# Econstudentlog

## Random stuff

i. Your Care Home in 120 Seconds. Some quotes:

“In order to get an overall estimate of mental power, psychologists have chosen a series of tasks to represent some of the basic elements of problem solving. The selection is based on looking at the sorts of problems people have to solve in everyday life, with particular attention to learning at school and then taking up occupations with varying intellectual demands. Those tasks vary somewhat, though they have a core in common.

Most tests include Vocabulary, examples: either asking for the definition of words of increasing rarity; or the names of pictured objects or activities; or the synonyms or antonyms of words.

Most tests include Reasoning, examples: either determining which pattern best completes the missing cell in a matrix (like Raven’s Matrices); or putting in the word which completes a sequence; or finding the odd word out in a series.

Most tests include visualization of shapes, examples: determining the correspondence between a 3-D figure and alternative 2-D figures; determining the pattern of holes that would result from a sequence of folds and a punch through folded paper; determining which combinations of shapes are needed to fill a larger shape.

Most tests include episodic memory, examples: number of idea units recalled across two or three stories; number of words recalled from across 1 to 4 trials of a repeated word list; number of words recalled when presented with a stimulus term in a paired-associate learning task.

Most tests include a rather simple set of basic tasks called Processing Skills. They are rather humdrum activities, like checking for errors, applying simple codes, and checking for similarities or differences in word strings or line patterns. They may seem low grade, but they are necessary when we try to organise ourselves to carry out planned activities. They tend to decline with age, leading to patchy, unreliable performance, and a tendency to muddled and even harmful errors. […]

A brain scan, for all its apparent precision, is not a direct measure of actual performance. Currently, scans are not as accurate in predicting behaviour as is a simple test of behaviour. This is a simple but crucial point: so long as you are willing to conduct actual tests, you can get a good understanding of a person’s capacities even on a very brief examination of their performance. […] There are several tests which have the benefit of being quick to administer and powerful in their predictions.[..] All these tests are good at picking up illness related cognitive changes, as in diabetes. (Intelligence testing is rarely criticized when used in medical settings). Delayed memory and working memory are both affected during diabetic crises. Digit Symbol is reduced during hypoglycaemia, as are Digits Backwards. Digit Symbol is very good at showing general cognitive changes from age 70 to 76. Again, although this is a limited time period in the elderly, the decline in speed is a notable feature. […]

The most robust and consistent predictor of cognitive change within old age, even after control for all the other variables, was the presence of the APOE e4 allele. APOE e4 carriers showed over half a standard deviation more general cognitive decline compared to noncarriers, with particularly pronounced decline in their Speed and numerically smaller, but still significant, declines in their verbal memory.

It is rare to have a big effect from one gene. Few people carry it, and it is not good to have.

Apparently the OP had second thoughts about this query so s/he deleted the question and marked the thread nsfw (??? …nothing remotely nsfw in that thread…). Fortunately the replies are all still there, there are quite a few good responses in the thread. I added some examples below:

“I think underestimating the domain/business side of things and focusing too much on tools and methodology. As a fairly new data scientist myself, I found myself humbled during this one project where I had I spent a lot of time tweaking parameters and making sure the numbers worked just right. After going into a meeting about it became clear pretty quickly that my little micro-optimizations were hardly important, and instead there were X Y Z big picture considerations I was missing in my analysis.”

[…]

• Forgetting to check how actionable the model (or features) are. It doesn’t matter if you have amazing model for cancer prediction, if it’s based on features from tests performed as part of the post-mortem. Similarly, predicting account fraud after the money has been transferred is not going to be very useful.

• Emphasis on lack of understanding of the business/domain.

• Lack of communication and presentation of the impact. If improving your model (which is a quarter of the overall pipeline) by 10% in reducing customer churn is worth just ~100K a year, then it may not be worth putting into production in a large company.

• Underestimating how hard it is to productionize models. This includes acting on the models outputs, it’s not just “run model, get score out per sample”.

• Forgetting about model and feature decay over time, concept drift.

• Underestimating the amount of time for data cleaning.

• Thinking that data cleaning errors will be complicated.

• Thinking that data cleaning will be simple to automate.

• Thinking that automation is always better than heuristics from domain experts.

• Focusing on modelling at the expense of [everything] else”

“unhealthy attachments to tools. It really doesn’t matter if you use R, Python, SAS or Excel, did you solve the problem?”

“Starting with actual modelling way too soon: you’ll end up with a model that’s really good at answering the wrong question.
First, make sure that you’re trying to answer the right question, with the right considerations. This is typically not what the client initially told you. It’s (mainly) a data scientist’s job to help the client with formulating the right question.”

iv. 5-HTTLPR: A Pointed Review. This one is hard to quote, you should read all of it. I did however decide to add a few quotes from the post, as well as a few quotes from the comments:

“…what bothers me isn’t just that people said 5-HTTLPR mattered and it didn’t. It’s that we built whole imaginary edifices, whole castles in the air on top of this idea of 5-HTTLPR mattering. We “figured out” how 5-HTTLPR exerted its effects, what parts of the brain it was active in, what sorts of things it interacted with, how its effects were enhanced or suppressed by the effects of other imaginary depression genes. This isn’t just an explorer coming back from the Orient and claiming there are unicorns there. It’s the explorer describing the life cycle of unicorns, what unicorns eat, all the different subspecies of unicorn, which cuts of unicorn meat are tastiest, and a blow-by-blow account of a wrestling match between unicorns and Bigfoot.

This is why I start worrying when people talk about how maybe the replication crisis is overblown because sometimes experiments will go differently in different contexts. The problem isn’t just that sometimes an effect exists in a cold room but not in a hot room. The problem is more like “you can get an entire field with hundreds of studies analyzing the behavior of something that doesn’t exist”. There is no amount of context-sensitivity that can help this. […] The problem is that the studies came out positive when they shouldn’t have. This was a perfectly fine thing to study before we understood genetics well, but the whole point of studying is that, once you have done 450 studies on something, you should end up with more knowledge than you started with. In this case we ended up with less. […] I think we should take a second to remember that yes, this is really bad. That this is a rare case where methodological improvements allowed a conclusive test of a popular hypothesis, and it failed badly. How many other cases like this are there, where there’s no geneticist with a 600,000 person sample size to check if it’s true or not? How many of our scientific edifices are built on air? How many useless products are out there under the guise of good science? We still don’t know.”

A few more quotes from the comment section of the post:

“most things that are obviously advantageous or deleterious in a major way aren’t gonna hover at 10%/50%/70% allele frequency.

Population variance where they claim some gene found in > [non trivial]% of the population does something big… I’ll mostly tend to roll to disbelieve.

But if someone claims a family/village with a load of weirdly depressed people (or almost any other disorder affecting anything related to the human condition in any horrifying way you can imagine) are depressed because of a genetic quirk… believable but still make sure they’ve confirmed it segregates with the condition or they’ve got decent backing.

And a large fraction of people have some kind of rare disorder […]. Long tail. Lots of disorders so quite a lot of people with something odd.

It’s not that single variants can’t have a big effect. It’s that really big effects either win and spread to everyone or lose and end up carried by a tiny minority of families where it hasn’t had time to die out yet.

Very few variants with big effect sizes are going to be half way through that process at any given time.

Exceptions are

1: mutations that confer resistance to some disease as a tradeoff for something else […] 2: Genes that confer a big advantage against something that’s only a very recent issue.”

“I think the summary could be something like:
A single gene determining 50% of the variance in any complex trait is inherently atypical, because variance depends on the population plus environment and the selection for such a gene would be strong, rapidly reducing that variance.
However, if the environment has recently changed or is highly variable, or there is a trade-off against adverse effects it is more likely.
Furthermore – if the test population is specifically engineered to target an observed trait following an apparently Mendelian inheritance pattern – such as a family group or a small genetically isolated population plus controls – 50% of the variance could easily be due to a single gene.”

“The most over-used and under-analyzed statement in the academic vocabulary is surely “more research is needed”. These four words, occasionally justified when they appear as the last sentence in a Masters dissertation, are as often to be found as the coda for a mega-trial that consumed the lion’s share of a national research budget, or that of a Cochrane review which began with dozens or even hundreds of primary studies and progressively excluded most of them on the grounds that they were “methodologically flawed”. Yet however large the trial or however comprehensive the review, the answer always seems to lie just around the next empirical corner.

With due respect to all those who have used “more research is needed” to sum up months or years of their own work on a topic, this ultimate academic cliché is usually an indicator that serious scholarly thinking on the topic has ceased. It is almost never the only logical conclusion that can be drawn from a set of negative, ambiguous, incomplete or contradictory data.” […]

“Here is a quote from a typical genome-wide association study:

“Genome-wide association (GWA) studies on coronary artery disease (CAD) have been very successful, identifying a total of 32 susceptibility loci so far. Although these loci have provided valuable insights into the etiology of CAD, their cumulative effect explains surprisingly little of the total CAD heritability.”  [1]

The authors conclude that not only is more research needed into the genomic loci putatively linked to coronary artery disease, but that – precisely because the model they developed was so weak – further sets of variables (“genetic, epigenetic, transcriptomic, proteomic, metabolic and intermediate outcome variables”) should be added to it. By adding in more and more sets of variables, the authors suggest, we will progressively and substantially reduce the uncertainty about the multiple and complex gene-environment interactions that lead to coronary artery disease. […] We predict tomorrow’s weather, more or less accurately, by measuring dynamic trends in today’s air temperature, wind speed, humidity, barometric pressure and a host of other meteorological variables. But when we try to predict what the weather will be next month, the accuracy of our prediction falls to little better than random. Perhaps we should spend huge sums of money on a more sophisticated weather-prediction model, incorporating the tides on the seas of Mars and the flutter of butterflies’ wings? Of course we shouldn’t. Not only would such a hyper-inclusive model fail to improve the accuracy of our predictive modeling, there are good statistical and operational reasons why it could well make it less accurate.”

Anyone who built software for a while knows that estimating how long something is going to take is hard. It’s hard to come up with an unbiased estimate of how long something will take, when fundamentally the work in itself is about solving something. One pet theory I’ve had for a really long time, is that some of this is really just a statistical artifact.

Let’s say you estimate a project to take 1 week. Let’s say there are three equally likely outcomes: either it takes 1/2 week, or 1 week, or 2 weeks. The median outcome is actually the same as the estimate: 1 week, but the mean (aka average, aka expected value) is 7/6 = 1.17 weeks. The estimate is actually calibrated (unbiased) for the median (which is 1), but not for the the mean.

A reasonable model for the “blowup factor” (actual time divided by estimated time) would be something like a log-normal distribution. If the estimate is one week, then let’s model the real outcome as a random variable distributed according to the log-normal distribution around one week. This has the property that the median of the distribution is exactly one week, but the mean is much larger […] Intuitively the reason the mean is so large is that tasks that complete faster than estimated have no way to compensate for the tasks that take much longer than estimated. We’re bounded by 0, but unbounded in the other direction.”

I like this way to conceptually frame the problem, and I definitely do not think it only applies to software development.

