Showing posts with label Science. Show all posts
Showing posts with label Science. Show all posts

Sunday, November 17, 2019

Lucy Jones, "The Big Ones"

Lucy Jones' The Big Ones talks about many major disasters, and what we can do to prepare for them. She is an earthquake specialist (working for the USGS), so she focuses on quakes, but she also spent time working on more general disaster preparedness for various California state and local agencies. The disasters include earthquakes, floods, tsunamis (flooding caused by earthquakes), and volcanoes. Each chapter focuses on a separate incident.

The introduction talks about the structure and geology of earthquakes. The San Andreas, for example, only produces big quakes. The surfaces that are pulling past each other have been ground smooth enough that they stick together. This means it can't release pressure a little at a time; it waits for a sizable build-up, and releases the tension all at once. The magnitude of a quake is determined by how much of the fault releases at once. If it's a short distance, it produces a small quake. Quakes that release a few yards of pressure would be under 2.0. If the rupture goes for a mile and then stops, you get a magnitude 5. A 100 mile long break would produce a magnitude 7.5 quake. Since the rupture front on the San Andreas is pretty smooth, a quake on it will continue to propagate once started, and will cover most of the length of the fault. The built up stresses (at two inches a year) on the southern end of the fault have accumulated about 26 feet of differential since the last major release more than 300 years ago. The section in northern California has had more recent quakes. If two hundred miles of the fault give way, we're talking about 7.8, while 350 miles is conceivable, and would reach 8.2. The section around Paso Robles releases pressure gradually, and should stop further propagation.

I was already pretty aware of the big picture for a major earthquake, since I've been part of the earthquake response teams both at Google and for Mountain View. After a major quake, some roads will be out, and all the fire, police and hospitals will be busy, so no one will get the mutual assistance that they can usually count on. Jones led a team of more than 300 experts as they explored what an 8.2 in LA would be like. Even though building codes have been improving for several decades in California, not enough have been retrofitted to keep this from being a serious disaster. 1500 buildings are likely to collapse including possibly some high-rises. When we drill in Mountain View, or at Google, we always assume that we'll be on our own--no fire or medical help should be expected for a few days. Google (and most other large employers) have plans to be able to feed employees for a few days, and the earthquake team is trained in triage and first aid. But anyone needing attention from a doctor is unlikely to get it.

And all that was in the introduction. The next few chapters cover the volcanoes that buried Pompeii in C.E. 79 (there were early warnings, so there are eyewitness reports from people who fled days or hours before the final eruption) and Iceland in 1783, and the earthquake that shook Lisbon in 1755.

I want to spend more time on chapter 4, which covers the great flood of California's central valley in 1861-2. Just that description should make you suspect that it was bigger than you'd expect. This was a flood that filled the Central Valley, and the water didn't recede for 9 months. California had only been a state for about 10 years at the time, and the only thing that most Californians today have heard about this event is that Sacramento raised its street level by 10 feet in response.

Most people who are familiar with California weather know that most of it is basically a desert. It usually only rains in the winter, and most of the rain falls in the mountains. We only have enough to drink because we dam the rivers, and store water from rainy years in the reservoirs. If you live here for a while, you get used to the idea that some winters are pretty dry, and other years, we'll get a couple of storms that seem to get stuck here, and we can get rain that lasts for a week or two.

Starting in December 1861, the rain throughout much of the state was continuous for nearly 45 days. Other than the mountainous areas, normal rainfall is 12-18 inches, with 24 inches being heavy. That storm apparently dropped 5-6 feet of rain in many places. There were no dams at the time, so by January 9th, the water in Sacramento was 24 foot above its normal level. Most of the city was at 16 feet, so the water was 8 feet deep. The water was still there 3 months later. But this was only what was visible at Sacramento, which is pretty much the northern tip of the central valley. The entire central valley: 30 miles wide and 200 miles long was inundated to a depth of thirty feet. Innumerable cities and towns were completely washed away. All the cattle grazing there died.

Modern California has dams and reservoirs, but they wouldn't have been able to hold back this much water. It was only 150 years ago, and there's no reason to think that extreme variation in annual rainfall has abated. Jones says that geologic records indicate we should expect this much rain "once every century or two", which is suitably vague, but scarily often. There's no way we're prepared for an event of this size. We now get decent alerts about rain two weeks ahead, but several recent winters have included anomalous weather patterns that persisted for longer than that, and the weather bureaus don't have much more to say than "we can't tell how long it'll last". If it starts raining and doesn't stop, we won't know until two weeks before all the dams are overtopped.

Later chapters cover flooding on the Mississippi and in New Orleans, tsunamis in the Indian Ocean, other disasters in Italy and China, and Japan's Fukushima, which combined earthquake, tsunami, and nuclear meltdown. She talks about emergency response, long-range preparedness, and our tendency to estimate the future based on past incidents we're familiar with.

Saturday, October 12, 2019

Order Without Law, Robert Ellickson


Robert Ellickson's Order Without Law is a study, as its sub-title says of "How Neighbors Settle Disputes". Ellickson starts with a deep dive into how ranchers and farmers in Shasta County, in the rural northern part of California actually deal with a problem that Richard Coase brought up in a classic paper on transactions costs. In "The Problem of Social Cost", Coase argued that if transaction costs were irrelevant, it wouldn't matter how property rights were allocated. Regardless of whether ranchers were responsible for keeping their cattle from straying or farmers were responsible for keeping unwelcome beasts out of their crops, the same solutions would be reached. If the law doesn't allocate responsibility to the low cost actor, then according to Coase the other party would find a way to pay the other party to do the cheaper thing. Of course, most of the argument since then has focused on the fact that transaction costs are seldom negligible.
Ellickson says that Shasta County is uniquely positioned for a study on this issue
Shasta County is "open range." In open range an owner of cattle is typically not legally liable for damages stemming from his cattle's accidental trespass upon unfenced land. Since 1945, however a special California statute has authorized the Shasta County Board of Supervisors, the county's elected governing body, to "close the range" in subareas of the county. A closed-range ordinance makes a cattleman strictly liable (that is liable even in the absence of negligence) for any damage his livestock might cause while trespassing within the territory described by the ordinance. The Shasta County Board of Supervisors has exercised its power to close the range on dozens of occasions since 1945, thus changing for selected territories the exact rule of liability that Coase used in his famous example.
This is the kind of change that economists love to study, because they can look at how behavior changes over time and treat the change of law as an independent variable. Any consistent changes in people's activity after the law changes can be treated as the result of the legal change.Ellickson focuses on how neighbors actually respond when trespasses occur. The book is filled with colorful stories giving details of what happened when particular responsible or irresponsible ranchers allowed their livestock to wander. The main observation is that while people were generally aware whether their property was in 'open' or 'closed' lands, their resolutions to incidents had little to do with what the law called for and more to do with a commonly accepted wisdom about that cattle owners are morally responsible for the damage. According to Ellickson, this fits Coase's model, since cattle owners are the low-cost provider. There are a variety of different types of pasture throughout Shasta County, and the cattle owners know more about how densely they are using any particular piece, and are more aware of which neighbors are most sensitive to their intrusions.
One of the most important enforcement mechanisms that Ellickson cites is plain simple gossip. Most of the people he talks about are eager to make things right, rather than be the subject of their neighbors' pointed comments. There is one member of the community who gets discussed a lot, but there are more extreme measures available when there are repeated run-ins, and one party is a consistent non-cooperator.
Ellickson is a good story teller and an astute observer. While the subjects of his study are less tight-knit than the farmers Ostrum described, there is enough social cohesion so that norms develop, and neighborliness is for the most part, a stronger limitation on people's interactions than actual laws.




Monday, November 13, 2017

Aging is a Group-Selected Adaptation, by Josh Mitteldorf

Josh Mitteldorf's Aging is a Group-Selected Adaptation places its thesis right in the title. Mitteldorf makes a strong case that aging is under the control of evolutionary pressures, and that the selection pressures for it are based on the benefits to groups, since it's clear there's no evolutionary gain to the individual. The evidence that aging is under evolution's control boils down to a comparison of many lineages that have long lives and have evolutionary cousins that do not. This is straightforward and hard to refute. The question is why.

