Monday, February 12, 2018

Walkaway by Cory Doctorow

I really enjoyed reading Cory Doctorow's Walkaway, though it was more the setting than the story that had me entranced.

Doctorow envisions a relatively high tech future with a strong upper class with strict controls on many aspects of society, but there's an informal, unsupported safety valve that makes it possible for people to get out from under the plutocrats (called Zottas here). Doctorow's society is fraying around the edges, so there are lots of abandoned industrial facilities and vacant land that people who are fed up can Walkaway to. Once there they create informal voluntary societies, and exploit the abandoned wealth they find around them. As with Doctorow's Down and Out in the Magic Kingdom this is a reputation based society, but many of the people who fuel this iteration explicitly reject the ideas of ratings and rankings and tracking contributions. People work together for the joy of it, and record their ideas and plans so others can replicate what works and improve on what doesn't.

In a focal early scene, Limpopo and her companions have been working for months to build a habitation called the Belt and Braces in the wilderness. Limpopo leads by doing a lot of the work, and she has argued convincingly that using leaderboards and rewarding people based on their contributions are ineffective ways to encourage desirable behaviors because they incentivize the wrong kinds of effort. Jimmy had lost an earlier round of this argument and been asked to leave. He returns with a crowd of allies one day when Limpopo is working outside, and his crowd uses the lack of formal rules to rewrite the software controls and impose a reward structure. A common response to this kind of disagreement would be to wage a "revert" battle in the software, but Limpopo uses this opportunity to demonstrate the depth of her commitment to the "Walkaway" philosophy by announcing that she's not going to fight over it. Instead, she'll go somewhere else and start over, leaving Jimmy with full possession of an empty shell. When pressed, she declares "I didn't make it. It wasn't mine. I didn't let him take it." The Walkaway philosophy is to not have belongings, so as not be attached to your stuff. It's impossible to steal from them because they don't acknowledge ownership.

For me, the model that strikes home is the ability to withdraw from an existing government and decamp to a new location to just start over. The current international order doesn't seem to leave any gaps for things like this, but I'm currently in the middle of reading James C. Scott's The Art of Not Being Governed, which presents a history of South East Asia that says that the shape of the societies in that part of the world has been driven for millennia largely by the people who moved to less accessible locations in order to escape governments that were getting unbearable. Scott argues that the sociology of the closely related peoples living in hills and valleys were driven more by which crops and living arrangements were easy for governments to count and tax in the valleys, and hard for them to find and more durable in the remote and higher settlements. I hope to write more about that when I've finished Scott's book.

Doctorow doesn't try to argue that it's easy, and in fact shows that the walkaway crowd is doing an immense amount of work in order to rebuild. I find this model of decentralized self government very sympathetic. There's no acknowledged government with territorial exclusivity, and people are able to leave if they don't like the way things are being run. There is plenty of open room to move to, and there's enough generalized wealth at hand and accessible know how that people don't feel tied down.

The unfortunate part of Walkaway is that Doctorow needed a conflict, and the one he sets up is that the Zottas are jealous of their control over society, and see the walkaways as a threat, so they're willing to kidnap, torture and send in the troops in order to regain control. In the final battle scene, a Zotta leader's daughter is in the target area, and the Zotta's back down. But in the meantime, the walkaway society's story is one of resisting violence from outside rather than the peaceful coexistence they're working so hard to get.

I agree with Doctorow's aesthetic sense; focusing on this society after the Zottas have ceded control wouldn't provide conflict at the same existential level, but it would be a much nicer place to live, both for those who walk away and those who remain behind in the "default" economy.

Doctorow knows how to tell a story: There are a lot of funny and touching scenes in the story, and he covers a lot of ground. In addition to the overall situation which I've focused on so far, the story covers many kinds of relationships, uploading makes a major sub-plot, and the unequal distribution of society's benefits is explored. He does have a darker outlook than I on where technology is heading. The reason there are riches lying around is that the Zottas would rather shutter outmoded plants than sell them and allow someone else to exploit the resources they contain. There are many highly trained mercenaries around that the Zottas can hire who will do their bidding, no matter how distasteful it might seem to us. But that's visible in many of his other stories, and he still manages to be entertaining and paint a hopeful picture about how people can get along together and build something great. This book is being considered for this year's Prometheus, and it's my current favorite.

