overall, the distribution of more than 100 estimates of heritability from recent papers approximates a bell-shaped normal curve. This distribution is to be expected from a sample of more than 100 imperfect estimates of a true effect that equals 50% in nature.

Further, we are currently undergoing dysgenics as the most violent mate with each other:

As well as the possibility that genes influence antisocial behaviour, it is also possible that antisocial experience can influence how genes are distributed in the population. This is an implication of the finding that men and women mate on the basis of similarity between the partners’ antisocial behaviour (this is called assortative mating), and that couples in which both people exhibit antisocial behaviour tend to have more children than the norm. Assortative mating on a genetically-influenced phenotype, such as antisocial behaviour has consequences for genetic variation in the population. Because people form unions with other people like themselves, the result is that families differ more from each other on average than they would if people mated randomly. If successive generations mate assortatively, genes relevant to the phenotype will become concentrated within families. Consider height as an example. Whole families clearly differ from other families in terms of height, yet families are made up of persons who are similar in height. Part of the explanation for this phenomenon is likely to lie in the positive assortative mating that occurs for this trait.

Castration of violent criminals, besides reducing the likelihood of a particular criminal breaking the law again (and quite possibly inflicting a punishment seen as worse than a 20 year sentence), does even more good to future generations. Violent criminal parents tend to have violent criminal children, so unless we want future generations to experience violent crime, we need to fight the causes of violent crime.

And part of the solution is eugenics.

On the web: Genetics and Human Behavior: The Ethical Context: Current findings: Quantitative Genetics.

Monday, January 14, 2008

When we began

When "we" began is a topic that's the subject of a lot of research but (considering the mutual hostility toward biological science by all parts of the political spectrum) not much publicized. The first physically modern humans probably weren't like us at all, except in outward appearance.

"Behaviorally modern humans" began about 80K year ago -- this marks the first time that humanity is able to circumvent the blockade imposed on us by Neanderthals and Homo Erecti (Peking Men). Before circa 80K, the boundary of our species was determined by climate so, for example, Palestine was settled by Neanderthals, taken by physically modern men, and then retaken by Neanderthals -- all basically a function of the temperature. 80K years ago, more or less, humans build boat, go along the coast of Asia (but apparently not entering -- Peking Men probably ate us) and got to Australia.

"Culturally modern humans" seem to have started roughly 10K years ago, when inhabitants of the fertile crescent -- who had not yet discovered farming -- started living in cities. Consider that: for the first time, our species was living in high-density because we wanted to -- because it was better to be with our fellows than be out in packs, even though we were still hunting animals and gathering plants. This doesn't mean that behaviorally modern humans would not be capable or willing to live in cities, but the for the first time a metastable equilibrium toward city life existed.

In A Farewell to Alms, Greg Clark argues that what might be called economically modern man finally emerged 200 years ago, in England, after an extremely long period of intense malthusian selection. Clark's politically smart enough to be coy about the mechanism, but it's pretty clear he's talking about genetic natural selection. (Malthusian selection really only operated in situations where starvation was a major cause of death. Among the Plains Indians, high rates of violence guaranteed there generally was enough food for everybody. So the Sioux were taller than some of the European settlers, because their more violent society was healthier for those who lived.)

Domestication is a continual process that produces dumber, weaker, and friendlier creatures. Our species is undergoing domestication -- at different rates in different places and in different times.


This is why shrinking the Gap is more important than global warming: climate change is easier to deal with the later you put it off, because economic and technological growth compounds, making the solution easier every year. Shrinking the Gap probably gets harder every generation, as populations continue to diverge. Further, as populations are much larger nowadays (increasing the rate of natural selection), every generation of divergent evolution now is worse than a generation, say, ten-thousand years ago.

16:04 Posted in Science | Permalink | Comments (11) | Tags: domestication

Sunday, January 06, 2008

The best video I have ever seen on the internet

Hackling Life, by a professor at MIT at a programming convention in Germany.

From inkjet DNA printers on eBay to programmer-style documentation for genes (with a new field, average time to mutation, added), infinitely fascinating.

06:55 Posted in Science | Permalink | Comments (2) | Tags: genetics, wetware, open source

Monday, December 31, 2007

Guns, Genomes, and Steel

I'm currently watching the PBS version of "Guns, Germs, and Steel," based on the book by Jared Diamond. My take is that Guns, Germs, and Steel is a story of the rise of the genomeplex -- that assortment of different species (cows, dogs, men, etc) that together make up the foundations for human culture.

In short, Diamond's argument is that biologically-driven efficiencies in every plant and animal in the genomeplex except for homo sapiens led to the rise of homo sapiens. Clearly, biologically-driven efficiency is a powerful argument. If one's crops provide less protein, or one's animals are less docile, one is not going to get as far in life.

But neglecting to mention our species in a story of the rise of our genomeplex is strange. One line from the documentary I think sums of Diamond's blindspot:

pigs do not give milk

This is obviously incorrect. Pigs are mammals. Pigs suckle their young.

Further, as far as human-drinkable milk goes -- neither did cows! The ability of adults to drink cow milk comes from a mutations (several of them, occurring independently, in different places and times). Our ancestors could not drink cow milk. But our ancestors' children were mutants.

Lactose tolerance is one mutation that occurred in some populations but not others, but there are other mutations like this too.

The rest of our genomeplex is not equal in productivity. Our species is not either.

The difference? The other animals and plants are to the extent they serve us. Humans are valuable in themselves.

Most of this world, like most of our genomeplex, has no inherent value. But humans do. And radically, all humans are equally precious.