The book's answer is that lineages that don't limit fecundity overshoot the carrying capacity of whatever environment they inhabit. The consequences are frequent population crashes. The alternative that leads to the possibility of stable populations is some feedback cycle that limits reproduction, combined with some way to ensure that deaths occur at a consistent rate. If the genes are optimized for the longest feasible life, then most deaths will occur in times of stress (resource exhaustion, unusual weather, or other cataclysm). This would lead to a much higher chance of ongoing boom and bust, which is a recipe for inevitable extinction.

There are some great graphs in the book illustrating the huge variety in life histories across many species. This one shows survivorship as a function of mortality and fecundity. When mortality is a horizontal line, survival falls consistently from birth to death. (hydra, hermit crabs, et. al.) Some species show decreasing mortality over their lifespan (desert tortoise, white mangrove, redleaf oak, ...), others only a slight uptick near the end (mute swan, tundra vole, sparrowhawk, ...).

According to Mitteldorf, the outcome of many experiments with artificial life show that one of the most valuable features of a species that has to cohabit with predators and prey is the ability to react to changes in its own population so that they have more progeny when the population density is low, and more individuals die when population density is high. The classical reaction to arguments about group selection says that this requires genes to have some kind of foresight, but the paradigm here is that populations that don't discover a way to reinforce this kind of response to population variation will be much more likely to go through frequent bottlenecks. Each bottleneck is another opportunity to go extinct.

One of the key ideas is that in order to contribute to ecosystem stability, rather than only to individual fitness, the genes must find a mechanism that leads to variation in robustness among the population. If some are slower, some are more susceptible to famine or cold, etc., then when a periodic stressor arises, some of the individuals will die. The alternative, if the genes design for uniform robustness is that all survive except when the stressor is severe, and in that case, nearly all will die. Aging, according to this thesis is a mechanism that causes variation within the population, ensuring a steady rate of death, which evens out rapid rises and falls in population. The population can still expand relatively rapidly when a niche opens up, but when living in a stable location, there are forces mitigating against population swings.

For those thinking about how to extend lifespan, a plausible first reaction to the idea that aging is selected for is to conclude that this means that aging will be harder to defeat. I would argue that the opposite may be true. Mitteldorf makes a good case that many lineages have found ways to allow individuals to live to arbitrarily long ages, so the biological mechanisms can't be infeasible or energetically unaffordable. Evolution's lesson is that we should be aware of the consequences of unlimited population growth, but given the demographic transition affecting most advanced economies, we can reasonably be more worried about the dangers of dropping population levels than of too many people. In any case, the hazards for human populations happen slowly enough that we'd be able to react before populations grow to be dangerous.

Aubrey de Grey wrote a response to Mitteldorf, but it looks like it was to an early version of the argument. (The book is dated 2017, but de Grey's 'response' is from 2015.) It looks to me as if de Grey had the reaction I described just above, and thought it was important to refute Mitteldorf's claims. I don't think de Grey directly addresses the arguments in the book. It seems to me that the argument presented here doesn't rule out the possibility of using de Grey's (SENS) approach to engineering fixes for the causes of aging, and it also provides for the possibility of other approaches that would directly intervene in the body's signaling that encourages aging and early senescence. If it's right, it doesn't reduce the number of possible approaches, it adds to them.

Saturday, April 01, 2017

The Vital Question, by Nick Lane

Nick Lane's The Vital Question seeks to explain why all eukaryotes share a large number of traits that are completely absent from all bacteria and other simple organisms. As Lane says in his opening page

All complex life shares an astonishing catalogue of elaborate traits, […]. Why, if all of these traits arose by natural selection, in which each step offers some small advantage, did equivalent traits not arise on other occasions in various bacterial groups?

Life arose around half a billion years after the earth's formation, perhaps 4 billion years ago, but then got stuck at the bacterial level of complexity for more than a billion years, half the age of our planet. […] In stark contrast, all morphologically complex organisms […] descend from that singular ancestor about 1.5—2 billion years ago. This ancestor was recognizably a 'modern' cell, with an exquisite internal structure and unprecedented nanomachines encoded by thousands of new genes that are largely unknown in bacteria. There are no surviving evolutionary intermediates, no 'missing links' to give any indication of how or why these complex traits arose, just an unexplained void between the morphological simplicity of bacteria and the awesome complexity of everything else.

Lane claims that this gap in our understanding should be glaringly obvious, and the scientific community should be struggling mightily to fill it in, but (he says) few are working on it, and fewer are talking about it as an important item on the agenda.

Lane's argument is that the combination of bacteria and archaeon that allowed the formation of eukaryotes happened once, and must have quickly evolved to have mitochondria, cilia, and to rely on sex for reproduction, and that all complex life descended from that single event. One of the surprising things is that eukaryotes didn't replace their ancestors; even though they have enough advantages that all complex life descends from that single event, there are still plenty of opportunities for the ancestral forms. The explanation Lane presents is that there's a delicate balance in the energy economy in bacteria and archaea, which doesn't allow the cells to grow much larger, and puts serious constraints on what kinds of mechanisms can be powered inside the cell. When that single archaeon engulfed a bacteria and turned it into the primal mitochondrion, the energy balance changed, and it became possible to store energy and distribute it around the cell, which made it possible to power more kinds of mechanisms, which led to the explosion in the variety of life and ways of living.

The usual story is that the environment changed (the Great Oxygenation) which enabled more styles of living. But what you'd expect if that was the cause would be a separate explosion from every kind of living creature, while what we really see in the evolutionary record is that when there are events like this (the cambrian explosion, e.g.) they radiate from a single progenitor, which tells us there was a significant discovery in that line that enabled the new directions of evolution.

Lynn Margulis' research shows that the form of modern eukaryotes derives from a series of mergers of adjacent bacteria and archaia. (One of the .sig lines I use refers to this) Lane says that while her results hold up, the mergers all occurred in a single line of descent, and all existant eukaryotes radiated out from the same end point of the serial events. Apparently none of the intermediate forms were good platforms from which to generate new life forms.

There are some simpler organisms (giardia among them) that are like eukaryotes in many ways, but lack mitochondria. They have long been viewed as an intermediate evolutionary point between archaia and eukaryotes, but modern phylogenetics (tracing the descent via gene similarity) shows that they're actually descended from eukaryotes, and merely discarded some of the internal structure because it wasn't needed in the environmental niches they occupied. This buttresses Lane's contention that all plants, animals, algae, fungi and protists share a common ancestor.

The common ancestor stored its DNA in a nucleus with a double membrane. The cell itself has a membrane with pores that were inherited by all the branches of its descendants. All the DNA has telomeres as well as introns which are spliced out using common machinery before proteins are built. The golgi apparatus, the form of the cytoskeleton, mitochondria, lysosomes, peroxisomes, the endoplasmic reticulum and the intra-cellular signaling mechanism are also common.

If you're interested, Lane goes into a lot of detail on his hypothesis on the energetic mechanisms that could have led to the evolution of the mitochondrial pathway starting from deep sea hydrothermal vents, where hydrogen and oxygen are bound in a way that can produce positive energy when the bonds are broken. I mostly understood it as I read it, but I'm going to have trouble doing it justice. Here's a precis of the argument; ATP is the end product, and is both stable and easy to extract energy from. A simple mechanism that can produce ATP has the effect of making many energy consuming processes possible.

Hydrothermal vents at the ocean bottom ("black smokers") are places where constantly renewed magma is in contact with sea water, which results in hot acidic water. Lane picks out nearby "alkaline vents" (also on the ocean bottom, but not where magma is exposed) as the plausible site for metabolism to arise. The alkaline version is rich in dissolved hydrogen, accompanied by "other reduced gases including methane, ammonia and sulphide". The rock is riddled with micropores from micrometers to millimeters in size. The flow of warmed sea water is relatively slow, so there's plenty of time for percolation and reaction. There are eddies in the flow, which allows reactive products to accumulate and concentrate locally. Before the Great Oxygenation, the most common gas in both the atmosphere and the ocean was CO2. In this environment, CO2 will react exergonically (releasing energy) with H2 to form CH4 (methane), but it needs a catalyst.

Lane considers it a crucial clue that all living cells drive their energy metabolism via proton gradients across thin membranes. To expand that, the claim is that the production of ATP always happens in the presence of cell membranes that separate proton-rich from proton-poor regions of a cell, and require a constant supply of H2 on the low-density side, and produces ATP on the high-density side. On the low density (alkaline) side, the H2 donates an electron, which is gobbled up in the production of ATP. Both of these reactions happen spontaneously.