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.

Thursday, July 06, 2017

Redemption Ark, by Alastair Reynolds

Alistair Reynolds's Redemption Ark is a great yarn, with action spaning a long time scale and many star systems. It takes quite a while to figure out that the Inhibitors have the same goals as Saberhagen's Berserkers—they want to eradicate intelligent life (though there's some hint that they're doing it to stave off a more thorough cleansing by unknown agencies). Unlike the Berserkers, these killers wait quietly while monitoring commerce between the stars so that when they strike, they'll be able to wipe out all traces of the civilizations they notice. And they don't attack with space ships and robotic warriors; they build megastructures to destroy entire star systems. The humans who figure out their objectives have to make even longer range plans in order to counter them.

And the main characters here are willing and able to think that far ahead, and set up long term goals. A few of them have the longevity to pursue this kind of plan, and still interact with shorter-lived people on a human level. The factions include a borg-like collective, though they seem to follow plausible physics, and members don't participate in the group mind when they're not on the same planet. They do have faster than light travel, though there are reasons it's rarely used. They still have a civilization that spans multiple star systems, so they have the ability to hibernate while on long journeys. Given time dilation at near light and other effects, they're used to (at a societal level) dealing with people who remember the distand past at first hand, and have institutions that allow people to carry out long term plans when the principals might be away for extended periods.

One of the things that has cut down the prevalence of interstellar travel is the presence of plague, a nano-scale infection that they seem unable to stop except by physical isolation. The story starts with the return of the ship captained by a revered long-lost ancestor which seems to have been infected or attacked by a new kind of agent. After this, we follow a couple of different story lines among the borg, on a colony world in political turmoil, and following a local transport rocket pilot around a densely inhabited system. Characters and events influence one another in various ways across the different story lines.

We gradually learn that an inner cabal within the closed leadership group inside a faction of the borg knows about some super weapons created in the distant past that might be useful in fighting the Inhibitors. The Inhibitors have recently become more active, and a few factions figure out that someone needs to act. The struggle to find and control the super weapons drives much of the conflict in one story line. Other groups pursue other schemes in the converging story lines, to keep things dramatic and interesting.

Anyway, the struggles between long-lived and widely traveling post humans and ordinary people living out their lives on planets in distant solar systems are fascinating to watch, and quite plausible. The further they are from an ordinary lifespan, the more alien their motivations and goals, but most of them seem to be trying to work towards a greater good as they understand it. Even the few with truly alien viewpoints know how to work with others to achieve mutual goals.

I've read a few of Reynolds ' books at this point, and I enjoy the broad scope, the immense vision, and the finely detailed characters. The stories are suspenseful, and even when they leave a hook for a follow-up story, the endings are satisfying.

Monday, July 03, 2017

Seeing Like a State, James C. Scott

I found a lot to like in James C. Scott's Seeing Like a State. It presents a way of thinking about the consequences of governments' interventions that makes a large category of unintended side effects appear coherent. Once you see this consistency, you can make predictions about other interventions and the ways they will turn out without needing to ascribe motivation to the planners behind them. In order to achieve their goals, bureaucrats and autocrats have to make the population they intend to help more surveyable, visible, and regular. That very act, independent of how much the rest of the change might be done with the best interests of the people in mind, reduces the relevance of the local knowledge and expertise that they have built up over time, making them more dependent on government, and less able to fill in the gaps in the ways that lead to smoothly functioning societies.