“I filed this in my brain under “curious toy models” for a long time, occasionally thinking that it’s a neat illustration of a real world phenomenon I’ve observed. But surfing around on the interwebs one day, I encountered an interesting dataset of project estimation and actual times. Fantastic! […] The median blowup factor turns out to be exactly 1x for this dataset, whereas the mean blowup factor is 1.81x. Again, this confirms the hunch that developers estimate the median well, but the mean ends up being much higher. […]

If my model is right (a big if) then here’s what we can learn:

• People estimate the median completion time well, but not the mean.
• The mean turns out to be substantially worse than the median, due to the distribution being skewed (log-normally).
• When you add up the estimates for n tasks, things get even worse.
• Tasks with the most uncertainty (rather the biggest size) can often dominate the mean time it takes to complete all tasks.”

“…the relentless focus on inequality among politicians is usually quite narrow: they tend to consider inequality only in monetary terms, and to treat “inequality” as basically synonymous with “income inequality.” There are so many other types of inequality that get air time less often or not at all: inequality of talent, height, number of friends, longevity, inner peace, health, charm, gumption, intelligence, and fortitude. And finally, there is a type of inequality that everyone thinks about occasionally and that young single people obsess over almost constantly: inequality of sexual attractiveness. […] One of the useful tools that economists use to study inequality is the Gini coefficient. This is simply a number between zero and one that is meant to represent the degree of income inequality in any given nation or group. An egalitarian group in which each individual has the same income would have a Gini coefficient of zero, while an unequal group in which one individual had all the income and the rest had none would have a Gini coefficient close to one. […] Some enterprising data nerds have taken on the challenge of estimating Gini coefficients for the dating “economy.” […] The Gini coefficient for [heterosexual] men collectively is determined by [-ll-] women’s collective preferences, and vice versa. If women all find every man equally attractive, the male dating economy will have a Gini coefficient of zero. If men all find the same one woman attractive and consider all other women unattractive, the female dating economy will have a Gini coefficient close to one.”

“A data scientist representing the popular dating app “Hinge” reported on the Gini coefficients he had found in his company’s abundant data, treating “likes” as the equivalent of income. He reported that heterosexual females faced a Gini coefficient of 0.324, while heterosexual males faced a much higher Gini coefficient of 0.542. So neither sex has complete equality: in both cases, there are some “wealthy” people with access to more romantic experiences and some “poor” who have access to few or none. But while the situation for women is something like an economy with some poor, some middle class, and some millionaires, the situation for men is closer to a world with a small number of super-billionaires surrounded by huge masses who possess almost nothing. According to the Hinge analyst:

On a list of 149 countries’ Gini indices provided by the CIA World Factbook, this would place the female dating economy as 75th most unequal (average—think Western Europe) and the male dating economy as the 8th most unequal (kleptocracy, apartheid, perpetual civil war—think South Africa).”

Btw., I’m reasonably certain “Western Europe” as most people think of it is not average in terms of Gini, and that half-way down the list should rather be represented by some other region or country type, like, say Mongolia or Bulgaria. A brief look at Gini lists seemed to support this impression.

Quartz reported on this finding, and also cited another article about an experiment with Tinder that claimed that that “the bottom 80% of men (in terms of attractiveness) are competing for the bottom 22% of women and the top 78% of women are competing for the top 20% of men.” These studies examined “likes” and “swipes” on Hinge and Tinder, respectively, which are required if there is to be any contact (via messages) between prospective matches. […] Yet another study, run by OkCupid on their huge datasets, found that women rate 80 percent of men as “worse-looking than medium,” and that this 80 percent “below-average” block received replies to messages only about 30 percent of the time or less. By contrast, men rate women as worse-looking than medium only about 50 percent of the time, and this 50 percent below-average block received message replies closer to 40 percent of the time or higher.

If these findings are to be believed, the great majority of women are only willing to communicate romantically with a small minority of men while most men are willing to communicate romantically with most women. […] It seems hard to avoid a basic conclusion: that the majority of women find the majority of men unattractive and not worth engaging with romantically, while the reverse is not true. Stated in another way, it seems that men collectively create a “dating economy” for women with relatively low inequality, while women collectively create a “dating economy” for men with very high inequality.”

I think the author goes a bit off the rails later in the post, but the data is interesting. It’s however important keeping in mind in contexts like these that sexual selection pressures apply at multiple levels, not just one, and that partner preferences can be non-trivial to model satisfactorily; for example as many women have learned the hard way, males may have very different standards for whom to a) ‘engage with romantically’ and b) ‘consider a long-term partner’.

“Intermittent fasting (IF) is a term used to describe a variety of eating patterns in which no or few calories are consumed for time periods that can range from 12 hours to several days, on a recurring basis. Here we focus on the physiological responses of major organ systems, including the musculoskeletal system, to the onset of the metabolic switch – the point of negative energy balance at which liver glycogen stores are depleted and fatty acids are mobilized (typically beyond 12 hours after cessation of food intake). Emerging findings suggest the metabolic switch from glucose to fatty acid-derived ketones represents an evolutionarily conserved trigger point that shifts metabolism from lipid/cholesterol synthesis and fat storage to mobilization of fat through fatty acid oxidation and fatty-acid derived ketones, which serve to preserve muscle mass and function. Thus, IF regimens that induce the metabolic switch have the potential to improve body composition in overweight individuals. […] many experts have suggested IF regimens may have potential in the treatment of obesity and related metabolic conditions, including metabolic syndrome and type 2 diabetes.()”

“In most studies, IF regimens have been shown to reduce overall fat mass and visceral fat both of which have been linked to increased diabetes risk.() IF regimens ranging in duration from 8 to 24 weeks have consistently been found to decrease insulin resistance.(, , , , , , , , , ) In line with this, many, but not all,() large-scale observational studies have also shown a reduced risk of diabetes in participants following an IF eating pattern.”

“…we suggest that future randomized controlled IF trials should use biomarkers of the metabolic switch (e.g., plasma ketone levels) as a measure of compliance and the magnitude of negative energy balance during the fasting period. It is critical for this switch to occur in order to shift metabolism from lipidogenesis (fat storage) to fat mobilization for energy through fatty acid β-oxidation. […] As the health benefits and therapeutic efficacies of IF in different disease conditions emerge from RCTs, it is important to understand the current barriers to widespread use of IF by the medical and nutrition community and to develop strategies for broad implementation. One argument against IF is that, despite the plethora of animal data, some human studies have failed to show such significant benefits of IF over CR [Calorie Restriction].() Adherence to fasting interventions has been variable, some short-term studies have reported over 90% adherence,() whereas in a one year ADMF study the dropout rate was 38% vs 29% in the standard caloric restriction group.()”

June 2, 2019

## Marine Biology (II)

Below some observations and links related to the second half of the book’s coverage:

[C]oral reefs occupy a very small proportion of the planet’s surface – about 284,000 square kilometres – roughly equivalent to the size of Italy [yet they] are home to an incredibly diversity of marine organisms – about a quarter of all marine species […]. Coral reef systems provide food for hundreds of millions of people, with about 10 per cent of all fish consumed globally caught on coral reefs. […] Reef-building corals thrive best at sea temperatures above about 23°C and few exist where sea temperatures fall below 18°C for significant periods of time. Thus coral reefs are absent at tropical latitudes where upwelling of cold seawater occurs, such as the west coasts of South America and Africa. […] they are generally restricted to areas of clear water less than about 50 metres deep. Reef-building corals are very intolerant of any freshening of seawater […] and so do not occur in areas exposed to intermittent influxes of freshwater, such as near the mouths of rivers, or in areas where there are high amounts of rainfall run-off. This is why coral reefs are absent along much of the tropical Atlantic coast of South America, which is exposed to freshwater discharge from the Amazon and Orinoco Rivers. Finally, reef-building corals flourish best in areas with moderate to high wave action, which keeps the seawater well aerated […]. Spectacular and productive coral reef systems have developed in those parts of the Global Ocean where this special combination of physical conditions converges […] Each colony consists of thousands of individual animals called polyps […] all reef-building corals have entered into an intimate relationship with plant cells. The tissues lining the inside of the tentacles and stomach cavity of the polyps are packed with photosynthetic cells called zooxanthellae, which are photosynthetic dinoflagellates […] Depending on the species, corals receive anything from about 50 per cent to 95 per cent of their food from their zooxanthellae. […] Healthy coral reefs are very productive marine systems. This is in stark contrast to the nutrient-poor and unproductive tropical waters adjacent to reefs. Coral reefs are, in general, roughly one hundred times more productive than the surrounding environment”.

“Overfishing constitutes a significant threat to coral reefs at this time. About an eighth of the world’s population – roughly 875 million people – live within 100 kilometres of a coral reef. Most of the people live in developing countries and island nations and depend greatly on fish obtained from coral reefs as a food source. […] Some of the fishing practices are very harmful. Once the large fish are removed from a coral reef, it becomes increasingly more difficult to make a living harvesting the more elusive and lower-value smaller fish that remain. Fishers thus resort to more destructive techniques such as dynamiting parts of the reef and scooping up the dead and stunned fish that float to the surface. People capturing fish for the tropical aquarium trade will often poison parts of the reef with sodium cyanide which paralyses the fish, making them easier to catch. An unfortunate side effect of this practice is that the poison kills corals. […] Coral reefs have only been seriously studied since the 1970s, which in most cases was well after human impacts had commenced. This makes it difficult to define what might actually constitute a ‘natural’ and healthy coral reef system, as would have existed prior to extensive human impacts.”

“Mangrove is a collective term applied to a diverse group of trees and scrubs that colonize protected muddy intertidal areas in tropical and subtropical regions, creating mangrove forests […] Mangroves are of great importance from a human perspective. The sheltered waters of a mangrove forest provide important nursery areas for juvenile fish, crabs, and shrimp. Many commercial fisheries depend on the existence of healthy mangrove forests, including blue crab, shrimp, spiny lobster, and mullet fisheries. Mangrove forests also stabilize the foreshore and protect the adjacent land from erosion, particularly from the effects of large storms and tsunamis. They also act as biological filters by removing excess nutrients and trapping sediment from land run-off before it enters the coastal environment, thereby protecting other habitats such as seagrass meadows and coral reefs. […] [However] mangrove forests are disappearing rapidly. In a twenty-year period between 1980 and 2000 the area of mangrove forest globally declined from around 20 million hectares to below 15 million hectares. In some specific regions the rate of mangrove loss is truly alarming. For example, Puerto Rico lost about 89 per cent of its mangrove forests between 1930 and 1985, while the southern part of India lost about 96 per cent of its mangroves between 1911 and 1989.”