Lane then describes a path via which permeable membranes (which don't benefit from better pumping) could evolve to be more selectively permeable, which would allow better pumping to be a benefit. This change makes it possible for the cell to escape from the natural proton gradient, since it can sustain its own internal gradient. Lane hyphothesizes that once selective permeability arises, archaea and bacteria evolved different membrane pumps (evidenced by the fact that they use steroisomers of glycerol) and split into evolutionarily distinct lines.

I'm not sure I explained that very well, but this felt like the first time I've read an explanation of basic cell metabolism that presented a mechanistic picture of the benefit of ATP (stores energy in an easily-extracted form), how the production of ATP is paid for energetically (proton gradients maintained by membranes and selective pumping), and why these designs are fundamental to the difference between bacteria, archaea, and eukaryotes, and eventually lead to the development of chloroplasts as an alternate energy source. Lane gives an explanation at a similar mechanistic level of what happens during apoptosis (programmed cell death; also conserved across the eukaryotes!)

Lane also argues that anti-oxidant supplements interfere with the apoptosis pathway, and thereby reduce health. He presents this as the currently accepted scientific viewpoint, though it's news to me. I need to do more research here.

I learned a lot of biology from this book, and thoroughly enjoyed it.

Sunday, October 02, 2016

The Secret of our Success, by Joseph Henrich

Joseph Henrich's The Secret of Our Success has a fair amount of overlap with Herculano-Houzel's The Human Advantage, which I reviewed in July. Both spend most of their attention on explaining why humans, of all the products of evolution, turned out to be the smartest and hence dominant species on the planet. The Human Advantage focused on what makes the human brain unique, and found some surprising neuronal traits that sets mammals apart from other other animals, and that make primates unique among mammals in their neuronal architecture. Henrich, on the other hand, takes pains to point out that individual humans (even very smart ones) aren't very good at figuring out how to survive in new environments. He uses that evidence to argue that communication and culture make the difference. As individuals, he claims, we aren't much smarter than other primates.

They both agree that cooking was a huge step forward for us, but Henrich takes pains to point out that this only an advantage when we're raised in a cultural group. Unlike practically all other animals, we don't instintively know how to unlock the nutrition in common foodstuffs—without training, it would take a long time (during which you have to be subsisting on something else) to figure out how to prepare most of what we eat.

The book starts out with several stories about lost european explorers becoming stranded, and if they didn't get help from locals, they would starve in the midst of what the locals would consider plenty. In Australia, the Arctic, and Florida, well-funded and trained explorers slowly starved because they couldn't figure out how to find, harvest, or prepare the foods the locals subsisted on, and they either didn't think to ask for help, or they drove away those who tried to help them. In contrast, there are a couple of stories of individual aborigines who are separated from their kin, and do just fine for years, since they grew up gathering and preparing the local bounty. His point is that our strength, as a species, is learning from one another, and picking up on every small increment in survivability.

I've been saying for years (since reading Jared Diamond's Guns, Germs, and Steel) that the thing to realize about the spread of humans and their ability to make use of local flora and fauna is that there were enough people, and people are curious enough that we tried to exploit everything, and we tried to make use of everything available in all conceivable ways. How else to explain the fact that people ate acorns, seal livers, and nardoo. In preparing nardoo, the Australian aborigines grind seeds, leech them with water, mix them with ash during heating, and use mussell shells to serve them. If you miss any step, then like the explorers, you'll die of poisoning or stavation with a full belly.

Along the way, this book has lots of interesting proposals about how culture affects prestige and dominance in ways that make it possible for us to live in larger groups and take advantage of the skills and abilities of more people; how competition for living space between groups leads to cultural differences, and how our ability and drive to share culture and learn from each other leads to increasing communication abilties and common grammar strength across the species. There are interesting tidbits spread throughout.

In talking about how living in larger groups with a larger repertoire of tools and techniques make us more capable without requiring more individual smarts or inventiveness, Henrich gave a list of simple tools that is more interesting than the standard list of 6 simple machines known since antiquity:

wheels, pulleys, springs, screws, projectiles, elastically stored energy (e.g. bows, spring traps), levers, poisons, compressed air (blow guns), rafts, leisters [a barbed spear], and heating (fire and coooking).
Instead of focusing on mechanical advantage as we do with the simple machines, this focuses on shared, reusable knowledge, and shows that there were ideas around to be re-used even in societies that were very primitive by modern standards.

Henrich has a longer more detailed time-line than Herculan-Houzel, and his focuses on evidence about tool use showing accumulation of culture rather than archeological evidence relating to brain size, cooking, and gut size. I enjoyed this book as much as Human Advantage, and it added an interesting, non-conflicting story about the roots of our intelligence. It didn't feel as if it has as much relevance to the question about our place in the universe—once we set out on the path toward communication and shared culture, Henrich didn't mention further roadblocks toward increasing advantage as we exploited the new niche better.

Sunday, July 17, 2016

Suzana Herculano-Houzel's The Human Advantage is a good book with some important insights hidden behind a fairly dry and dense presentation on "how I made these important discoveries." Herculano-Houzel (by her own account) pioneered a technique for determining the number of neurons in brain tissue, and managed (through a fair number of mildly interesting adventures) to bring together samples of many different primate, rodent, and other mammalian brains in order to work out the scaling laws that govern how brains and neuron counts grow with body mass in different tissues across different lineages. She shows a lot of graphs and charts to demonstrate that (with two exceptions) for most mammals, neuron counts scale up with an exponent of .5 with body mass, but in primates, the scaling factor is .8. If neurons have to be added in order to increase intelligence, this means that primates have a huge advantage. In order to get smarter, brains and neuron count have to increase. Larger bodies are necessary in order to sustain a larger brain, and if neuron count or neuron density is the limiting factor in intelligence, then you want to be able to pack more neurons into a denser brain in order not to require an enormous body.

Once Herculano-Houzel has established the basic scaling laws, she delves into the economics of maintaining a sufficiently neuron rich brain. The comparative scaling laws mean that as you look at bigger and bigger species of mammals, the neuron counts increase with the square root of the body mass. As primate species get larger, their neuron count increases much more quickly, which means that for a given body size, a primate is capable of supporting a larger brain than would a mammal. The cross-over point where the two lineages have comparable neuron sizes are with body sizes in the 10 gram range. At any larger size, if you compare a primate with another similar sized mammal, the primate is probably smarter.

There is a separate literature showing the energy requirements for many particular species. Herculano-Houzel used her new numbers on neurons for rodent and primate species to show that there is a direct correlation between the number of neurons and the amount of glucose consumed per minute by the brain. For humans (and others in the Homo lineage, being able to take advantage of the primate scaling laws gives a big boost, but you still have to find a way to ingest sufficient calories to afford the bigger brain.

Humans have two main advantages on this score compared to other primates. Walking on two legs is much more energy efficient than knuckle-walking like other (primarily arboreal) primates or on four legs. This increases the range over which foragers could range, and also freed up hands for gathering and carrying. It's not clear what originally drove bipedalism in the homo line, but it occurs at the same branch point that leads to the massive growth in cranial capacity.

The other big human advantage is cooking. I've seen discussions before that cooking increases the efficiency of digestion, and led to our shorter digestive tract, which allowed us to switch energy resources from digestion to our brains, but Herculano-Houzel points out that even before control of fire, other kinds of preparation (chopping and mashing for example) reduce the energy required for digestion. The anthropological evidence for food preparation goes back much further than the evidence of cooking, and significantly after bipedalism. The earliest evidence of eating meat is swiftly followed by anatomic adaptations to a more efficient diet, which is quickly followed by better tools, and the then bigger brains. Part of the evolutionary adaptation for bigger brains included smaller jaws.