Scott describes several grand schemes, mostly done to help various populations, though often in ignorance of the ways of the people living in the affected area. He discusses state-sponsored forestry, Corbusier's city planning, government-sponsored (and private) experiments in industrial agriculture, China's Great Leap Forward, resettlements in Tanzania, as well as touching on other examples. In each case he shows how the (necessarily) high level plans of of the top officials were translated into concrete details for the convenience of those implementing the plan, in ignorance of the deleterious consequences for the affected villagers. The end result in each case conformed to the planners' specifications, but left an unlivable environment in which the inhabitants were more dependent on the government, and often much poorer than they started out.

Whether the results of all these grand schemes ended up being helpful is questionable, and is certainly independent of what the original intent was, or how much effort was spent during the planning stage in considering ways to make the outcome closer to what the subjects would have asked for. Since plans and maps are necessarily abstractions from reality, and since the plans must be carried out by intermediaries whose interests are distinct from both the rulers and the people being 'helped', those doing the work will have to have to fill in details about how to get the work done. This will often be done in ignorance of the intent, and more usually without concern for the extended well-being of the future of the community.

As with Jacobs' Death and Life of Great American Cities, the point isn't to move towards a conclusion on how to do a better job of redesigning a society, so much as of having skepticism that it's possible to achieve humane objectives by trying. In most cases, hubris would lead to addressing problems by allowing people to adjust things in an incremental manner. Otherwise we risk replacing things that seems suboptimal to an outsider with situations that are truly dismal for those left behind. While discussing Soviet collective farms, Scott talks about some attempts by American industrial agricultural firms to do something similar in the midwest. Their grand plans for integrated industrial farms didn't succeed any better, but the difference was that when the outcome became clear, the companies involved backed off and the land reverted to more local, context-sensitive control.

Sunday, May 21, 2017

Insurgence, by Ken MacLeod

Ken MacLeod's The Corporation Wars: Insurgence, is the second book of a trilogy. It (along with the first book in the series, Dissidence, is a finalist for the Prometheus award this year.

Insurgence continues the story of awakened robots struggling for freedom, and uploaded human ex-combatants fighting to retake the planetary system the robots had been mining and exploring.

This installment focuses less on the robots' claim to be agents worthy of separate respect, and more on the uploaded warriors struggle to figure out the nature of the reality they inhabit while mostly following orders to fight the battles their supervisors are pursuing. Their ultimate worry is that they don't have enough information to tell which side they're fighting on or who they are battling to subdue. When you live in a simulation (particularly when you can tell that someone else has access to the control panel) it's a little difficult to be sure that your choices aren't effectively controlled by someone else.

Next, cracks appear in the simulation, and "real" revived people see the shortcomings, but non-player-characters (MacLeod calls them philosophical zombies) think everything is normal, so the real people can tell who's just a simulated person. The idea of zombies in philosophy (sometimes "p-zombies") is an exploration of the idea of consciousness. What if there were beings that acted just like people, but had no consciousness? Would it make a difference to them? Should we accord them lesser rights?

I consider the idea of p-zombies to be incoherent, but many smart people treat the question as exploring an important distinction. MacLeod here undercuts the point of the argument since there are actual behavioral differences. It isn't an exploration of whether consciousness matters, it's just that some characters in the story are imperfect simulations without an inner life, and the actual thinking beings can tell who they are. At the same time, MacLeod makes sure we notice that the robots and AIs who are active in the battles and the scheming do have an inner dialogue, and are making plans and collaborating with others to get things done.

The starting position for the agencies that represent the current Earth government and act under its protection is that only humans are allowed to be sentient. Even AIs' powers are circumscribed. Whenever self awareness arises otherwise, it must be stamped out. It's not clear why this would be a plausible stance, since it's clearly the case that the AIs can become self-aware for short periods, and autonomously operating robots have the capacity for spontaneous self awareness given the right trigger. So they must be constantly battling to defeat uprisings, and track down newly minted sophonts who either try to escape from control, or hide in occupied systems. It would make more sense to forbid use of tools with the capacity for self awareness, than to constantly try to stomp them out. I'd also have a hard time going along with a regime that wanted to outlaw and destroy a class of beings because they were self aware. Self aware and hostile is a separate thing, but that's not the distinction they've settled on.