“[A]bout 80 per cent of the entire volume of the Global Ocean, or roughly one billion cubic kilometres, consists of seawater with depths greater than 1,000 metres […] The deep ocean is a permanently dark environment devoid of sunlight, the last remnants of which cannot penetrate much beyond 200 metres in most parts of the Global Ocean, and no further than 800 metres or so in even the clearest oceanic waters. The only light present in the deep ocean is of biological origin […] Except in a few very isolated places, the deep ocean is a permanently cold environment, with sea temperatures ranging from about 2° to 4°C. […] Since there is no sunlight, there is no plant life, and thus no primary production of organic matter by photosynthesis. The base of the food chain in the deep ocean consists mostly of a ‘rain’ of small particles of organic material sinking down through the water column from the sunlit surface waters of the ocean. This reasonably constant rain of organic material is supplemented by the bodies of large fish and marine mammals that sink more rapidly to the bottom following death, and which provide sporadic feasts for deep-ocean bottom dwellers. […] Since food is a scarce commodity for deep-ocean fish, full advantage must be taken of every meal encountered. This has resulted in a number of interesting adaptations. Compared to fish in the shallow ocean, many deep-ocean fish have very large mouths capable of opening very wide, and often equipped with numerous long, sharp, inward-pointing teeth. […] These fish can capture and swallow whole prey larger than themselves so as not to pass up a rare meal simply because of its size. These fish also have greatly extensible stomachs to accommodate such meals.”

“In the pelagic environment of the deep ocean, animals must be able to keep themselves within an appropriate depth range without using up energy in their food-poor habitat. This is often achieved by reducing the overall density of the animal to that of seawater so that it is neutrally buoyant. Thus the tissues and bones of deep-sea fish are often rather soft and watery. […] There is evidence that deep-ocean organisms have developed biochemical adaptations to maintain the functionality of their cell membranes under pressure, including adjusting the kinds of lipid molecules present in membranes to retain membrane fluidity under high pressure. High pressures also affect protein molecules, often preventing them from folding up into the correct shapes for them to function as efficient metabolic enzymes. There is evidence that deep-ocean animals have evolved pressure-resistant variants of common enzymes that mitigate this problem. […] The pattern of species diversity of the deep-ocean benthos appears to differ from that of other marine communities, which are typically dominated by a small number of abundant and highly visible species which overshadow the presence of a large number of rarer and less obvious species which are also present. In the deep-ocean benthic community, in contrast, no one group of species tends to dominate, and the community consists of a high number of different species all occurring in low abundance. […] In general, species diversity increases with the size of a habitat – the larger the area of a habitat, the more species that have developed ways to successfully live in that habitat. Since the deep-ocean bottom is the largest single habitat on the planet, it follows that species diversity would be expected to be high.”

Seamounts represent a special kind of biological hotspot in the deep ocean. […] In contrast to the surrounding flat, soft-bottomed abyssal plains, seamounts provide a complex rocky platform that supports an abundance of organisms that are distinct from the surrounding deep-ocean benthos. […] Seamounts support a great diversity of fish species […] This [has] triggered the creation of new deep-ocean fisheries focused on seamounts. […] [However these species are generally] very slow-growing and long-lived and mature at a late age, and thus have a low reproductive potential. […] Seamount fisheries have often been described as mining operations rather than sustainable fisheries. They typically collapse within a few years of the start of fishing and the trawlers then move on to other unexplored seamounts to maintain the fishery. The recovery of localized fisheries will inevitably be very slow, if achievable at all, because of the low reproductive potential of these deep-ocean fish species. […] Comparisons of ‘fished’ and ‘unfished’ seamounts have clearly shown the extent of habitat damage and loss of species diversity brought about by trawl fishing, with the dense coral habitats reduced to rubble over much of the area investigated. […] Unfortunately, most seamounts exist in areas beyond national jurisdiction, which makes it very difficult to regulate fishing activities on them, although some efforts are underway to establish international treaties to better manage and protect seamount ecosystems.”

“Hydrothermal vents are unstable and ephemeral features of the deep ocean. […] The lifespan of a typical vent is likely in the order of tens of years. Thus the rich communities surrounding vents have a very limited lifespan. Since many vent animals can live only near vents, and the distance between vent systems can be hundreds to thousands of kilometres, it is a puzzle as to how vent animals escape a dying vent and colonize other distant vents or newly created vents. […] Hydrothermal vents are [however] not the only source of chemical-laden fluids supporting unique chemosynthetic-based communities in the deep ocean. Hydrogen sulphide and methane also ooze from the ocean buttom at some locations at temperatures similar to the surrounding seawater. These so-called ‘cold seeps‘ are often found along continental margins […] The communities associated with cold seeps are similar to hydrothermal vent communities […] Cold seeps appear to be more permanent sources of fluid compared to the ephemeral nature of hot water vents.”

“Seepage of crude oil into the marine environment occurs naturally from oil-containing geological formations below the seabed. It is estimated that around 600,000 tonnes of crude oil seeps into the marine environment each year, which represents almost half of all the crude oil entering the oceans. […] The human activities associated with exploring for and producing oil result in the release on average of an estimated 38,000 tonnes of crude oil into the oceans each year, which is about 6 per cent of the total anthropogenic input of oil into the oceans worldwide. Although small in comparison to natural seepage, crude oil pollution from this source can cause serious damage to coastal ecosystems because it is released near the coast and sometimes in very large, concentrated amounts. […] The transport of oil and oil products around the globe in tankers results in the release of about 150,000 tonnes of oil worldwide each year on average, or about 22 per cent of the total anthropogenic input. […] About 480,000 tonnes of oil make their way into the marine environment each year worldwide from leakage associated with the consumption of oil-derived products in cars and trucks, and to a lesser extent in boats. Oil lost from the operation of cars and trucks collects on paved urban areas from where it is washed off into streams and rivers, and from there into the oceans. Surprisingly, this represents the most significant source of human-derived oil pollution into the marine environment – about 72 per cent of the total. Because it is a very diffuse source of pollution, it is the most difficult to control.”

“Today it has been estimated that virtually all of the marine food resources in the Mediterranean sea have been reduced to less than 50 per cent of their original abundance […] The greatest impact has been on the larger predatory fish, which were the first to be targeted by fishers. […] It is estimated that, collectively, the European fish stocks of today are just one-tenth of their size in 1900. […] In 1950 the total global catch of marine seafood was just less than twenty million tonnes fresh weight. This increased steadily and rapidly until by the late 1980s more than eighty million tonnes were being taken each year […] Starting in the early 1990s, however, yields began to show signs of levelling off. […] By far the most heavily exploited marine fishery in the world is the Peruvian anchoveta (Engraulis ringens) fishery, which can account for 10 per cent or more of the global marine catch of seafood in any particular year. […] The anchoveta is a very oily fish, which makes it less desirable for direct consumption by humans. However, the high oil content makes it ideal for the production of fish meal and fish oil […] the demand for fish meal and fish oil is huge and about a third of the entire global catch of fish is converted into these products rather than consumed directly by humans. Feeding so much fish protein to livestock comes with a considerable loss of potential food energy (around 25 per cent) compared to if it was eaten directly by humans. This could be viewed as a potential waste of available energy for a rapidly growing human population […] around 90 per cent of the fish used to produce fish meal and oil is presently unpalatable to most people and thus unmarketable in large quantities as a human food”.

“On heavily fished areas of the continental shelves, the same parts of the sea floor can be repeatedly trawled many times per year. Such intensive bottom trawling causes great cumulative damage to seabed habitats. The trawls scrape and pulverize rich and complex bottom habitats built up over centuries by living organisms such as tube worms, cold-water corals, and oysters. These habitats are eventually reduced to uniform stretches of rubble and sand. For all intents and purposes these areas are permanently altered and become occupied by a much changed and much less rich community adapted to frequent disturbance.”

“The eighty million tonnes or so of marine seafood caught each year globally equates to about eleven kilograms of wild-caught marine seafood per person on the planet. […] What is perfectly clear […] on the basis of theory backed up by real data on marine fish catches, is that marine fisheries are now fully exploited and that there is little if any headroom for increasing the amount of wild-caught fish humans can extract from the oceans to feed a burgeoning human population. […] This conclusion is solidly supported by the increasingly precarious state of global marine fishery resources. The most recent information from the Food and Agriculture Organization of the United Nations (The State of World Fisheries and Aquaculture 2010) shows that over half (53 per cent of all fish stocks are fully exploited – their current catches are at or close to their maximum sustainable levels of production and there is no scope for further expansion. Another 32 per cent are overexploited and in decline. Of the remaining 15 per cent of stocks, 12 per cent are considered moderately exploited and only 3 per cent underexploited. […] in the mid 1970s 40 per cent of all fish stocks were in [the moderately exploited or unexploited] category as opposed to around 15 per cent now. […] the real question is not so much whether we can get more fish from the sea but whether we can sustain the amount of fish we are harvesting at present”.

March 16, 2018

## Systems Biology (II)

Some observations from the book’s chapter 3 below:

“Without regulation biological processes would become progressively more and more chaotic. In living cells the primary source of information is genetic material. Studying the role of information in biology involves signaling (i.e. spatial and temporal transfer of information) and storage (preservation of information). Regarding the role of the genome we can distinguish three specific aspects of biological processes: steady-state genetics, which ensure cell-level and body homeostasis; genetics of development, which controls cell differentiation and genesis of the organism; and evolutionary genetics, which drives speciation. […] The ever growing demand for information, coupled with limited storage capacities, has resulted in a number of strategies for minimizing the quantity of the encoded information that must be preserved by living cells. In addition to combinatorial approaches based on noncontiguous genes structure, self-organization plays an important role in cellular machinery. Nonspecific interactions with the environment give rise to coherent structures despite the lack of any overt information store. These mechanisms, honed by evolution and ubiquitous in living organisms, reduce the need to directly encode large quantities of data by adopting a systemic approach to information management.”

Information is commonly understood as a transferable description of an event or object. Information transfer can be either spatial (communication, messaging or signaling) or temporal (implying storage). […] The larger the set of choices, the lower the likelihood [of] making the correct choice by accident and — correspondingly — the more information is needed to choose correctly. We can therefore state that an increase in the cardinality of a set (the number of its elements) corresponds to an increase in selection indeterminacy. This indeterminacy can be understood as a measure of “a priori ignorance”. […] Entropy determines the uncertainty inherent in a given system and therefore represents the relative difficulty of making the correct choice. For a set of possible events it reaches its maximum value if the relative probabilities of each event are equal. Any information input reduces entropy — we can therefore say that changes in entropy are a quantitative measure of information. […] Physical entropy is highest in a state of equilibrium, i.e. lack of spontaneity (G = 0,0) which effectively terminates the given reaction. Regulatory processes which counteract the tendency of physical systems to reach equilibrium must therefore oppose increases in entropy. It can be said that a steady inflow of information is a prerequisite of continued function in any organism. As selections are typically made at the entry point of a regulatory process, the concept of entropy may also be applied to information sources. This approach is useful in explaining the structure of regulatory systems which must be “designed” in a specific way, reducing uncertainty and enabling accurate, error-free decisions.

The fire ant exudes a pheromone which enables it to mark sources of food and trace its own path back to the colony. In this way, the ant conveys pathing information to other ants. The intensity of the chemical signal is proportional to the abundance of the source. Other ants can sense the pheromone from a distance of several (up to a dozen) centimeters and thus locate the source themselves. […] As can be expected, an increase in the entropy of the information source (i.e. the measure of ignorance) results in further development of regulatory systems — in this case, receptors capable of receiving signals and processing them to enable accurate decisions. Over time, the evolution of regulatory mechanisms increases their performance and precision. The purpose of various structures involved in such mechanisms can be explained on the grounds of information theory. The primary goal is to select the correct input signal, preserve its content and avoid or eliminate any errors.”