Evidence of tool use and manufacture date back to 3.3 MYA (Million Years Ago). This date was recently pushed back from 2.6 MYA. These tools were simple flint knives. Archaeologists wouldn't count rocks that were used for pounding, since they are impossible to distinguish from unworked rocks. The flint knives would have been useful for cutting up meat, which would make it more digestible, and is necessary in order to survive with smaller jaws. Presumably, eating primitively processed foods had to become habitual before later evolutionary steps that relied on it would have survived in the population. The archaeological evidence gives the following timeline:

  1. 4.4 MYA: bipedalism appears
  2. 3.3 MYA: earliest tool use
  3. 2.5 MYA: eating meat
  4. 2.4 MYA: beginning of the reduction in size of the jaw
  5. 1.9 MYA: smaller gut is clearly present
  6. 1.7 MYA to 300 KYA: The Acheulean hand axe
  7. 1.5 MYA-100 KYA: start of the increase in cranial capacity
  8. 1 MYA: Clear indications of cooking

Another tantalizing clue is that the taste for cooked food may pre-date adoption of the habit. Herculano-Houzel refers to two studies that show that chimpanzees have a very strong preference for the taste of cooked food over raw. I don't know whether this has been investigated in other lineages, but if so, (even if it's just the body innately being able to detect foods that are provide big efficiency gains) it provides a boost for any lineage that can figure out how to reliably prepare foods--once you start, it would be an easy habit to keep, providing that the right food sources and tools are accessible.

Earlier, I mentioned that there are two exceptions to the laws regulating the number of neurons in primates and in all other mammals. The first is gorillas, which have brains and neuron counts much closer to those of other mammals rather than those expected of a primate. This fact about gorillas has been throwing off the results of previous researchers, who could only measure brain capacity. They concluded that the rules for primates would be the same as for other mammals, and argued that it was humans that were outliers. Once you plot the detailed data from small and medium primates and compare to mammals, it's easy to see a different trend line applies, and that humans fit on the primate line and gorillas do not. The other exception is elephants. (Herculano-Houzel has an entertaining section about her adventures getting elephant brains to analyze.) Elephants have brains whose size follows the standard scaling rule for mammals. They're huge, and they have huge brains. But their neurons are distributed very differently from all other species. 98% of the neurons are in the cerebellum, while the normal number doesn't get much above 80%. So elephants have big brains and a lot of neurons, but this explains why they're not even smarter than us, presuming neurons in the cerebral cortex are the thing that matters most.

Anyway, the later clues about cooking and bipedalism only added to my reaction that this work may provide an improved answer to the Fermi paradox. Herculano-Houzel doesn't appear to have data about the brains of animals beyond mammals, but if all the mammals outside of primates share a common scaling factor, then that's an indication that it's hard to evolve intelligence given the standard energy budget. It takes a special trick (which didn't have an immediate obviously benefit in the small primates in which it evolved) which was only discovered in one previously obscure branch of the mammal family tree to enable the efficient scaling that allows bodies to grow large enough to support brains supporting enough neurons to enable tool use. This enables (with other accidents like bipedalism and prepared food appearing in the same lineage) the feedback cycle that led to our massive growth in intelligence.

I've never been very worried by the argument that says the Fermi paradox indicates that there's a Great Filter, and if we can't figure out what the hard step was in our past, we should expect to encounter a hurdle in our future that has stopped other species from getting to space. The Human Advantage makes me even more sanguine. It's hard to evolve an intelligent species. There are a lot of happy accidents in our past, and the likely number of extra-terrestrial species in our light cone may be smaller than we thought. It would be nice to see more data showing the scaling laws that apply outside the primates (and in the cetaceans, which she didn't give much data about). I'll be surprised if any of them show divergent scaling progression compared to baseline mammals.

Tuesday, July 05, 2016

To Explain The World: by Steven Weinberg

Steven Weinberg's To Explain The World provides a very good introduction to the age of scientific discovery. Weinberg's goal is to explain how the early scientists incrementally developed the scientific method as they were learning, developing new theory, and testing their ideas, but I thought the presentation also did an amazing job of explaining the context of the discoveries in a way that made each contribution much more understandable. I've read many histories of science, so few of the foreground facts (who discovered what and when) were new to me, but being reminded about what else was going on at the time, and which people had been talking to (or arguing with) one another gave more context and made it easier to judge the relevance and difficulty of their accomplishments.

Weinberg starts with the ancient greeks, and explains how they were interested in the nature of reality, and our place in the cosmos, but had no concept of comparing their proposed explanations to the world or in any way testing their ideas. In some ways, some of those whose names live on were proposing better solutions than any that would appear for thousands of years, but without demonstrations of their truth or applicability, they wouldn't be influential until rediscovered in later circumstances, where better scientific methods would allow them to take part in a system of understanding.

In the hellenistic period in Egypt after the death of Alexander, individuals were able to figure out that falling objects accelerate, that air is a real substance that can displace water, and to invent effective pumps and accurate water clocks. When they made useful artifacts, their ideas had consequences and were remembered. When they theorized ex nihilo, they were more evanescent and didn't effect many later thinkers. Around this time, Archimedes systematized approaches to the simple machines, and recorded drawings of many useful tools built from screws, ramps, levers, and pulleys.

Starting from their certainty that heavenly bodies must move in circles, Plato asked some of his students what combinations of circular motions could produce the wandering motions of the seven known planets against the starry background that the Greeks could see with their unaided eyes. The pattern of inventing and compounding epicycles would continue until the time of Kepler.

Weinberg's final word on Leibniz and Newton is illustrative of how he analyzes the interactions between scientists, and looks for their influences on one another and on progress generally.

The judgement of contemporary scholars is that Leibniz and Newton had discovered the calculus independently. Newton accomplished this a decade earlier than Leibniz, but Leibniz deserves great credit for publishing his work. In contrast, after his original effort in 1671 to find a publisher for his treatise on calculus, Newton allowed this work to remain hidden until he was forced into the open by the controversy with Leibniz. The decision to go public is generally a critical element in the process of scientific discovery. It represents a judgement by the author that the work is correct and ready to be used by other scientists. For this reason, the credit for a scientific discovery today usually goes to the first to publish. But though Leibniz was the first to publish on calculus, as we shall see it was Newton rather than Leibniz who applied calculus to problems in science. Though, like Descartes, Leibniz was a great mathematics whose philosophical work is much admired, he made no important contributions to natural science.

Weinberg gives credit to the Greeks for discovering and passing on the idea that nature follows consistent rules, and that we can use mathematics to build models which will help us explain and understand them. It wasn't until the 17th century however, that scientists realized that this can be applied pervasively, and actively looked for opportunities to explore new phenomena and describe them mathematically. The final two thirds of the book is a discussion of the conversation that arose among scientists as they investigated, shared observations, and looked for ways to apply fewer and broader explanations to more and more fields.

Monday, August 24, 2015

Eifelheim, by Michael Flynn



Michael Flynn's Eifelheim is a nice twist on a first-contact story. The contact takes place when insectoid aliens traveling through string theory's seventh folded dimension get stranded on Earth in 1300s medieval Germany. They are a relatively small party, but they have just the right physical form to trigger everyone's prejudices about devils. Flynn does a great job of depicting a highly religious society with a few educated (for the time) leaders.
Unfortunately for the Germans trying to figure out whether to welcome or vilify their visitors, the plague is sweeping through Europe, and it's going to kill most of them. The scenes with the survivors taking care of their loved ones are touching and gruesome. Meanwhile, the aliens are wasting away because earth's biota is missing an essential protein for them. "They eat their fill, but are not nourished".
In a parallel stream, a pair of scientist (living together, but drifting apart) are searching for answers that intersect this distant past. Sharon is trying to piece together a grand-unified theory to explain anomalous measurements, and being inspired by random phrases uttered by Tom. Tom is a sociologist tring to figure out why Eifelheim, an obscure German hill town, was never resettled after the plagues. Of course there are enough clues in obscure historical records to inspire a theory.
Of course many of the villagers are simple superstitious peasants, but Dietrich, their Pastor was educated in Paris and Vienna, and has a more open mind. Dietrich struggles to convince the villagers and the manorial lord that the visitors are "men" by the meaning of the Bible, rather than devils, and then works to convert the visitors to his faith. He has some small successes; apparently the aliens don't recognize superstition when they see it. The linguistic difficulties are enough that it's not always clear when he is speaking literally or metaphorically. Similar issues impede his understanding of the science they understand--both biology to explain the diseases afflicting both parties and astronomy.
The characters are compelling, the science is a plausible stretch, the historicism is infecting, and their travails are affecting. Dietrich treats visiting Jews (escaping from pogroms and rabble afraid that they may have brought the plague, intentionally or not) the same as he does the visitors; all are "men" in God's sight are worthy of respect and an attempt to convince them to act as their best instincts direct them. The final scene, in modern times, left tears in my eyes.