Before one of the final battles, one of the leaders of the simulated humans challenges the combatants to each eat a slice of p-zombie flesh to prove that they believe they're in a simulation, and that there can't be any moral issues with simulated eating of simulated meat from simulated people that were never actually alive or aware. Except for a few who object to the initiation-ceremony aspect of the act, they all partake.

So there's a lot of exploration here of of philosophical questions of identity, and what it means to be human. The questions of liberty are mostly focussed on what kinds of agents deserve respect as actual people, though I think MacLeod fumbled some of the issues. The action is interesting and the conflict exciting. Besides there are also weaponized communications packets, interrogations of potentially hostile agents by sending them into a dungeon simulation, double and triple agents, and terraforming. It's a pretty good read, and the lead-in to part three, of course leaves a few things to be resolved.

Saturday, April 15, 2017

Dissidence, by Ken MacLeod

Ken MacLeod's The Corporation Wars: Dissidence, is the first book of trilogy. It (along with the second book in the series, Insurgence) is a finalist for the Prometheus award this year.

The story starts with a scene in which a pair of mining robots exploring an asteroid (in a distant solar system) and representing different corporate interests have an encounter, which leads them to realize they have opposing interests, which leads them each to recognize that they have interests, which leads them to self-awareness. The corporations are in a tenuous situation, trying to assert their ownership of the robots, trying to be civil about their contractual cooperation, but objecting strenuously to breaches by the opposing robots. The corporations end up fighting one another, and the robots band together and spread the concept of self-awareness to other nearby robots with sufficient computing capacity. Since the corporations don't seem likely to grant them independence, the robots form an independent faction in the upcoming battle. The corporations are loath to destroy their valuable property just yet.

When they do decide that military actions are called for, they end up dredging up opposing troops of uploaded warriors from past wars. All the AIs and non-self-aware robots, and other actors are under a deep compulsion that only humans and their uploads can actually be armed for combat, even against rogue self-aware robots. So the "humans" spent parts of their time embodied as people in a planetary environment, training and relaxing between missions. In the missions, they're downloaded into articulated space battle suits. Every time they die in battle, they return to the training site to start again. Over time, they find reason to doubt the reality of their home, and eventually detect serious cracks.

The uploads gradually learn enough about their realities to doubt that they're still fighting for the side they were loyal to in their first lives. Apparently part of the distinction between uploads and awakened AIs is that the operators can't tinker with opinions and loyalties directly, but they can easily lie and mislead about who they're representing, and what their opponents are fighting for. Of course, it wouldn't be an interesting story if the operator's control couldn't be subverted.

Ken MacLeod tells a good story, and gets us to think about what kinds of entities should have rights. The authorial point of view allows him to show the action in the eyes alternately of the awakened robots and the revived soldiers, so we feel their fundamental humanness. The characters, ex-human and non-human alike, think about who they should allow into their coalition, whether other actors are actually aware or just act like it, and have varying motives.

My biggest complaint about the story and the characters' attitudes is a simple acceptance among all the characters that some other characters are not real, based simply on statements from people in authority roles. In war, it doesn't make much sense to worry about whether the people shooting at you are actually thinking beings, but deciding that some category of bystanders don't have inner lives should be a cause for more intensive investigation. It's an easy allegation to make, and not far from standard attitudes about our enemies that we've mostly moved past.

Saturday, April 08, 2017

Johanna Sinisalo's The Core of the Sun is a finalist for the Prometheus award this year.

It has enough SF elements to qualify as standard near future fiction, and provides biting social commentary. In feel, it reminds me a lot of Margaret Atwood's The Handmaid's Tale, but I liked this better in several ways.

The story takes place in a future Finland that has managed to selectively breed its women so that they're either docile sex dolls and mothers ("eloi"), or sterile, powerless but competent workers ("morlocks"). They've also outlawed psycho-active drugs from alcohol to heroin, and somehow included capsacin (hot peppers) on that list. The protagonist (Vanna) is a morlock who was raised as an eloi, which allows her to pass in polite company. She's also hooked on hot peppers, and has started dealing in whole, dried, and preserved peppers in order to afford her next fix.