09:09 Posted in Science | Permalink | Comments (7) | Tags: jared diamond, genomeplex

Categorization and the Nature of Science

Does the Core and the Gap exist? That is, does a generally well-off realm known as the Functioning Core contain goods associated with globalization (wealth, peace, etc), while a realm known as the Non-Integrating Gap lack these goods?

Mountainrunner, surprisingly, appears to say the answer is no. While he does not say so directly, he notes that (in general) anything that exists in the Gap exists within the Core, and vice versa. In response to my claim that the assassination of former Pakistani Prime Minister Bhutto is not surprising because it happened in the Gap, Mountainrunner wrote:

My point is this: this is about violence and death and ideology that is not specific to Islamists or the Gap. Heads of state were targeted. The IRA reminded Thatcher they only needed to be lucky once, she needed to be lucky all the time. Italy, Greece, Hungry, etc. Take your pick and you'll find attacks on leadership.

A similar mistake is made by those who deny the existence of "race," or often the "generations of warfare:" a misunderstanding about what categories are.

Categories are not Platonic ideals, true forms that are immutable through time and space. Categories allow us to explain variance. That is, a categorization is useful if categories within it correlate with clusters in frequencies of some traits. Consider again the Core and the Gap. There are rich people in the Gap, and poor people in the Core. There are those with IPTV in the Gap, and those without electricity in the core. For that matter, there are gang rapes in Darfur and gang rapes in Dallas.

But the terms "Core" and "Gap" really do explain variation in these things. Don't believe it? Run the numbers yourself. The same is true with regard to race, and my assumption is that the same is true with regards to the generation of war.

Objecting to the Core/Gap categorization because you can cite assassinations in Core countries is like objecting to the concept of race because you know some East Asians who drink milk. (Because I am unaware of any large dataset on war that's been used to test xGW theory, sadly we're still in the realm of mixed methods when it comes to the generations of war.)

The moral of the story: categories explain variation. That does not mean they explain all variation. That does not mean they are supposed to.

Anything else is just... unscientific.

Also on the web: Against xGW, for William Lind? On another aspect of Mountainrunner's post.

Friday, December 21, 2007

Human Genetic Variation is Science's Breakthrough of the Year!

Pennisi, E. (2007). Breakthrough of the year: Human genetic variation. Science, 318(5858), 1842-1843, available online: http://www.sciencemag.org/cgi/content/full/318/5858/1842 (from John Hawks).

We have gone from using genes to contrast us with the chimpanzees, to using genes to contrast us with each other:

The unveiling of the human genome almost 7 years ago cast the first faint light on our complete genetic makeup. Since then, each new genome sequenced and each new individual studied has illuminated our genomic landscape in ever more detail. In 2007, researchers came to appreciate the extent to which our genomes differ from person to person and the implications of this variation for deciphering the genetics of complex diseases and personal traits.

Less than a year ago, the big news was triangulating variation between us and our primate cousins to get a better handle on genetic changes along the evolutionary tree that led to humans. Now, we have moved from asking what in our DNA makes us human to striving to know what in my DNA makes me me.

Techniques that scan for hundreds of thousands of genetic differences at once are linking particular variations to particular traits and diseases in ways not possible before. Efforts to catalog and assess the effects of insertions and deletions in our DNA are showing that these changes are more common than expected and play important roles in how our genomes work--or don't work. By looking at variations in genes for hair and skin color and in the "speech" gene, we have also gained a better sense of how we are similar to and different from Neandertals.


In one study, geneticists discovered 3600 so-called copy number variants among 95 individuals studied. Quite a few overlapped genes, including some implicated in our individuality--blood type, smell, hearing, taste, and metabolism, for example. Individual genomes differed in size by as many as 9 million bases. This fall, another group performed an extensive analysis using a technique, called paired-end mapping, that can quickly uncover even smaller structural variations.

These differences matter. One survey concluded that in some populations almost 20% of differences in gene activity are due to copy-number variants; SNPs account for the rest. People with high-starch diets--such as in Japan--have extra copies of a gene for a starch-digesting protein compared with members of hunting-gathering societies. By scanning the genomes of autistic and healthy children and their parents for copy-number variation, other geneticists have found that newly appeared DNA alterations pose a risk for autism.

Relatedly: does genetics make Karl Popper obsolete? (Hat-tip to gnxp.)

07:20 Posted in Science | Permalink | Comments (1) | Tags: genetics

Sunday, December 16, 2007

An Artificial World

(From my comment over at DM's blog, inspired by a conversation with Sean and a post by Shlok.)

The greatest change every to befall earth is not climate, or glaciation, or any of that: it is the rising-up of a artificial genome-plex -- that giant interspecies culture that began with a few proto-chimpanzees kicked out of the forest and now stands at hundreds of species that that are "artificial" --- man, dog, cat, cow, horse, and others. Of all large animals that existed before this new community, every one has since been domesticated (that is, breeding has led to the survival of docile offspring while the rest have been allowed to die off) or kept around for amusement (elephants, rhinos, and the rest)

This has never happened before.

10,000 years ago the artificial genome-plex radically expanded its scope, adding plants to its army. Corn, wheat, barley, potatoes -- all manner of plant species that could not exist by themselves in the wild -- were artificially created from free ancestors.

When Jurassic Park came out, the idea of bringing dinosaurs back to life seemed incredible. I think now it's just as much a matter of time. Same thing for other extinct animals, and extinct plants.

The genome-plex is preparing to cross time.

What Jurassic fruits taste the sweetest? Which plants eaten by the triceratops would make good raw material for ethanol? I think we'll live to have a good idea of the answer to these questions.

We live in a world, radically artificial twice over, and we haven't begun to see what it will hold.

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