Genetic information stored in nucleotide sequences can be expressed and transmitted in two ways:
a. via replication (in cell division);
b. via transcription and translation (also called gene expression […]
)
Both processes act as effectors and can be triggered by certain biological signals transferred on request.
Gene expression can be defined as a sequence of events which lead to the synthesis of proteins or their products required for a particular function. In cell division, the goal of this process is to generate a copy of the entire genetic code (S phase), whereas in gene expression only selected fragments of DNA (those involved in the requested function) are transcribed and translated. […] Transcription calls for exposing a section of the cell’s genetic code and although its product (RNA) is short-lived, it can be recreated on demand, just like a carbon copy of a printed text. On the other hand, replication affects the entire genetic material contained in the cell and must conform to stringent precision requirements, particularly as the size of the genome increases.”

The magnitude of effort involved in replication of genetic code can be visualized by comparing the DNA chain to a zipper […]. Assuming that the zipper consists of three pairs of interlocking teeth per centimeter (300 per meter) and that the human genome is made up of 3 billion […] base pairs, the total length of our uncoiled DNA in “zipper form” would be equal to […] 10,000 km […] If we were to unfasten the zipper at a rate of 1 m per second, the entire unzipping process would take approximately 3 months […]. This comparison should impress upon the reader the length of the DNA chain and the precision with which individual nucleotides must be picked to ensure that the resulting code is an exact copy of the source. It should also be noted that for each base pair the polymerase enzyme needs to select an appropriate matching nucleotide from among four types of nucleotides present in the solution, and attach it to the chain (clearly, no such problem occurs in zippers). The reliability of an average enzyme is on the order of 10-3–10-4, meaning that one error occurs for every 1,000–10,000 interactions between the enzyme and its substrate. Given this figure, replication of 3*109 base pairs would introduce approximately 3 million errors (mutations) per genome, resulting in a highly inaccurate copy. Since the observed reliability of replication is far higher, we may assume that some corrective mechanisms are involved. Really, the remarkable precision of genetic replication is ensured by DNA repair processes, and in particular by the corrective properties of polymerase itself.

Many mutations are caused by the inherent chemical instability of nucleic acids: for example, cytosine may spontaneously convert to uracil. In the human genome such an event occurs approximately 100 times per day; however uracil is not normally encountered in DNA and its presence alerts defensive mechanisms which correct the error. Another type of mutation is spontaneous depurination, which also triggers its own, dedicated error correction procedure. Cells employ a large number of corrective mechanisms […] DNA repair mechanisms may be treated as an “immune system” which protects the genome from loss or corruption of genetic information. The unavoidable mutations which sometimes occur despite the presence of error correction-mechanisms can be masked due to doubled presentation (alleles) of genetic information. Thus, most mutations are recessive and not expressed in the phenotype. As the length of the DNA chain increases, mutations become more probable. It should be noted that the number of nucleotides in DNA is greater than the relative number of aminoacids participating in polypeptide chains. This is due to the fact that each aminoacid is encoded by exactly three nucleotides — a general principle which applies to all living organisms. […] Fidelity is, of course, fundamentally important in DNA replication as any harmful mutations introduced in its course are automatically passed on to all successive generations of cells. In contrast, transcription and translation processes can be more error-prone as their end products are relatively short-lived. Of note is the fact that faulty transcripts appear in relatively low quantities and usually do not affect cell functions, since regulatory processes ensure continued synthesis of the required substances until a suitable level of activity is reached. Nevertheless, it seems that reliable transcription of genetic material is sufficiently significant for cells to have developed appropriate proofreading mechanisms, similar to those which assist replication. […] the entire information pathway — starting with DNA and ending with active proteins — is protected against errors. We can conclude that fallibility is an inherent property of genetic information channels, and that in order to perform their intended function, these channels require error correction mechanisms.”

The discrete nature of genetic material is an important property which distinguishes prokaryotes from eukaryotes. […] The ability to select individual nucleotide fragments and construct sequences from predetermined “building blocks” results in high adaptability to environmental stimuli and is a fundamental aspect of evolution. The discontinuous nature of genes is evidenced by the presence of fragments which do not convey structural information (introns), as opposed to structure-encoding fragments (exons). The initial transcript (pre-mRNA) contains introns as well as exons. In order to provide a template for protein synthesis, it must undergo further processing (also known as splicing): introns must be cleaved and exon fragments attached to one another. […] Recognition of intron-exon boundaries is usually very precise, while the reattachment of adjacent exons is subject to some variability. Under certain conditions, alternative splicing may occur, where the ordering of the final product does not reflect the order in which exon sequences appear in the source chain. This greatly increases the number of potential mRNA combinations and thus the variety of resulting proteins. […] While access to energy sources is not a major problem, sources of information are usually far more difficult to manage — hence the universal tendency to limit the scope of direct (genetic) information storage. Reducing the length of genetic code enables efficient packing and enhances the efficiency of operations while at the same time decreasing the likelihood of errors. […] The number of genes identified in the human genome is lower than the number of distinct proteins by a factor of 4; a difference which can be attributed to alternative splicing. […] This mechanism increases the variety of protein structures without affecting core information storage, i.e. DNA sequences. […] Primitive organisms often possess nearly as many genes as humans, despite the essential differences between both groups. Interspecies diversity is primarily due to the properties of regulatory sequences.”

The discontinuous nature of genes is evolutionarily advantageous but comes at the expense of having to maintain a nucleus where such splicing processes can be safely conducted, in addition to efficient transport channels allowing transcripts to penetrate the nuclear membrane. While it is believed that at early stages of evolution RNA was the primary repository of genetic information, its present function can best be described as an information carrier. Since unguided proteins cannot ensure sufficient specificity of interaction with nucleic acids, protein-RNA complexes are used often in cases where specific fragments of genetic information need to be read. […] The use of RNA in protein complexes is common across all domains of the living world as it bridges the gap between discrete and continuous storage of genetic information.”

Epigenetic differentiation mechanisms are particularly important in embryonic development. […] Unlike the function of mature organisms, embryonic programming refers to structures which do not yet exist but which need to be created through cell proliferation and differentiation. […] Differentiation of cells results in phenotypic changes. This phenomenon is the primary difference between development genetics and steady-state genetics. Functional differences are not, however, associated with genomic changes: instead they are mediated by the transcriptome where certain genes are preferentially selected for transcription while others are suppressed. […] In a mature, specialized cell only a small portion of the transcribable genome is actually expressed. The remainder of the cell’s genetic material is said to be silenced. Gene silencing is a permanent condition. Under normal circumstances mature cells never alter their function, although such changes may be forced in a laboratory setting […] Cells which make up the embryo at a very early stage of development are pluripotent, meaning that their purpose can be freely determined and that all of their genetic information can potentially be expressed (under certain conditions). […] At each stage of the development process the scope of pluripotency is reduced until, ultimately, the cell becomes monopotent. Monopotency implies that the final function of the cell has already been determined, although the cell itself may still be immature. […] functional dissimilarities between specialized cells are not associated with genetic mutations but rather with selective silencing of genes. […] Most genes which determine biological functions have a biallelic representation (i.e. a representation consisting of two alleles). The remainder (approximately 10 % of genes) is inherited from one specific parent, as a result of partial or complete silencing of their sister alleles (called paternal or maternal imprinting) which occurs during gametogenesis. The suppression of a single copy of the X chromosome is a special case of this phenomenon.”

Evolutionary genetics is subject to two somewhat contradictory criteria. On the one hand, there is clear pressure on accurate and consistent preservation of biological functions and structures while on the other hand it is also important to permit gradual but persistent changes. […] the observable progression of adaptive traits which emerge as a result of evolution suggests a mechanism which promotes constructive changes over destructive ones. Mutational diversity cannot be considered truly random if it is limited to certain structures or functions. […] Approximately 50 % of the human genome consists of mobile segments, capable of migrating to various positions in the genome. These segments are called transposons and retrotransposons […] The mobility of genome fragments not only promotes mutations (by increasing the variability of DNA) but also affects the stability and packing of chromatin strands wherever such mobile sections are reintegrated with the genome. Under normal circumstances the activity of mobile sections is tempered by epigenetic mechanisms […]; however in certain situations gene mobility may be upregulated. In particular, it seems that in “prehistoric” (remote evolutionary) times such events occurred at a much faster pace, accelerating the rate of genetic changes and promoting rapid evolution. Cells can actively promote mutations by way of the so-called AID process (activity-dependent cytosine deamination). It is an enzymatic mechanism which converts cytosine into uracil, thereby triggering repair mechanisms and increasing the likelihood of mutations […] The existence of AID proves that cells themselves may trigger evolutionary changes and that the role of mutations in the emergence of new biological structures is not strictly passive.”

Regulatory mechanisms which receive signals characterized by high degrees of uncertainty, must be able to make informed choices to reduce the overall entropy of the system they control. This property is usually associated with development of information channels. Special structures ought to be exposed within information channels connecting systems of different character as for example linking transcription to translation or enabling transduction of signals through the cellular membrane. Examples of structures which convey highly entropic information are receptor systems associated with blood coagulation and immune responses. The regulatory mechanism which triggers an immune response relies on relatively simple effectors (complement factor enzymes, phages and killer cells) coupled to a highly evolved receptor system, represented by specific antibodies and organized set of cells. Compared to such advanced receptors the structures which register the concentration of a given product (e.g. glucose in blood) are rather primitive. Advanced receptors enable the immune system to recognize and verify information characterized by high degrees of uncertainty. […] In sequential processes it is usually the initial stage which poses the most problems and requires the most information to complete successfully. It should come as no surprise that the most advanced control loops are those associated with initial stages of biological pathways.”

February 10, 2018

## The Biology of Moral Systems (III)

This will be my last post about the book. It’s an important work which deserves to be read by far more people than have already read it. I have added some quotes and observations from the last chapters of the book below.

“If egoism, as self-interest in the biologists’ sense, is the reason for the promotion of ethical behavior, then, paradoxically, it is expected that everyone will constantly promote the notion that egoism is not a suitable theory of action, and, a fortiori, that he himself is not an egoist. Most of all he must present this appearance to his closest associates because it is in his best interests to do so – except, perhaps, to his closest relatives, to whom his egoism may often be displayed in cooperative ventures from which some distant- or non-relative suffers. Indeed, it may be arguable that it will be in the egoist’s best interest not to know (consciously) or to admit to himself that he is an egoist because of the value to himself of being able to convince others he is not.”

“The function of [societal] punishments and rewards, I have suggested, is to manipulate the behavior of participating individuals, restricting individual efforts to serve their own interests at others’ expense so as to promote harmony and unity within the group. The function of harmony and unity […] is to allow the group to compete against hostile forces, especially other human groups. It is apparent that success of the group may serve the interests of all individuals in the group; but it is also apparent that group success can be achieved with different patterns of individual success differentials within the group. So […] it is in the interests of those who are differentially successful to promote both unity and the rules so that group success will occur without necessitating changes deleterious to them. Similarly, it may be in the interests of those individuals who are relatively unsuccessful to promote dissatisfaction with existing rules and the notion that group success would be more likely if the rules were altered to favor them. […] the rules of morality and law alike seem not to be designed explicitly to allow people to live in harmony within societies but to enable societies to be sufficiently united to deter their enemies. Within-society harmony is the means not the end. […] extreme within-group altruism seems to correlate with and be historically related to between-group strife.”