Compared to Handmaid's Tale, the viewpoint character is a more active agent, with more freedom to act for her own interests and to undermine the system; her allies against the state are more fully bought into the fight; the state she fights has taken more reprehensible steps, though it seems to have less thorough control of its subjugated females.

The story is told with a mix of present-tense action, and recollections by Vanna of how she got to her present situation, mostly written as letters to her long-lost eloi sister, Manna. The two were raised away from the city by their eccentric aunt, which gave Vanna the opportunity to act naturally most of the time, and mimic her sister when visitors were around. This gave her the tools to pass as eloi when she grew up.

After the aunt dies, Manna finds a husband who Vanna suspects to be after the family farm, since neither Manna nor Vanna (passing as an eloi) can legally hold title to it. Vanna finds a man to partner with who values her for her unusual intellect and her ability to act independently (a useful tool for his black market activities).

Vanna pursues the secrets behind her sister's disappearance until events force her to escape with her partner. I found the prose (and occasional poetry) to be delightful and very evocative. The characters were convincing, and Vanna's struggle to be her own person in the face of societal expectations was heart breaking.

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, September 04, 2016

Seveneves, by Neal Stephenson

Neal Stephenson's Seveneves is a fun read — it won this year's Prometheus Award against a strong field of authors including previous winners and SF greats. That's most of what I can say without spoilers. Alright, also this: the story starts with an unidentified object causing the breakup of the Moon into seven large chunks. Scientists and astronomers quickly run their simulations and analyses and agree that it'll be about two years of bumping against one another and breaking into finer and finer pieces before it all ends in a "White Sky" where fragments blanket the sky and soon start falling in the "Hard Rain" which will kill basically all macroscopic life on the surface. The initial breakup of the moon and the subsequent analysis happens in the opening pages, so this doesn't feel like a spoiler to me. If you're likely to read the book (it's Neal Stephenson, and it won the Prometheus Award), and don't like spoilers, I recommend reading just to the end of this paragraph. I enjoyed the book, and it qualifies as a Prometheus winner because nearly everything that happens does so without the presence of anything like a government. There are many failures of coordination but also a lot of successes. The ending is hopeful.

The first part of the book is about what happens over those approximately two years as everyone pulls together. The next part is what happens next to those who survive in space, and the final section is about what happens much later to the descendents of those who survived. In the first part, there's a lot of cooperation even though everyone agrees that the vast majority are going to die very soon. An astonishing number of people and institutions pull together to do what can be done to save a representative sample of humanity, and ensure they have enough supplies and tools to stand a decent chance of surviving. There is a little bit of cowboy heroics, but for the most part, people are putting the species before themselves. Stephenson does a good job of depicting the impact of politics and struggles between factions, while also showing the technology that could make it all work, and the interesting personal dynamics that go into creating a new society from scratch in an inhospitable environment.

The main conflict in the second part is set up because the President of the US violates the broad agreement that politicians wouldn't be allowed on the rescue fleet. At the very last minute before it becomes impossible, she gets on the last rocket to take off and joins those expected to survive. She is not welcomed by the leaders of the expedition, but being a consummate politician, she recruits followers from the least powerful, and ends up splitting the escape fleet into two that are both too small to carry out the planned mission. The survivors face the challenge of moving from a low orbit under constant threat from the remaining chunks (which are predicted to eventually coalesce into a ring) to someplace higher and safer. Disastrous events ensue, and a tiny remnant group manages to find refuge in one of the remaining large chunks of the Moon, a nickel-iron lump with a crevice big enough to shelter them while they recover, repair, and deploy their remaining technology to sustainably feed themselves and begin the process of procreation so there can be a next chapter. Most of the action is interpersonal, with politics and factional struggles driving the plot. Stephenson keeps this section short, and skips fairly quickly to a time a few thousand years in the future.