Monday, November 24, 2014

Confusion about AI

I like Brockman's Edge.org. I think of it as smart people talking to smart people, and I usually find the discussions very interesting. But I was unable to read the recent conversation on the Myth of AI, started by Jaron Lanier, and mostly focussed on Bostrom's Superintelligence. I expect Bostrom's work to be very important, but I haven't found time to read it yet. Superintelligence talks about the likely emergence of super-human intelligences, and what there is to look forward to, as well as what we should worry about. I consider these to be very important issues, though I don't think they're going to make a huge difference in the next 10-20 years. But further out it is indeed going to be crucial that we spend time planning out how to make these intelligences not act in a way that is inimical to our interests. It's not that there's any reason to expect them to be out to get us, it's just that they'll have goals, and if we don't make the right moves ahead of time, we'll be in the way of their achieving their goals.
Anyway, starting out with Lanier, the discussion seemed ill-informed. The opening quote has him saying "The idea that computers are people has a long and storied history." This conflates so many threads that it's hard to know where to start. It's like trying to have a discussion about free speech with someone whose opening point is a complaint about the Supreme Court having decided that "companies are people". As far as I can tell, the Court decided that corporations are one of the ways that people act in concert, and that they don't lose their free speech rights when they use that kind of organizational structure to speak publicly. The fact that this decision applies just as much to giant mega-corporations and to unions as to the two-person public outreach institute that was the actual subject of the case at issue is more due to the Court's belief in consistency.
The point of AI isn't that "computers are people", it's that thinking and acting can be reduced to computational processes (it all comes down to atoms and meat, after all) and so there's no reason to believe that we won't eventually be able to build machines out of silicon that do the same thing, and aren't subject to the same constraints as apply to biological mechanism made out of Carbon.
I was very happy to read Luke Muehlhauser's review (hat tip to Yvain). Luke agrees that the discussants at Edge are confused, and had the patience to analyze some of the misconceptions, and point back to the actual subjects of disagreement.

Sunday, February 09, 2014

The Righteous Mind, by Jonathan Haidt

Jonathan Haidt's The Righteous Mind argues that our political leanings are strongly tied to our moral intuitions, and explains that people in each of the main political categories have different fundamental tenets that they each believe in strongly. There's some overlap between the various groups, but Haidt presents evidence that there's a lot of consistency within each group. If you hope to convince people on the opposite side of these divides of anything important, it's crucial to understand the foundations their reasoning is based on. If you believe the people you argue with are confused or evil, rather than reasoning from different premises, your arguments will fail to sway them.

In part one, Righteous Mind argues that intuition comes first, and strategic reasoning second. People enter a discussion of morality with instincts that tell them the answers. Most of the arguments they make are driven by their instincts, and little follows from intellectual considerations. Haidt relies heavily on the metaphor of a rider on an elephant. It's possible for the rider to decide which direction they go, but the elephant makes the first choice, and the driver has to convince the elephant if they're to end up somewhere else.

The second part covers the common foundations of our moral instincts. Most philosophers have concluded that morality is based on fairness or avoidance of harm. Haidt's research has shown that across cultures, there are actually six relatively consistent value frameworks that different political camps choose among. He says "The righteous mind is like a tongue with six taste receptors."

The third part shows that common feelings about morality bind communities together and blinds members of those communities to the goals, tastes, and priorities of their neighbors. He argues that religion evolved because of its contribution to social cohesion in contrast to the common atheist accusation that it's mostly religion is a memetic parasite that wins at the cost of its carriers.

Haidt is a master at presenting short vignettes that adherents to one viewpoint will say shows immoral behavior and others will be fine with. Whatever your outlook, he knows some stories that your group will be the only one to approve of, and other stories that you'll find to be disturbing while people with other political views won't be bothered. This technique seems to have been the core of the research underlying the book. He uses it to good effect in teasing apart the most basic drivers of people's instincts about right and wrong.

The underlying drives presented in the book. The names represent virtues and the adaptive challenge in the evolutionary environment that they protected us from. Haidt often refers to them just by the name of the virtue, and so will I.

  • care/harm
  • fairness/cheating
  • liberty/oppression
  • loyalty/betrayal
  • authority/subversion
  • sanctity/degradation
Liberals rely on caring, then fairness and liberty. Conservatives rely on all six, somewhat equally. Libertarians rely most on liberty, and a little on fairness. On the left, fairness often implies equality, but on the right it means proportionality—people should be rewarded in proportion to what they contribute, even if that guarantees unequal outcomes. Liberals also have a streak of sanctity, but it usually applies to nature and cleanliness rather than religious faith. Notice that there is no foundation used by the left that is not also important to the right. Liberals reject altogether some of the values that matter to Conservatives. To Liberals, loyalty and respect for authority can be outright negatives.

If you have trouble seeing how virtues other than the ones you believe in can be seen as fundamental, you're going to miss most of the point of the book.

When Haidt's research team asked liberals and conservatives to predict one another's responses to his Moral Foundations survey, they found that conservatives were the best able to understand other's motivations. Liberals seem to assume that where others hold values more weakly than liberals do (because there are other values they hold more strongly) that those with whom they disagree hold the opposite position from them rather than understanding that value but having another, higher priority. Many Liberals, when asked to describe Conservative values, say that they are actively pursuing evil ends. Conservatives, since they use all 6 metrics, can recognize when others are relying on particular values. Libertarians are most handicapped by this standard (having only one prime value), but their advantage is that, being in the minority, they are more used to talking to people with different points of view.

Part three of the book argues first, that humans are uniquely social creatures (He cites Tomasello, an expert on chimpanzee cognition, who said "It is inconceivable that you would ever see two chimpanzees carrying a log together.") Bees and ants sacrifice themselves for the hive, but individual cooperation is extremely rare if you exclude sex and other instinctive behavior. Second, that religion is mostly used to bind us into communities. He argues that we have a built-in "hive switch" that makes us bind more tightly and unthinkingly into groups. The release of oxytocin binds people to their groups, not to humanity as a whole. Finally, he argues that the New Atheists (Dennett, Dawkins, and Harris, primarily) miss the main point of religion, which is to bind people into groups. The fact that they naturally divide everyone into insider and enemy is a consequence of human psychology. The rituals "that the New Atheists dismiss as costly, inefficient, and irrational turn out to be a solution to one of the hardest problems human [societies] face: cooperation without kinship." Haidt uses these points to support his conclusion that treating people who disagree with us (or merely act differently) as repugnant is a deep-seated reaction.

Haidt says he grew up a liberal, and it was partly due to his studies of different political approaches that led him to a conservative viewpoint. It was also as a result of his studies that he came to see that libertarians have a distinct approach that is straightforward to describe in his framework. The descriptions of the liberal progress narrative (a quote from Christian Smith's Moral, Believing Animals) and the conservative mindset (a description of the "Reagan narrative" from Westen's The Political Brain) are masterful in their contrasts. Smith wrote

Once upon a time, the vast majority of human persons suffered in societies and social institutions that were unjust, unhealthy, repressive, and oppressive. These traditional societies were reprehensible because of their deep-rooted inequality, exploitation, and irrational traditionalism…But the noble human aspiration for autonomy, equality, and prosperity struggled mightily against the forces of misery and oppression, and eventually succeeded in establishing modern, liberal, democratic, capitalist, welfare societies. While modern social conditions hold the potential to maximize the individual freedom and pleasure of all, there is much work to be done to dismantle the powerful vestiges of inequality, exploitations, and repression.
Westen's description is
Once upon a time, America was a shining beacon. Then liberals came along and erected an enormous federal bureaucracy that handcuffed the invisible hand of the free market. They subverted our traditional American values and opposed God and Faith at every step of the way. … Instead of requiring that people work for a living, they siphoned money from hardworking Americans and gave it to Cadillac-driving drug addicts and welfare queens. Instead of punishing criminals, they tried to "understand" them. Instead of worrying about the victims of crime, they worried about the rights of criminals, … Instead of adhering to traditional American values of family, fidelity, and personal responsibility, they preached promiscuity, premarital sex, and the gay lifestyle … and they encouraged a feminist agenda that undermined traditional family roles. … Instead of projecting strength to those who would do evil around the world, they cut military budgets, disrespected our soldiers in uniform, burned our flag, and chose negotiation and multilateralism.
Haidt points out that these are very much descriptions of the American liberal and conservative viewpoints. In other countries, the narrative would be different, and in some, the constellation of values wouldn't align the same way. But in all the countries he's studied, the same 6 underlying values keep coming up in different combinations, and his story problems elicit the same distinctions, when adjusted for local customs and unique traditions.