“There are often few or no legitimate or rational expectations of reciprocity or “fairness” between social groups (especially warring or competing groups such as tribes or nations). Perhaps partly as a consequence, lying, deceit, or otherwise nasty or even heinous acts committed against enemies may sometimes not be regarded as immoral by others withing the group of those who commit them. They may even be regarded as highly moral if they seem dramatically to serve the interests of the group whose members commit them.”

“Two major assumptions, made universally or most of the time by philosophers, […] are responsible for the confusion that prevents philosophers from making sense out of morality […]. These assumptions are the following: 1. That proximate and ultimate mechanisms or causes have the same kind of significance and can be considered together as if they were members of the same class of causes; this is a failure to understand that proximate causes are evolved because of ultimate causes, and therefore may be expected to serve them, while the reverse is not true. Thus, pleasure is a proximate mechanism that in the usual environments of history is expected to impel us toward behavior that will contribute to our reproductive success. Contrarily, acts leading to reproductive success are not proximate mechanisms that evolved because they served the ultimate function of bringing us pleasure. 2. That morality inevitably involves some self-sacrifice. This assumption involves at least three elements: a. Failure to consider altruism as benefits to the actor. […] b. Failure to comprehend all avenues of indirect reciprocity within groups. c. Failure to take into account both within-group and between-group benefits.”

“If morality means true sacrifice of one’s own interests, and those of his family, then it seems to me that we could not have evolved to be moral. If morality requires ethical consistency, whereby one does not do socially what he would not advocate and assist all others also to do, then, again, it seems to me that we could not have evolved to be moral. […] humans are not really moral at all, in the sense of “true sacrifice” given above, but […] the concept of morality is useful to them. […] If it is so, then we might imagine that, in the sense and to the extent that they are anthropomorphized, the concepts of saints and angels, as well as that of God, were also created because of their usefulness to us. […] I think there have been far fewer […] truly self-sacrificing individuals than might be supposed, and most cases that might be brought forward are likely instead to be illustrations of the complexity and indirectness of reciprocity, especially the social value of appearing more altruistic than one is. […] I think that […] the concept of God must be viewed as originally generated and maintained for the purpose – now seen by many as immoral – of furthering the interests of one group of humans at the expense of one or more other groups. […] Gods are inventions originally developed to extend the notion that some have greater rights than others to design and enforce rules, and that some are more destined to be leaders, others to be followers. This notion, in turn, arose out of prior asymmetries in both power and judgment […] It works when (because) leaders are (have been) valuable, especially in the context of intergroup competition.”

“We try to move moral issues in the direction of involving no conflict of interest, always, I suggest, by seeking universal agreement with our own point of view.”

“Moral and legal systems are commonly distinguished by those, like moral philosophers, who study them formally. I believe, however, that the distinction between them is usually poorly drawn, and based on a failure to realize that moral as well as legal behavior occurs as a result of probably and possible punishments and reward. […] we often internalize the rules of law as well as the rules of morality – and perhaps by the same process […] It would seem that the rules of law are simply a specialized, derived aspect of what in earlier societies would have been a part of moral rules. On the other hand, law covers only a fraction of the situations in which morality is involved […] Law […] seems to be little more than ethics written down.”

“Anyone who reads the literature on dispute settlement within different societies […] will quickly understand that genetic relatedness counts: it allows for one-way flows of benefits and alliances. Long-term association also counts; it allows for reliability and also correlates with genetic relatedness. […] The larger the social group, the more fluid its membership; and the more attenuated the social interactions of its membership, the more they are forced to rely on formal law”.

“[I]ndividuals have separate interests. They join forces (live in groups; become social) when they share certain interests that can be better realized for all by close proximity or some forms of cooperation. Typically, however, the overlaps of interests rarely are completely congruent with those of either other individuals or the rest of the group. This means that, even during those times when individual interests within a group are most broadly overlapping, we may expect individuals to temper their cooperation with efforts to realize their own interests, and we may also expect them to have evolved to be adept at using others, or at thwarting the interests of others, to serve themselves (and their relatives). […] When the interests of all are most nearly congruent, it is essentially always due to a threat shared equally. Such threats almost always have to be external (or else they are less likely to affect everyone equally […] External threats to societies are typically other societies. Maintenance of such threats can yield situations in which everyone benefits from rigid, hierarchical, quasi-military, despotic government. Liberties afforded leaders – even elaborate perquisites of dictators – may be tolerated because such threats are ever-present […] Extrinsic threats, and the governments they produce, can yield inflexibilities of political structures that can persist across even lengthy intervals during which the threats are absent. Some societies have been able to structure their defenses against external threats as separate units (armies) within society, and to keep them separate. These rigidly hierarchical, totalitarian, and dictatorial subunits rise and fall in size and influence according to the importance of the external threat. […] Discussion of liberty and equality in democracies closely parallels discussions of morality and moral systems. In either case, adding a perspective from evolutionary biology seems to me to have potential for clarification.”

“It is indeed common, if not universal, to regard moral behavior as a kind of altruism that necessarily yields the altruist less than he gives, and to see egoism as either the opposite of morality or the source of immorality; but […] this view is usually based on an incomplete understanding of nepotism, reciprocity, and the significance of within-group unity for between-group competition. […] My view of moral systems in the real world, however, is that they are systems in which costs and benefits of specific actions are manipulated so as to produce reasonably harmonious associations in which everyone nevertheless pursues his own (in evolutionary terms) self-interest. I do not expect that moral and ethical arguments can ever be finally resolved. Compromises and contracts, then, are (at least currently) the only real solutions to actual conflicts of interest. This is why moral and ethical decisions must arise out of decisions of the collective of affected individuals; there is no single source of right and wrong.

I would also argue against the notion that rationality can be easily employed to produce a world of humans that self-sacrifice in favor of other humans, not to say nonhuman animals, plants, and inanimate objects. Declarations of such intentions may themselves often be the acts of self-interested persons developing, consciously or not, a socially self-benefiting view of themselves as extreme altruists. In this connection it is not irrelevant that the more dissimilar a species or object is to one’s self the less likely it is to provide a competitive threat by seeking the same resources. Accordingly, we should not be surprised to find humans who are highly benevolent toward other species or inanimate objects (some of which may serve them uncomplainingly), yet relatively hostile and noncooperative with fellow humans. As Darwin (1871) noted with respect to dogs, we have selected our domestic animals to return our altruism with interest.”

“It is not easy to discover precisely what historical differences have shaped current male-female differences. If, however, humans are in a general way similar to other highly parental organisms that live in social groups […] then we can hypothesize as follows: for men much of sexual activity has had as a main (ultimate) significance the initiating of pregnancies. It would follow that when a man avoids copulation it is likely to be because (1) there is no likelihood of pregnancy or (2) the costs entailed (venereal disease, danger from competition with other males, lowered status if the event becomes public, or an undesirable commitment) are too great in comparison with the probability that pregnancy will be induced. The man himself may be judging costs against the benefits of immediate sensory pleasures, such as orgasms (i.e., rather than thinking about pregnancy he may say that he was simply uninterested), but I am assuming that selection has tuned such expectations in terms of their probability of leading to actual reproduction […]. For women, I hypothesize, sexual activity per se has been more concerned with the securing of resources (again, I am speaking of ultimate and not necessarily conscious concerns) […]. Ordinarily, when women avoid or resist copulation, I speculate further, the disinterest, aversion, or inhibition may be traceable eventually to one (or more) of three causes: (1) there is no promise of commitment (of resources), (2) there is a likelihood of undesirable commitment (e.g., to a man with inadequate resources), or (3) there is a risk of loss of interest by a man with greater resources, than the one involved […] A man behaving so as to avoid pregnancies, and who derives from an evolutionary background of avoiding pregnancies, should be expected to favor copulation with women who are for age or other reasons incapable of pregnancy. A man derived from an evolutionary process in which securing of pregnancies typically was favored, may be expected to be most interested sexually in women most likely to become pregnant and near the height of the reproductive probability curve […] This means that men should usually be expected to anticipate the greatest sexual pleasure with young, healthy, intelligent women who show promise of providing superior parental care. […] In sexual competition, the alternatives of a man without resources are to present himself as a resource (i.e., as a mimic of one with resources or as one able and likely to secure resources because of his personal attributes […]), to obtain sex by force (rape), or to secure resources through a woman (e.g., allow himself to be kept by a relatively undesired woman, perhaps as a vehicle to secure liaisons with other women). […] in nonhuman species of higher animals, control of the essential resources of parenthood by females correlates with lack of parental behavior by males, promiscuous polygyny, and absence of long-term pair bonds. There is some evidence of parallel trends within human societies (cf. Flinn, 1981).” [It’s of some note that quite a few good books have been written on these topics since Alexander first published his book, so there are many places to look for detailed coverage of topics like these if you’re curious to know more – I can recommend both Kappeler & van Schaik (a must-read book on sexual selection, in my opinion) & Bobby Low. I didn’t think too highly of Miller or Meston & Buss, but those are a few other books on these topics which I’ve read – US].

“The reason that evolutionary knowledge has no moral content is [that] morality is a matter of whose interests one should, by conscious and willful behavior, serve, and how much; evolutionary knowledge contains no messages on this issue. The most it can do is provide information about the reasons for current conditions and predict some consequences of alternative courses of action. […] If some biologists and nonbiologists make unfounded assertions into conclusions, or develop pernicious and fallible arguments, then those assertions and arguments should be exposed for what they are. The reason for doing this, however, is not […should not be..? – US] to prevent or discourage any and all analyses of human activities, but to enable us to get on with a proper sort of analysis. Those who malign without being specific; who attack people rather than ideas; who gratuitously translate hypotheses into conclusions and then refer to them as “explanations,” “stories,” or “just-so-stories”; who parade the worst examples of argument and investigation with the apparent purpose of making all efforts at human self-analysis seem silly and trivial, I see as dangerously close to being ideologues at least as worrisome as those they malign. I cannot avoid the impression that their purpose is not to enlighten, but to play upon the uneasiness of those for whom the approach of evolutionary biology is alien and disquieting, perhaps for political rather than scientific purposes. It is more than a little ironic that the argument of politics rather than science is their own chief accusation with respect to scientists seeking to analyze human behavior in evolutionary terms (e.g. Gould and Levontin, 1979 […]).”

“[C]urrent selective theory indicates that natural selection has never operated to prevent species extinction. Instead it operates by saving the genetic materials of those individuals or families that outreproduce others. Whether species become extinct or not (and most have) is an incidental or accidental effect of natural selection. An inference from this is that the members of no species are equipped, as a direct result of their evolutionary history, with traits designed explicitly to prevent extinction when that possibility looms. […] Humans are no exception: unless their comprehension of the likelihood of extinction is so clear and real that they perceive the threat to themselves as individuals, and to their loved ones, they cannot be expected to take the collective action that will be necessary to reduce the risk of extinction.”