The ring has stabilized and civilization has spread around it and developed in some interesting directions. This is where the projections of plausible technologies get extra interesting. What kinds of technologies would develop in a society with an abundance of hard metals and no gravity? Where the challenge isn't getting into space, but getting around in the vast emptiness? The society takes advantage of their location (it's easier to build a sky-hook from the middle than from the ground) and finds ways to thrive.

Stephenson's expectation that starting from a very small base the population would fracture into competing polities and separate societies seems thin to me, but he uses it to drive the plot in interesting directions. At the end the residents of the ring start making attempts to explore the newly habitable surface of Earth and encounter descendents of two groups of people who found ways to survive the "Hard Rain" on the surface. One of them seems somewhat plausible, and was reasonably foreseeable from the first part of the story. The other group seemed like a real stretch to me, and the mechanism of their survival is just hinted at. But that's a small part of the story.

Stephenson tells a fascinating story about the struggle to survive and the collaboration it takes to succeed in an extreme situation. Along the way, we meet some interesting characters, and read about some new technologies that it would be great fun to play with.

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.

Thursday, July 14, 2016

Jo Walton's The Just City investigates the nature of justice, while telling an enchanting story involving gods, mortals and robots trying to actually build the Just City hypothesized by Plato. The goddess Pallas Athene brings together 10,000 children and a few hundred adults from many different times and places to found a new city (on the island of Atlantis) according to Plato's prescriptions in The Republic. Plato's main goal in The Republic was to explain the nature of Justice (the words 'Just' and 'Justice' occur more than 150 times on the wikipedia page), so Walton has plenty of room to explore the idea from several different directions.

In order to get infrastructure in place without burdening the new inhabitants (who are supposed to be coddled and trained so they can understand Justice) the goddess brings in robots to build housing and meeting rooms. The robots are kept around to take care of maintenance and other tasks that Plato didn't describe the city's inhabitants as handling. When the historical Socrates (as envisioned by Walton) joins the city, he turns out to be a very inquisitive man. Since the robots display some autonomy, Socrates wonders whether they have individual personalities and whether they're thinking and aware. This leads to even more opportunities for questions about Justice.

Pallas Athene wants to populate the city with willing participants, so the children (exactly half girls and half boys) all are from disadvantaged circumstances. The adults are all people who prayed for a chance to live in Plato's Republic, so (considering how often the book is actually read in the original greek, and in what historical periods) most are men from antiquity, and the women are nearly all from more modern times. This leads to some interesting political factions, and changing of practices as time goes on and the oldest denizens die off first.

Not all of the children are happy to be there, even though all of them agree that their previous lives (most were slaves) were worse. Even so, not having been given a choice rankles with a few, and their reactions are also interesting.

Many of Plato's ideas are reasonably modern, but others are very outdated, like assigning citizens to societal roles according to their metal. The adults of The Just City spend a lot of effort training and testing the children in order to place them appropriately. Many of the adults are uncomfortable with this duty, but they carry it out, and even put their thumbs on the scales as necessary in order to make the numbers come out right according to Plato's very Greek ideas about numerical harmony. When some of the children figure out that test rankings are being adjusted in order to fit pre-defined notions of how many should be in each category, they challenge the adults, and as with everything else that goes on in the city, philosophical discussion and socratic dialogue ensues.

Since there's limited space on the island, procreation must be limited and sexual activity controlled. The children (and adults) find creative ways around the restrictions, but this means discussion of sexual mores and prohibitions are necessary. We hear about everything from rape and unwanted intimacy to Plato's ignorance of issues of women's hygiene. For the most part the adults attempt to do everything according to Plato's prescriptions, but there are several clear gaps in Plato's planning which leads to the need for endless committee meetings (most of which we, mercifully, hear about afterward, rather than having to endure.)

Walton does a wonderful job of presenting these philosophical questions of freedom, choice, and justice through the character's activity and interactions. In the end, we get to know these people who are all striving to be their best, and to create an environment in which justice is available to all, even though humans always have incompatible desires. We even get some satisfying answers to new and old questions and some unresolved issues to ponder on our own.