Haidt believes that the crucial value that liberals misunderstand is moral capital (he's careful to draw a distinction from social capital). He cites Bertrand Russell to make the point: "Every community is exposed to two opposite dangers: ossification through too much discipline and reverence of tradition, on the one hand; on the other hand, dissolution, or subjection to foreign conquest, through the growth of an individualism and personal independence that makes cooperation impossible." Haidt then says

If you are trying to change an organization or a society and you do not consider the effects of your changes on moral capital, you're asking for trouble. This, I believe, is the fundamental blind spot of the left. It explains why liberal reforms so often backfire, and why communist revolutions usually end up in despotism. It is the reason I believe that liberalism—which has done so much to bring about freedom and equal opportunity—is not sufficient as a governing philosophy. It tends to overreach, change too many things too quickly, and reduce the stock of moral capital inadvertently. Conversely, while conservatives do a better job of preserving moral capital, they often fail to notice certain classes of victims, fail to limit the predations of certain powerful interests, and fail to see the need to change or update institutions as times change.

I found this to be a very helpful book, explaining how different factions see the world, and it's presented in a way that's sympathetic to everyone's views. If you want to argue constructively with people it helps tremendously to be able to understand where they're coming from. Having more of an understanding of other points of view also makes it much easier to hear what someone else's concerns are so you can address those directly. When we misunderstand one another we often talk past one another, not realizing that the other party has different values, rather than misunderstanding our position. Too much of politics today is based on ascribing bad motives to the opposition.

Saturday, September 14, 2013

Space Elevator Competitions

A couple of weeks ago someone mentioned Space Elevators, and I said "Oh, it's the end of August, there ought to be results from a Space Elevator challenge. Weren't they doing that annually?" That started me down a path of research and compiling information. It turned out that the International Space Elevator Association was having their annual conference that weekend in Redmond, but without a competition, and the Japan Space Elevator Association had held their competition a week earlier, but there didn't seem to be a place where results were compiled.

As I collected links and results and cross-checked them, and wrote up results, a wikipedia page came into being. I've just posted it, though there's no telling whether it'll last, given wikipedia's unknowable rules and processes.

I've found some details about 9 different competitions, mostly for fast climbers and/or strong tethers. There were a few other competitions that were announced, but which never took place either because no one was ready, no one qualified, or the site fell through.

The most recent climbing results were in Japan in August, where two different teams built climbers that climbed more than a kilometer. The most recent Tether competition I found was in 2011, but I haven't found results for any finisher since 2007, which I think, means the competitors haven't been beating the existing benchmark by a large enough margin. I'm disappointed that the best finishers haven't been published, so we could see how capabilities are growing each year.

Wednesday, February 13, 2013

Thinking Fast and Slow: Daniel Kahneman

Daniel Kahneman's Thinking Fast and Slow was much better than I expected it to be. Not that I wasn't expecting it to be well written or interesting, just that I expected that since Kahneman's results and views have been covered in great depth in a lot of other works I've read, I didn't expect much to be new. Even if you're fairly familiar with Kahneman's results and ideas, the book presents them well, and gives good advice on how to take advantage of your brain's predilections and work around its shortcomings.


Kahneman is well known as the progenitor (with Amos Tversky) of the Heuristics and Biases literature. You will find references to their research and results in lots of popular presentations on how people think, and the various ways in which people are prone to mistaken beliefs and sub-optimal actions. In Thinking Fast and Slow, he presents a unified discussion of this work, along with some solid suggestions for integrating the conclusions into your approach to life so that you can get more of what you want and be happier.


The basic theory is that we have two main approaches to problem solving with divergent benefits. The fast thinking part ("System One") is ready to make snap judgements on any subject at any time. It is fast, but it takes lots of shortcuts, and doesn't even bother to choose an optimal shortcut. Whatever answer first presents itself to this part of our minds is latched onto, because the evolutionary benefit was in having some answer quickly in case our ancestors needed to react immediately. The other approach is slow and deliberate, and involves evaluating lots of alternatives and consciously weighing benefits as well as the appropriateness of each approach to the current problem. The problem with System Two is that it's expensive, and for good evolutionary reasons your instincts always offer a quick and dirty response before there's time to consider more carefully.


Kahneman spends the bulk of the book giving lots of examples of particular, named, classes of mistakes we make ("Availability Heuristic", "Illusion of Validity", "Endowment effect", etc). It's probably useful to be aware of these classes if you want to reason more clearly, but I see the main value of Kahneman's approach to be in making us aware that our snap judgements are suspect. There are good reasons for each bias, which explains why evolution selected for that particular outcome, but whenever you're not in a life-and-death race to escape a lion, it pays to be attentive to your innate biases and consider your options more carefully. Having names for a catalog of short-sighted trade-offs you are likely to have gravitated to makes it easier to see which first guesses to re-think.


The final section of the book follows another perspective, also first identified by Kahneman and Tversky. This is the idea that our "Experiencing Self" and our "Remembering Self" have different evaluations when comparing things we do, which can lead to strange trade-offs when choosing what to do. The author argues that our memories systematically underweight pain we experience and consistently get some things wrong about enjoyable times, leading us to guess incorrectly about what kinds of situations we'd prefer in the future.


Experimental evidence shows that peoples' memories of painful episodes (dentist visits, for example) are dominated by the experience of the final moments of the experience, neglecting how painful earlier parts were. This means that adding 5 minutes of sligtly painful procedures to the end of a very-painful 15 minute procedure actually makes people remember the whole incident as having been less painful. Many people argue that it's clearly wrong to choose 20 minutes of pain over 15 minutes of pain, but this is not obvious to me. The 15 minute session should also carry the burden of all the subsequent time when the patient had to remember the more painful portions more clearly. The 20 minute session may have included more pain while in the chair, but the experiments show that the patients were less upset long afterward, partly because they had less gripping memories subsequently. So, as I see it, it's less of a contradiction than Kahneman believes.


On the other side, our recollections of enjoyable situations are also skewed. We tend to neglect long periods of time spent in pleasurable avocations (Kahneman calls it "duration neglect"), and when asked to choose how to spend our time or money, people often opt for the choice with a more easily recalled high point, regardless of the duration or enjoyability of the entire experience. Kahneman recommends that when planning vacations, or choosing other ways to spend our time, we focus more on the ongoing experience rather than the extremes. He's pretty convinced that we'll get more out of life that way. The counter is that when recalling our lives we'll be subject to just these biases, and regardless of how much joy there was in the small moments, we'll focus on the highs and lows when remembering our story or telling it to other people. It's food for thought in either case.

Monday, January 07, 2013

Steven Pinker: The Better Angels of Our Nature

Steven Pinker's The Better Angels of our Nature argues that violence has been declining over the last several centuries, and continues to decline, even though the common wisdom seems to say the opposite. Pinker marshalls an enormous quantity of data to buttress his story, and fills in with enough explanation to make a very convincing case. At the end, he tries to explain this long term trend, and comes up with several mechanisms, but since this section is less data driven, it's less convincing than the fact that the change is broad, pervasive, and has continued for a very long time.


Pinker starts out with wars, genocide, and other large scale killings. He amasses a dataset of all known mass killings before the modern age. The data is spotty, so it's hard to draw many conclusions, but it is clear that the distant past included its share of conflicts resulting in lots of deaths, and the twentieth century's war are memorable more for their recency than their scale. In addition, there's a pretty clear trend that the great power conflicts of the early twentieth have disappeared. At the end of his chapter on the Long Peace, Pinker points out that since the end of WWII there have been zero:

  1. nuclear weapons used
  2. battlefield fights between great powers
  3. armies crossing the Rhine (longest interval since 200 BCE)
  4. wars between european states
  5. wars between developed countries anywhere in the world
  6. territorial expansions by conquest for a developed country
As we're getting close to 50 or 60 years without a conflict between major powers, it becomes more plausible that it's a trend rather than an aberration.