“In examining ourselves […] we are forced to use the attributes we wish to analyze to carry out the analysis, while resisting certain aspects of the analysis. At the very same time, we pretend that we are not resisting at all but are instead giving perfectly legitimate objections; and we use our realization that others will resist the analysis, for reasons as arcane as our own, to enlist their support in our resistance. And they very likely will give it. […] If arguments such as those made here have any validity it follows that a problem faced by everyone, in respect to morality, is that of discovering how to subvert or reduce some aspects of individual selfishness that evidently derive from our history of genetic individuality.”

“Essentially everyone thinks of himself as well-meaning, but from my viewpoint a society of well-meaning people who understand themselves and their history very well is a better milieu than a society of well-meaning people who do not.”

September 22, 2017

## Quantifying tumor evolution through spatial computational modeling

Two general remarks: 1. She talks very fast, in my opinion unpleasantly fast – the lecture would have been at least slightly easier to follow if she’d slowed down a little. 2. A few of the lectures uploaded in this lecture series (from the IAS Mathematical Methods in Cancer Evolution and Heterogeneity Workshop) seem to have some sound issues; in this lecture there are multiple 1-2 seconds long ‘chunks’ where the sound drops out and some words are lost. This is really annoying, and a similar problem (which was likely ‘the same problem’) previously lead me to quit another lecture in the series; however in this case I decided to give it a shot anyway, and I actually think it’s not a big deal; the sound-losses are very short in duration, and usually no more than one or two words are lost so you can usually figure out what was said. During this lecture there was incidentally also some issues with the monitor roughly 27 minutes in, but this isn’t a big deal as no information was lost and unlike the people who originally attended the lecture you can just skip ahead approximately one minute (that was how long it took to solve that problem).

A few relevant links to stuff she talks about in the lecture:

August 22, 2017

## The Biology of Moral Systems (II)

There are multiple really great books I have read ‘recently’ and which I have either not blogged at all, or not blogged in anywhere near the amount of detail they deserve; Alexander’s book is one of those books. I hope to get rid of some of the backlog soon. You can read my first post about the book here, and it might be a good idea to do so as I won’t allude to material covered in the first post here. In this post I have added some quotes from and comments related to the book’s second chapter, ‘A Biological View of Morality’.

“Moral systems are systems of indirect reciprocity. They exist because confluences of interest within groups are used to deal with conflicts of interest between groups. Indirect reciprocity develops because interactions are repeated, or flow among a society’s members, and because information about subsequent interactions can be gleaned from observing the reciprocal interactions of others.
To establish moral rules is to impose rewards and punishments (typically assistance and ostracism, respectively) to control social acts that, respectively, help or hurt others. To be regarded as moral, a rule typically must represent widespread opinion, reflecting the fact that it must apply with a certain degree of indiscrimininateness.”

“Moral philosophers have not treated the beneficence of humans as a part, somehow, of their selfishness; yet, as Trivers (1971) suggested, the biologist’s view of lifetimes leads directly to this argument. In other words, the normally expressed beneficence, or altruism, of parenthood and nepotism and the temporary altruism (or social investment) of reciprocity are expected to result in greater returns than their alternatives.
If biologists are correct, all that philosophers refer to as altruistic or utilitarian behavior by individuals will actually represent either the temporary altruism (phenotypic beneficence or social investment) of indirect somatic effort [‘Direct somatic effort refers to self-help that involves no other persons. Indirect somatic effort involves reciprocity, which may be direct or indirect. Returns from direct and indirect reciprocity may be immediate or delayed’ – Alexander spends some pages classifying human effort in terms of such ‘atoms of sociality’, which are useful devices for analytical purposes, but I decided not to cover that stuff in detail here – US] or direct and indirect nepotism. The exceptions are what might be called evolutionary mistakes or accidents that result in unreciprocated or “genetic” altruism, deleterious to both the phenotype and genotype of the altruist; such mistakes can occur in all of the above categories” [I should point out that Boyd and Richerson’s book Not by Genes Alone – another great book which I hope to blog soon – is worth having a look at if after reading Alexander’s book you think that he does not cover the topic of how and why such mistakes might happen in the amount of detail it deserves; they also cover related topics in some detail, from a different angle – US]

“It is my impression that many moral philosophers do not approach the problem of morality and ethics as if it arose as an effort to resolve conflicts of interests. Their involvement in conflicts of interest seems to come about obliquely through discussions of individuals’ views with respect to moral behavior, or their proximate feelings about morality – almost as if questions about conflicts of interest arise only because we operate under moral systems, rather than vice versa.”

“The problem, in developing a theory of moral systems that is consistent with evolutionary theory from biology, is in accounting for the altruism of moral behavior in genetically selfish terms. I believe this can be done by interpreting moral systems as systems of indirect reciprocity.
I regard indirect reciprocity as a consequence of direct reciprocity occurring in the presence of interested audiences – groups of individuals who continually evaluate the members of their society as possible future interactants from whom they would like to gain more than they lose […] Even in directly reciprocal interactions […] net losses to self […] may be the actual aim of one or even both individuals, if they are being scrutinized by others who are likely to engage either individual subsequently in reciprocity of greater significance than that occurring in the scrutinized acts. […] Systems of indirect reciprocity, and therefore moral systems, are social systems structured around the importance of status. The concept of status implies that an individual’s privileges, or its access to resources, are controlled in part by how others collectively think of him (hence, treat him) as a result of past interactions (including observations of interactions with others). […] The consequences of indirect reciprocity […] include the concomitant spread of altruism (as social investment genetically valuable to the altruist), rules, and efforts to cheat […]. I would not contend that we always carry out cost-benefit analyses on these issues deliberately or consciously. I do, however, contend that such analyses occur, sometimes consciously, sometimes not, and that we are evolved to be exceedingly accurate and quick at making them […] [A] conscience [is what] I have interpreted (Alexander, 1979a) as the “still small voice that tells us how far we can go in serving our own interests without incurring intolerable risks.””

“The long-term existence of complex patterns of indirect reciprocity […] seems to favor the evolution of keen abilities to (1) make one’s self seem more beneficent than is the case; and (2) influence others to be beneficent in such fashions as to be deleterious to themselves and beneficial to the moralizer, e.g. to lead others to (a) invest too much, (b) invest wrongly in the moralizer or his relatives and friends, or (c) invest indiscriminately on a larger scale than would otherwise be the case. According to this view, individuals are expected to parade the idea of much beneficence, and even of indiscriminate altruism as beneficial, so as to encourage people in general to engage in increasing amounts of social investment whether or not it is beneficial to their interests. […] They may also be expected to depress the fitness of competitors by identifying them, deceptively or not, as reciprocity cheaters (in other words, to moralize and gossip); to internalize rules or evolve the ability to acquire a conscience, interpreted […] as the ability to use or own judgment to serve our own interests; and to self-deceive and display false sincerity as defenses against detection of cheating and attributions of deliberateness in cheating […] Everyone will with to appear more beneficent than he is. There are two reasons: (1) this appearance, if credible, is more likely to lead to direct social rewards than its alternatives; (2) it is also more likely to encourage others to be more beneficent.”

“Consciousness and related aspects of the human psyche (self-awareness, self-reflection, foresight, planning, purpose, conscience, free will, etc.) are here hypothesized to represent a system for competing with other humans for status, resources, and eventually reproductive success. More specifically, the collection of these attributes is viewed as a means of seeing ourselves and our life situations as others see us and our life situations – most particularly in ways that will cause (the most and the most important of) them to continue to interact with us in fashions that will benefit us and seem to benefit them.
Consciousness, then, is a game of life in which the participants are trying to comprehend what is in one another’s minds before, and more effectively than, it can be done in reverse.”

“Provided with a means of relegating our deceptions to the subconsciousness […] false sincerity becomes easier and detection more difficult. There are reasons for believing that one does not need to know his own personal interests consciously in order to serve them as much as he needs to know the interests of others to thwart them. […] I have suggested that consciousness is a way of making our social behavior so unpredictable as to allow us to outmaneuver others; and that we press into subconsciousness (as opposed to forgetting) those things that remain useful to us but would be detrimental to us if others knew about them, and on which we are continually tested and would have to lie deliberately if they remained in our conscious mind […] Conscious concealment of interests, or disavowal, is deliberate deception, considered more reprehensible than anything not conscious. Indeed, if one does not know consciously what his interests are, he cannot, in some sense, be accused of deception even though he may be using an evolved ability of self-deception to deceive others. So it is not always – maybe not usually – in our evolutionary or surrogate-evolutionary interests to make them conscious […] If people can be fooled […] then there will be continual selection for becoming better at fooling others […]. This may include causing them to think that it will be best for them to help you when it is not. This ploy works because of the thin line everybody must continually tread with respect to not showing selfishness. If some people are self-destructively beneficent (i.e., make altruistic mistakes), and if people often cannot tell if one is such a mistake-maker, it might be profitable even to try to convince others that one is such a mistake-maker so as to be accepted as a cooperator or so that the other will be beneficent in expectation of large returns (through “mistakes”) later. […] Reciprocity may work this way because it is grounded evolutionarily in nepotism, appropriate dispensing of nepotism (as well as reciprocity) depends upon learning, and the wrong things can be learned. [Boyd and Richerson talk about this particular aspect, the learning part, in much more detail in their books – US] Self-deception, then may not be a pathological or detrimental trait, at least in most people most of the time. Rather, it may have evolved as a way to deceive others.”

“The only time that utilitarianism (promoting the greatest good to the greatest number) is predicted by evolutionary theory is when the interests of the group (the “greatest number”) and the individual coincide, and in such cases utilitarianism is not really altruistic in either the biologists’ or the philosophers’ sense of the term. […] If Kohlberg means to imply that a significant proportion of the populace of the world either implicitly or explicitly favors a system in which everyone (including himself) behaves so as to bring the greatest good to the greatest number, then I simply believe that he is wrong. If he supposes that only a relatively few – particularly moral philosophers and some others like them – have achieved this “stage,” then I also doubt the hypothesis. I accept that many people are aware of this concept of utility, that a small minority may advocate it, and that an even smaller minority may actually believe that they behave according to it. I speculate, however, that with a few inadvertent or accidental exceptions, no one actually follows this precept. I see the concept as having its main utility as a goal towards which one may exhort others to aspire, and towards which one may behave as if (or talk as if) aspiring, which actually practicing complex forms of self-interest.”

“Generally speaking, the bigger the group, the more complex the social organization, and the greater the group’s unity of purpose the more limited is individual entrepreneurship.”

“The function or raison d’etre [sic] of moral systems is evidently to provide the unity required to enable the group to compete successfully with other human groups. […] the argument that human evolution has been guided to some large extent by intergroup competition and aggression […] is central to the theory of morality presented here”.