From large-scale conflicts, Pinker moves on to socially-approved violence, and then to individual violence. Socially-approved violence includes things like slavery and wide-spread repression as of jews and gays as well as public execution and public torture and punishment. All these have gone from common to unacceptable over the long term. Pinker shows that, in parallel with granting rights to more and more groups the statistics on personal violence in a very broad range of contexts have been declining. Historic attitudes toward blacks, women, gays, ethnic groups, children, and animals have all changed dramatically.

Finally, Pinker tries to figure out what's been driving this change. He starts out by describing some broad trends: The Long Peace, and The Rights Revolution, but he admits they're just names, not a description of causes. From there he looks for factors that could have caused these trends. Empathy may have been increased because of the spread of literacy and mass entertainment that give us more access to other points of view. Self control, likewise may have been improved by the promulgation of personal habits that enable people to make their short-term desires subservient to their longer-range goals. He considers biological evolution, but concludes that while it would have been capable of producing a change, we don't have any evidence for the hypothesis. Next Pinker discusses whether humanity's moral sense or rationality has improved in some way to produce the improvement. He accepts that people are getting smarter (i.e. "the Flynn effect") and argues that once we reach a certain level, we can use reason to see that cooperation is more in our interest than violence, first at the personal level, and gradually at broader levels on interaction.

Finally, Pinker presents a framework for thinking about how various changes have impacted people's incentive structures, and what consequences they have for interactions. It's all based on the basic prisoner's dilemma payoff matrix, showing the options two parties face when they can make independent choices as they interact. The first version is called the Pacifist's dilemma, and shows that wars and fights are costly, but it's better to be the aggressor than the defeated. A second shows that "Leviathan" (a government) can change everyone's incentives by penalizing agression. Next is a chart showing that trade ("Gentle Commerce") improves things for everyone by improving the payoffs as long as agression is avoided. His final chart assumes that empathy and reason are added in, and everyone feels not only their own gains and losses, but those of the other party as well. At that point only positive sum outcomes make sense, since each player gains no advantage by imposing costs that are felt by both sides.

This model is plausible, but not compelling. Something like this might be going on, but it's hard to say that he's actually found the mechanism driving things. An interesting postscript is provided by Nassim Nicholas Taleb, who argues that Pinker doesn't understand the statistics of the fat tail that Taleb has been writing about for a while. If the proper curve is not a normal distribution, but instead a fat-tailed curve with most of the weight in the extremes, then the stats demonstrating that there is an effect to be explained are worthless. Taleb gives a bunch of (not well-explained) possible mechanisms for supposing that Pinker might have missed something, but he doesn't analyze whether the historical data looks more like a normal distribution or a fat-tail distribution. I suspect that the near-constant level of violence in the past makes Pinker's position more believable that violence has in fact gone down. It's possible that large-scale conflicts will occasionally arise with enormous body counts, but the drop in violence on all lesser scales doesn't seem likely to be reversed, and that doesn't seem consistent with Taleb's models of financial system variability.

Overall, the book provides good news, and more fodder I can use to try to convince people that what appears in the news is exceptions rather than trends.

Saturday, November 19, 2011

Sex at Dawn: Ryan and Jethá


Christopher Ryan and Cacilda Jethá's Sex at Dawn argues convincingly that monogamy isn't particularly natural for humans. It certainly is one common choice, but many modern people have a lot of trouble sticking to the program despite a lot of exhortation and systemic incentives promoting the practice. Ryan and Jethá marshall evidence from anthropology, evolutionary evidence, comparisons with other primates, and examinations of current practices. Their main argument is that a reasonable definition of "naturally monogamous" would mean that most people pair up with someone from the opposite sex, and aren't tempted to stray. There are a few species that mostly act that way, but looking at the broad range of what humans do, we're not like that. It's an interesting question as to why sociologists, and anthropologists seem to want us to believe that it is natural in the face of all the evidence.

There are several places in the book where the authors don't seem to really understand how evolution works. When talking about male parental investment, they ridicule the notion that maximum reproductive productivity is anyone's goal. It's clear from context that they're misunderstanding a discussion in which individuals are described as acting as if maximizing fecundity is the goal. But the evolutionary reasoning is just that those individuals who produce more offspring end up predominating in subsequent generations, regardless of why they acted that way. But regardless of this, they still make a strong case.

When biologists compare anatomy and mating behavior across species, human genitalia and sexual cycles don't make sense for a species in which couples stick together over the long term and don't cheat on one another. The size of male Genitalia, timing and (lack of) visibility of ovulation, breast prominence, are all unnecessary if the pair bond is unshakeable. They make sense when you assume each individual normally mates with multiple individuals of the opposite sex.

Our close relatives the chimpanzees and bonobos don't restrict themselves to single partners and we look more like humans evolved in an environment where individuals didn't restrict their attention to a single partner. In this kind of environment, evolutionary pressures push toward the large penises (by body weight), external scrotum, long duration of intercourse, and large volume of ejaculate you see in humans. If our ancestors had had reliable access to a partner, they wouldn't have needed these (evolutionarily) expensive features.

Another myth they take on is that of the demure female, uninterested in sex. It certainly occurs, but it's not predominant, either in societies (like ours) that constantly promote the idea or in societies that don't. Ryan and Jethá also make it clear that, evolutionarily speaking, homosexuality is nothing to be ashamed of. Our nearest relatives and many other species engage in the practice, though seldom exclusively. Mainstream society's insistance that each person can be categorized as either heterosexual or homosexual, is just not consistent with our behavior or the evolutionary or anthropological evidence.

Anyway, if you're not sqeamish about these topics, it's a fun, eye-opening read. Not likely to change anyone's behavior, but maybe some people will feel less constrained about their choices. It'll probably also provide grist for some arguments, but that's a fine thing, too.

Wednesday, November 09, 2011

Deutsch on the Evolution of DNA

I posted this on Google+ on Monday. I'll repost here for anyone who's not following me there. It's from David Deutsch's The Beginning of Infinity on the evolutionary origins of DNA as a universal language. I'll post a complete review when I finish the book, but these paragraphs really caught my attention.
Initially, the genetic code and the mechanism that interpreted it were both evolving along with everything else in the organisms. But there came a moment when the code stopped evolving yet the organisms continued to do so. At that moment the system was coding for nothing more complex than primitive, single celled creatures. Yet virtually all subsequent organisms on Earth, to this day, have not only been based on DNA replicators but have used exactly the same alpahabet of bases, grouped into three-base 'words', with only small variations in the meanings of those 'words'.

That means that, considered as a language for specifying organisms, the genetic code has displayed phenomenal reach. It evolved only to specify organisms with no nervous systems, no ability to move or exert forces, no internal organs and no sense organs, whose lifestyle consisted of little more than synthesizing their own structural constituents and then dividing in two. An yet the same language today specifies the hardware and software for countless multicellular behaviours that had no close analogue in those organisms, such as running and flying and breathing and mating and recognizing predators and prey. It also specifies engineering structures such as wings and teeth, and nanotechnology such as immune systems, and even a brain that is capable of explaining quasars, designing other organisms from scratch, and wondering why it exists.

Sunday, February 27, 2011

The Checklist Manifesto, by Atul Gawande

Atul Gawande has been writing on medical practice, provocatively and informatively, for the New Yorker for several years. His comments on price differences and what drives disparities between different areas garnered a lot of attention, but that area hasn't been his main focus. His recent book, The Checklist Manifesto, is closer to the main line of his writings. In this short book, Gawande presents his argument that medicine as currently practiced is far from a rigorous, science-driven field. He shows how aviation and construction are at least as complex and time-constrained as medicine, and that both have benefited from the use of checklists to help practitioners get the details right when performing complex operations.

Individual errors and mistakes of coordination are far more common in medicine than in other modern highly-technical fields. If medicine followed the standards of professional practice common in other areas, there would be a dramatic improvement in our overall health. Gawande discusses how checklists are constructed and used in aviation, another field where routine work is occasionally suddenly interrupted by situation requiring split second decision making at a rapid pace in a distracting environment with enormous consequences. Safety experts in aviation have learned how to put together checklists that can be found quickly, and that enable professionals to correctly address situations that arise in one flight in a million.

The safety record in aviation world-wide is amazingly good. I've long ascribed that difference between aviation and medicine to the fact that accidents in aviation are scrutinized thoroughly, and every mistake drives new corrective processes that quickly make it less likely that the same thing will happen again anywhere in the world. Every airframe manufacturer ensures that all of its vehicles are quickly updated with the most up-to-date procedures. In medicine, individual hospitals sometimes conduct reviews, but any knowledge gained is used sporadically and locally. There is also no standard for how to conduct these inquiries, so some investigations are derailed by politics, infighting, or a desire to deflect blame (which is exacerbated by medical malpractice risks.) The inquiries conducted in aviation have been designed to find correctable causes, and not to place blame. Focusing on the checklists that result from these inquiries would be a big improvement on what we have in medicine now. It's even plausible that a coordinated process for producing checklists would drive an improvement in the checklists based on measured effectiveness.

The book is very readable. The main story is about how Gawande led a task force for WHO testing out some simple checklists for a few common surgical procedures with high rates of routine errors. The results were spectacular, leading to a 36 percent reduction in complications and 47 percent drop in deaths from a variety of hospitals in rich and poor communities all over the world. Getting doctors and hospitals to actually adopt this simple improvement is a far harder task than getting a pilot program demonstrating its effectiveness. The side trips Gawande makes into aviation and construction to show how checklists work there and how they're constructed are engaging.

Monday, February 14, 2011

Going Inside, John McCrone

John McCrone's Going Inside provides a lot of insightful observations about how the brain works, but fails to tie them together into a cohesive picture. McCrone focuses on recent findings from new brain scanning technologies, and is particularly fascinated by timing studies that give details on how long it takes us to process incoming information, the specific times at which decisions are made, and how our subjective experience of when choices happen comport with the underlying brain circuitry. In particular, the studies show that it takes a half second to react to new information, even when we're expecting it, but our subjective experience is that the decision is made instantaneously at the end of that period. The experiments that show this are ingenious: by cutting off or distracting the process at various points, we can compare the reported subjective feel about the decision state that was reached with the brain scanner's details of how far into the process the brain actually got. All this works experimentally, because repeated sessions show that there's a lot of consistency in the information processing, so the scientists can pinpoint when the incoming information started being processed, and how long it would have taken to reach a choice.

The problem with the presentation is that McCrone doesn't provide an overview of the whole picture until the closing chapter, so as a reader, I had no framework onto which to attach all the facts as he presented them so as to build up a cohesive picture. I was left with the feeling that he'd presented good evidence that seemed to bear on the issue he was investigating, but I didn't know how it fit as I encountered it, so each tidbit vanished as I encountered the next one. I'm not sure things would be much improved on a re-reading. With a familiarity with the whole story, I could figure out how most of the pieces buttress the argument, but I'd have to make up my own argument structure for why his is the best explanation for the workings of the entire system.

McCrone also flubs up on the evolutionary explanation. At various points, he attempts to show why evolution would have produced just the structures and relationships that he has revealed, but his descriptions are unconvincing--he sometimes speaks as if evolutionary pressures are pushing toward a known result, rather than explaining why some abilities would have been selectively favored and why random mutations could have produced the effects. I think the correctly formed arguments could have been constructed, but McCrone's failed attempts were distracting.

One of McCrone's goals is to show how quickly brain scanning technologies advanced over the last few decades. The best tools for peering into the deepest details of timing and interaction in the brain have only recently been developed, so the insights that are most crucial to the book's argument aren't presented until a third of the way into the book, when he has set the historical context. Benjamin Libet did a series of experiments on patients (who were getting brain surgery already) that showed that direct electrical stimulation of the brain wasn't noticed unless it continued for a full half-second. If the stimulation was cut off earlier the patient wouldn't notice anything; if it continued for longer, the subject would report that they had been aware of it from the beginning. Later experiments showed that a second stimulus could mask the first one, as much as a third of a second later. This is pretty convincing evidence that processing inputs takes us up to half a second, and our experience of the present is cobbled together after the fact. Explaining "Libet's half-second" and figuring out what it implies about consciousness occupies the bulk of the book.

Libet did other studies later in which subjects were asked to notice the position of a rotating second hand at the moment they made a decision to lift a hand or take a similar action. With these and other similar experiments by other researchers it became clear that there isn't a precise moment at which decisions are made. The state of the brain changes somewhat continuously over a period from a half second to a full second, and subjects report somewhat arbitrary times as "the moment" of decision.

I would have to re-read the whole book (I've re-skimmed about the first half) in order to provide a detailed synopsis of it. I did feel like McCrone brought quite a few fascinating and important insights to light that would clarify an understanding of brain mechanisms, but the organization makes it hard to put them together on first reading. Maybe someone else will (or has) pull the material together in a better order, and that will be a more worthwhile book.

Saturday, June 26, 2010

Microcosmos: Lynn Margulis and Dorian Sagan

Lynn Margulis and Dorion Sagan's Microcosmosis a recapitulation of the history of evolution of microbes and how it affects us. The work that Margulis & Sagan report on also led to an article at Edge.org that produced a quote I've been using as one of my email signatures.

All sensory cells [in all animals] have in common the presence of ... cilia [with a constant] structure. It provides a strong argument for common ancestry. The common ancestor ... was a spirochete bacterium.

The copyright date is 1986. A lot has been learned about evolution and microbes since then. Even so, this book is a good introduction to the subject; it's very readable and has lots of detail that is still accepted. The story starts with the very beginnings of life on earth, and is always connected to its affect on how our biology works now:

As we examine ourselves as products of symbiosis over billions of yeaaar, the supporting evidence of our multimicrobe ancestry becomes overwhelming. Our bodies contain a veritable history of life on Earth. Our cells maintain an environment that is carbon- and hydrogen-rich, like that of the Earth when life began. They live in a medium of water and salts like the composition of the early seas.

The presentation is ordered chronologically, starting with the formation of stars and planets, proceeding through the cooling of the earth and the formation of the first entities that could reproduce reliably, the invention of sex and the alternative means of exchanging genetic information, and the change in composition of Earth's atmosphere to something that supported oxygen breathers and was toxic to their precursors. That takes us through the first 3.5 Billion years of the history of the earth, and all of the evolution of macroscopic life occupies the most recent 500 Million years. The emergence of cells, multi-cellular life, and then plants and animals follows, but the microbes are still around and still affecting both metabolism and evolution.

Margulis & Sagan provide a very readable introduction to modern microbiology and modern thinking about evolution. There are certainly more recent books that cover the details of the modern understanding in more detail, but this is a good overview and doesn't miss much that's important.

Tuesday, February 23, 2010

Daniel Kennefick: Travelling at the Speed of Thought

Daniel Kennefick's Traveling at the Speed of Thought tries to untangle the current state of science with respect to gravitational waves. The approach is mostly historical, with a focus on what Einstein thought at various times, and how others reacted to his analyses. The book is also fairly recent (2007) and doesn't seem to have been eclipsed by new discoveries yet. (There are active experiments looking for physical evidence of gravity waves. The effect is expected to be minuscule, so proponents are bothered by lack of success so far.)

A lot of the story is driven by a referee's report on a paper Einstein and Rosen submitted to Physical Review in 1936. Einstein was apparently used to European deference to authority on submitted papers, and was so upset that an anonymous referee had been consulted that he sent it to an obscure journal. By the time it was published there, Einstein had changed his mind about the primary conclusions.

The primary question seems to be whether gravitational waves carry energy with them as they propagate. If they do, then their sources (black holes, for instance) ought to lose mass over time. If they don't carry energy, then we don't have a sufficient theory of what could be propagating.

Another question that has to be answered is how fast gravity travels, and what it is that moves. In waves in water, individual water molecules only move locally, while the wave can travel great distances. With electromagnetism, actual photons move from place to place, carrying the influence. Which kind of thing is gravity? In one case, we should try to identify the medium in which the disturbance propagates, in the other, we should be able to find the particles themselves.

I may be over-simplifying, but the skeptical viewpoint seems to be that symmetrical motion or ballistic motion of any isolated mass wouldn't radiate energy, since changes in trajectory are required to produce gravity waves. If the present crop of detectors fails to find anything, this may be the best interpretation. It's hard to reconcile this suggestion with the presence of supernovas and binary star collapses. Those seem like dynamic enough changes that they should result in a change in the gravitational field that would have to propagate at some finite velocity.

Kennefick's book provides a good, general introduction to the area, without getting too technical. If you're interested in the history it would make sense to read it. If you're looking for more details on what is know, how the math works, or how to interpret the results from the detectors, you should probably look elsewhere.