June 29, 2017

## Quotes

(The Pestallozzi quotes below are from The Education of Man, a short and poor aphorism collection I can not possibly recommend despite the inclusion of quotes from it in this post.)

i. “Only a good conscience always gives man the courage to handle his affairs straightforwardly, openly and without evasion.” (Johann Heinrich Pestalozzi)

ii. “An intimate relationship in its full power is always a source of human wisdom and strength in relationships less intimate.” (-ll-)

iii. “Whoever is unwilling to help himself can be helped by no one.” (-ll-)

iv. “He who has filled his pockets in the service of injustice will have little good to say on behalf of justice.” (-ll-)

v. “It is Man’s fate that no one knows the truth alone; we all possess it, but it is divided up among us. He who learns from one man only, will never learn what the others know.” (-ll-)

vi. “No scoundrel is so wicked that he cannot at some point truthfully reprove some honest man” (-ll-)

vii. “The man too keenly aware of his good reputation is likely to have a bad one.” (-ll-)

viii. “Many words make an excuse anything but convincing.” (-ll-)

ix. “Fashions are usually seen in their true perspective only when they have gone out of fashion.” (-ll-)

x. “A thing that nobody looks for is seldom found.” (-ll-)

xi. “Many discoveries must have been stillborn or smothered at birth. We know only those which survived.” (William Ian Beardmore Beveridge)

xii. “Time is the most valuable thing a man can spend.” (Theophrastus)

xiii. “The only man who makes no mistakes is the man who never does anything.” (Theodore Roosevelt)

xiv. “It is hard to fail, but it is worse never to have tried to succeed.” (-ll-)

xv. “From their appearance in the Triassic until the end of the Creta­ceous, a span of 140 million years, mam­mals remained small and inconspicuous while all the ecological roles of large ter­restrial herbivores and carnivores were monopolized by dinosaurs; mammals did not begin to radiate and produce large species until after the dinosaurs had al­ready become extinct at the end of the Cretaceous. One is forced to conclude that dinosaurs were competitively su­perior to mammals as large land vertebrates.” (Robert T. Bakker)

xvi. “Plants and plant-eaters co-evolved. And plants aren’t the passive partners in the chain of terrestrial life. […] A birch tree doesn’t feel cosmic fulfillment when a moose munches its leaves; the tree species, in fact, evolves to fight the moose, to keep the animal’s munching lips away from vulnerable young leaves and twigs. In the final analysis, the merciless hand of natural selection will favor the birch genes that make the tree less and less palatable to the moose in generation after generation. No plant species could survive for long by offering itself as unprotected fodder.” (-ll-)

xvii. “… if you look at crocodiles today, they aren’t really representative of what the lineage of crocodiles look like. Crocodiles are represented by about 23 species, plus or minus a couple. Along that lineage the more primitive members weren’t aquatic. A lot of them were bipedal, a lot of them looked like little dinosaurs. Some were armored, others had no teeth. They were all fully terrestrial. So this is just the last vestige of that radiation that we’re seeing. And the ancestor of both dinosaurs and crocodiles would have, to the untrained eye, looked much more like a dinosaur.” (Mark Norell)

xviii. “If we are to understand the interactions of a large number of agents, we must first be able to describe the capabilities of individual agents.” (John Henry Holland)

xix. “Evolution continually innovates, but at each level it conserves the elements that are recombined to yield the innovations.” (-ll-)

xx. “Model building is the art of selecting those aspects of a process that are relevant to the question being asked. […] High science depends on this art.” (-ll-)

June 19, 2017

## The Biology of Moral Systems (I)

I have quoted from the book before, but I decided that this book deserves to be blogged in more detail. I’m close to finishing the book at this point (it’s definitely taken longer than it should have), and I’ll probably give it 5 stars on goodreads; I might also add it to my list of favourite books on the site. In this post I’ve added some quotes and ideas from the book, and a few comments. Before going any further I should note that it’s frankly impossible to cover anywhere near all the ideas covered in the book here on the blog, so if you’re even remotely interested in these kinds of things you really should pick up a copy of the book and read all of it.

“I believe that something crucial has been missing from all of the great debates of history, among philosophers, politicians, theologians, and thinkers from other and diverse backgrounds, on the issues of morality, ethics, justice, right and wrong. […] those who have tried to analyze morality have failed to treat the human traits that underlie moral behavior as outcomes of evolution […] for many conflicts of interest, compromises and enforceable contracts represent the only real solutions. Appeals to morality, I will argue, are simply the invoking of such compromises and contracts in particular ways. […] the process of natural selection that has given rise to all forms of life, including humans, operates such that success has always been relative. One consequence is that organisms resulting from the long-term cumulative effects of selection are expected to resist efforts to reveal their interests fully to others, and also efforts to place limits on their striving or to decide for them when their interests are being “fully” satisfied. These are all reasons why we should expect no “terminus” – ever – to debates on moral and ethical issues.” (these comments I also included in the quotes post to which I link at the beginning, but I thought it was worth including them in this post as well even so – US).

“I am convinced that biology can never offer […] easy or direct answers to the questions of what is right and wrong. I explicitly reject the attitude that whatever biology tells us is so is also what ought to be (David Hume’s so-called “naturalistic fallacy”) […] there are within biology no magic solutions to moral problems. […] Knowledge of the human background in organic evolution can [however] provide a deeper self-understanding by an increasing proportion of the world’s population; self-understanding that I believe can contribute to answering the serious questions of social living.”

“If there had been no recent discoveries in biology that provided new ways of looking at the concept of moral systems, then I would be optimistic indeed to believe that I could say much that is new. But there have been such discoveries. […] The central point in these writings [Hamilton, Williams, Trivers, Cavalli-Sforza, Feldman, Dawkins, Wilson, etc. – US] […] is that natural selection has apparently been maximizing the survival by reproduction of genes, as they have been defined by evolutionists, and that, with respect to the activities of individuals, this includes effects on copies of their genes, even copies located in other individuals. In other words, we are evidently evolved not only to aid the genetic materials in our own bodies, by creating and assisting descendants, but also to assist, by nepotism, copies of our genes that reside in collateral (nondescendant) relatives. […] ethics, morality, human conduct, and the human psyche are to be understood only if societies are seen as collections of individuals seeking their own self-interests […] In some respects these ideas run contrary to what people have believed and been taught about morality and human values: I suspect that nearly all humans believe it is a normal part of the functioning of every human individual now and then to assist someone else in the realization of that person’s own interests to the actual net expense of those of the altruist. What [the above-mentioned writings] tells us is that, despite our intuitions, there is not a shred of evidence to support this view of beneficence, and a great deal of convincing theory suggests that any such view will eventually be judged false. This implies that we will have to start all over again to describe and understand ourselves, in terms alien to our intuitions […] It is […] a goal of this book to contribute to this redescription and new understanding, and especially to discuss why our intuitions should have misinformed us.”

“Social behavior evolves as a succession of ploys and counterploys, and for humans these ploys are used, not only among individuals within social groups, but between and among small and large groups of up to hundreds of millions of individuals. The value of an evolutionary approach to human sociality is thus not to determine the limits of our actions so that we can abide by them. Rather, it is to examine our life strategies so that we can change them when we wish, as a result of understanding them. […] my use of the word biology in no way implies that moral systems have some kind of explicit genetic background, are genetically determined, or cannot be altered by adjusting the social environment. […] I mean simply to suggest that if we wish to understand those aspects of our behavior commonly regarded as involving morality or ethics, it will help to reconsider our behavior as a product of evolution by natural selection. The principal reason for this suggestion is that natural selection operates according to general principles which make its effects highly predictive, even with respect to traits and circumstances that have not yet been analyzed […] I am interested […] not in determining what is moral and immoral, in the sense of what people ought to be doing, but in elucidating the natural history of ethics and morality – in discovering how and why humans initiated and developed the ideas we have about right and wrong.”

I should perhaps mention here that sort-of-kind-of related stuff is covered in Aureli et al. (see e.g. this link), and that some parts of that book will probably make you understand Alexander’s ideas a lot better even if perhaps he didn’t read those specific authors – mainly because it gets a lot easier to imagine the sort of mechanisms which might be at play here if you’ve read this sort of literature. Here’s one relevant quote from the coverage of that book, which also deals with the question Alexander discusses above, and in a lot more detail throughout his book, namely ‘where our morality comes from?’

“we make two fundamental assertions regarding the evolution of morality: (1) there are specific types of behavior demonstrated by both human and nonhuman primates that hint at a shared evolutionary background to morality; and (2) there are theoretical and actual connections between morality and conflict resolution in both nonhuman primates and human development. […] the transition from nonmoral or premoral to moral is more gradual than commonly assumed. No magic point appears in either evolutionary history or human development at which morality suddenly comes into existence. In both early childhood and in animals closely related to us, we can recognize behaviors (and, in the case of children, judgments) that are essential building blocks of the morality of the human adult. […] the decision making and emotions underlying moral judgments are generated within the individual rather than being simply imposed by society. They are a product of evolution, an integrated part of the human genetic makeup, that makes the child construct a moral perspective through interactions with other members of its species. […] Much research has shown that children acquire morality through a social-cognitive process; children make connections between acts and consequences. Through a gradual process, children develop concepts of justice, fairness, and equality, and they apply these concepts to concrete everyday situations […] we assert that emotions such as empathy and sympathy provide an experiential basis by which children construct moral judgments. Emotional reactions from others, such as distress or crying, provide experiential information that children use to judge whether an act is right or wrong […] when a child hits another child, a crying response provides emotional information about the nature of the act, and this information enables the child, in part, to determine whether and why the transgression is wrong. Therefore, recognizing signs of distress in another person may be a basic requirement of the moral judgment process. The fact that responses to distress in another have been documented both in infancy and in the nonhuman primate literature provides initial support for the idea that these types of moral-like experiences are common to children and nonhuman primates.”

Alexander’s coverage is quite different from that found in Aureli et al.,, but some of the contributors to the latter work deal with similar questions to the ones in which he’s interested, using approaches not employed in Alexander’s book – so this is another place to look if you’re interested in these topics. Margalit’s The Emergence of Norms is also worth mentioning. Part of the reason why I mention these books here is incidentally that they’re not talked about in Alexander’s coverage (for very natural reasons, I should add, in the case of the former book at least; Natural Conflict Resolution was published more than a decade after Alexander wrote his book…).

“In the hierarchy of explanatory principles governing the traits of living organisms, evolutionary reductionism – the development of principles from the evolutionary process – tends to subsume all other kinds. Proximate-cause reductionism (or reduction by dissection) sometimes advances our understanding of the whole phenomena. […] When evolutionary reduction becomes trivial in the study of life it is for a reason different from incompleteness; rather, it is because the breadth of the generalization distances it too significantly from the particular problem that may be at hand. […] the greatest weakness of reduction by generalization is not that it is likely to be trivial but that errors are probable through unjustified leaps from hypothesis to conclusion […] Critics such as Gould and Lewontin […] do not discuss the facts that (a) all students of human behavior (not just those who take evolution into account) run the risk of leaping unwarrantedly from hypothesis to conclusion and (b) just-so stories were no less prevalent and hypothesis-testing no more prevalent in studies of human behavior before evolutionary biologists began to participate. […] I believe that failure by biologists and others to distinguish proximate- or partial-cause and evolutionary- or ultimate-cause reductionism […] is in some part responsible for the current chasm between the social and the biological sciences and the resistance to so-called biological approaches to understanding humans. […] Both approaches are essential to progress in biology and the social sciences, and it would be helpful if their relationship, and that of their respective practitioners, were not seen as adversarial.”

(Relatedly, love is motivationally prior to sugar. This one also seems relevant, though in a different way).

“Humans are not accustomed to dealing with their own strategies of life as if they had been tuned by natural selection. […] People are not generally aware of what their lifetimes have been evolved to accomplish, and, even if they are roughly aware of this, they do not easily accept that their everyday activities are in any sense means to that end. […] The theory of lifetimes most widely accepted among biologists is that individuals have evolved to maximize the likelihood of survival of not themselves, but their genes, and that they do this by reproducing and tending in various ways offspring and other carriers of their own genes […] In this theory, survival of the individual – and its growth, development, and learning – are proximate mechanisms of reproductive success, which is a proximate mechanism of genic survival. Only the genes have evolved to survive. […] To say that we are evolved to serve the interests of our genes in no way suggests that we are obliged to serve them. […] Evolution is surely most deterministic for those still unaware of it. If this argument is correct, it may be the first to carry us from is to ought, i.e., if we desire to be the conscious masters of our own fates, and if conscious effort in that direction is the most likely vehicle of survival and happiness, then we ought to study evolution.”

“People are sometimes comfortable with the notion that certain activities can be labeled as “purely cultural” because they also believe that there are behaviors that can be labeled “purely genetic.” Neither is true: the environment contributes to the expression of all behaviors, and culture is best described as part of the environment.”

“Happiness and its anticipation are […] proximate mechanisms that lead us to perform and repeat acts that in the environments of history, at least, would have led to greater reproductive success.”

“The remarkable difference between the patterns of senescence in semelparous (one-time breeding) and iteroparous (repeat-breeding) organisms is probably one of the best simple demonstrations of the central significance of reproduction in the individual’s lifetime. How, otherwise, could we explain the fact that those who reproduce but once, like salmon and soybeans, tend to die suddenly right afterward, while those like ourselves who have residual reproductive possibilities after the initial reproductive act decline or senesce gradually? […] once an organism has completed all possibilities of reproducing (through both offspring production and assistance, and helping other relatives), then selection can no longer affect its survival: any physiological or other breakdown that destroys it may persist and even spread if it is genetically linked to a trait that is expressed earlier and is reproductively beneficial. […] selection continually works against senescence, but is just never able to defeat it entirely. […] senescence leads to a generalized deterioration rather than one owing to a single effect or a few effects […] In the course of working against senescence, selection will tend to remove, one by one, the most frequent sources of mortality as a result of senescence. Whenever a single cause of mortality, such as a particular malfunction of any vital organ, becomes the predominant cause of mortality, then selection will more effectively reduce the significance of that particular defect (meaning those who lack it will outreproduce) until some other achieves greater relative significance. […] the result will be that all organs and systems will tend to deteriorate together. […] The point is that as we age, and as senescence proceeds, large numbers of potential sources of mortality tend to lurk ever more malevolently just “below the surface,” so that, unfortunately, the odds are very high against any dramatic lengthening of the maximum human lifetime through technology. […] natural selection maximizes the likelihood of genetic survival, which is incompatible with eliminating senescence. […] Senescence, and the finiteness of lifetimes, have evolved as incidental effects […] Organisms compete for genetic survival and the winners (in evolutionary terms) are those who sacrifice their phenotypes (selves) earlier when this results in greater reproduction.”

“altruism appears to diminish with decreasing degree of relatedness in sexual species whenever it is studied – in humans as well as nonhuman species”

October 5, 2016

## A Cooperative Species

First, people cooperate not only for self-interested reasons but also because they are genuinely concerned about the well-being of others, try to uphold social norms, and value behaving ethically for its own sake. People punish those who exploit the cooperative behavior of others for the same reasons. Contributing to the success of a joint project for the benefit of one’s group, even at a personal cost, evokes feelings of satisfaction, pride, even elation. Failing to do so is often a source of shame or guilt.
Second, we came to have these “moral sentiments” because our ancestors lived in environments, both natural and socially constructed, in which groups of individuals who were predisposed to cooperate and uphold ethical norms tended to survive and expand relative to other groups, thereby allowing these prosocial motivations to proliferate. The first proposition concerns proximate motivations for prosocial behavior, the second addresses the distant evolutionary origins and ongoing perpetuation of these cooperative dispositions.”

Here’s my goodreads review of the book – I gave the book five stars on goodreads. In the post I have included some illustrative quotes below, but really you should read all of it if you find this sort of stuff interesting and you’re not mathematically illiterate (and as the authors note early on, they have given the way they present their ideas some thought: “We have presented technical material in verbal as well as mathematical form wherever possible, and avoided mathematical formulations entirely where that was possible without sacrificing clarity.” Even so, the book is somewhat dense and it takes some work to get through).

“In short, humans became the cooperative species that we are because cooperation was highly beneficial to the members of groups that practiced it, and we were able to construct social institutions that minimized the disadvantages of those with social preferences in competition with fellow group members, while heightening the group-level advantages associated with the high levels of cooperation that these social preferences allowed. These institutions proliferated because the groups that adopted them secured high levels of within-group cooperation, which in turn favored the groups’ survival as a biological and cultural entity in the face of environmental, military and other challenges.”

The regulation of social interactions by group-level institutions plays no less a role than altruistic individual motives in understanding how this cooperative species came to be. Institutions affect the rewards and penalties associated with particular behaviors, often favoring the adoption of cooperative actions over others, so that even the self-regarding are often induced to act in the interest of the group. […] the individual motives and group-level institutions that account for cooperation among humans include not only the most elevated, including a concern for others, fair-mindedness, and democratic accountability of leaders, but also the most wicked, such as vengeance, racism, religious bigotry, and hostility toward outsiders.

“Optimizing models are commonly used to describe behavior not because they mimic the cognitive processes of the actors, which they rarely do, but because they capture important influences on individual behavior in a succinct and analytically tractable way.”

“Culture is an evolutionary force in its own right, not simply an effect of the interaction of genes and natural environments. […] human preferences and beliefs are the product of a dynamic whereby genes affect cultural evolution and culture affects genetic evolution, the two being tightly intertwined in the evolution of our species. [I have of course talked about gene-culture coevolution before here on the blog and I don’t like to repeat myself, but this idea/notion really is unknown to many people who should know better, and so is perhaps worth repeating here even so – US] […] The idea of treating culture as a form of epigenetic transmission was pioneered by Cavalli-Sforza and Feldman (1973), Karl Popper (1979), and Richard Dawkins, who coined the term “meme” […] to represent an integral unit of information that could be transmitted phenotypically. There quickly followed several major contributions to a biological approach to culture, all based on the notion that culture, like genes, could evolve through replication (intergenerational transmission), mutation, and selection […] Richard Dawkins added a second fundamental mechanism of epigenetic information transmission in The Extended Phenotype (1982), noting that organisms can directly transmit environmental artifacts to the next generation […] Creating a fitness-relevant aspect of an environment and stably transmitting this environment across generations, known as niche construction, is a widespread form of epigenetic transmission […] niche construction gives rise to what might be called a gene-environment coevolutionary process, since a genetically induced environmental regularity becomes the basis for genetic selection, and genetic mutations that give rise to mutant niches will tend to survive if they are fitness enhancing for their constructors. […] Human cultures, along with the institutional structures they support, are instances of niche construction”.

“while genetic transmission of information plays a central role in our account, the genetics of non-pathological social behavior is for the most part unknown. […] No “gene for cooperation” has been discovered. Nor is it likely that one will ever be found, for the idea of a one-to-one mapping between genes and behavior is unlikely given what is now known about gene expression, and is implausible in light of the complexity and cultural variation of cooperative behaviors. […] an explanation of the evolution of human cooperation must hinge on the empirical evidence. The question is not “Which model works?” They all work, if mathematical coherence is the bar. The question we are asking is about something that actually happened in the human past. Thus we measure the empirical plausibility of alternative explanations against the conditions under which early humans lived during the Pleistocene, roughly 1.6 million years before the present, until the advent of agriculture beginning about 12,000 years ago, and especially the last 100 or so millennia of this period.”

“in small-scale societies punishment can be highly effective even when it takes the form of ridicule or gossip and it inflicts no material costs on its targets. […] People are sensitive to others’ evaluation of their moral worth or intentions and will cooperate in social dilemmas when the punishment for free-riding takes the form of criticism by peers rather than a reduction in material payoffs. […] People punish not only those who have hurt them, but also those who hurt others. […] even self-regarding individuals may engage in third-party punishment if they believe that this will induce other-regarding individuals to behave favorably toward them. […] recent experimental results are consistent with the view that the social preferences that become salient in a population depend critically on the manner in which a people’s institutions and livelihood frame social interactions and shape the process of social learning. An expected result, confirmed by a growing body of international comparative evidence, is substantial cross-cultural differences in the nature and extent of social preferences.”

In experimental and natural settings, people often behave differently toward others, depending on the organizational, linguistic, ethnic, and religious groups to which they belong. People choose to associate with others who are similar to themselves in some salient respect […] Among the salient characteristics on which this choice operates are racial and ethnic identification, and religion […] Conversely, people often seek to avoid interactions with those who are different from themselves. […] Those who condition their behavior on the group membership of the other may do this because group membership is thought to provide information about the other’s likely behavior. Or group membership may matter because people would like to help or to interact with members of some groups more than others. In the first case the actor’s beliefs are involved. In the second case, group-sensitive preferences are at work. […] a series of experiments by Toshio Yamagishi and his associates […] show that experimental subjects’ allocations favor in-group members not because of altruistic sentiments toward those who are similar to themselves, but because they expected reciprocation from in-groupers and not from out-groupers. […] taking account of ethnic, racial and other characteristics of those with whom one interacts appears to be a quite common human trait. We seem quite attuned to noticing and treating as salient the ascriptive markers of group difference. For example, Americans of European and African origin are better at recognizing faces of their own ancestral group, and faces of their own group induce greater activation in the part of the brain associated with face recognition.” (my bold)

“The most parsimonious and compelling proximate explanation of behavior in the ultimatum game, public goods game, and other social dilemma experiments is that people think that cooperating is the right thing to do and enjoy doing it, and that they dislike unfair treatment and enjoy punishing those who violate norms of fairness. […] Recent studies of brain functioning provide some support for this hedonic view of cooperative behavior.

Differential group success […] plays a central role in the evolution of human behaviors and institutions, members of less successful groups copying the more successful or being eliminated by them. […] the speed of an evolutionary process is proportional to the differences on which it works […] reduction in within-group differences slows down the selection against altruistic individuals. Insider biases and individual preferences to interact with like individuals lead to large between-group differences in behavior and, to a lesser but not negligible extent, in genotypes too […] insider biases result in frequent between-group conflicts as well as high levels of positive assortment in interactions both within and between groups. […] All of these aspects of human social life enhance the force of between-group selection relative to within-group selection.” (my bold)

“The fact that helping behaviors are […] motivated by [a] wide range of proximate motives, from maternal love, to enlightened self-interest, to solidarity with one’s coethnics or conationals, is consistent with our view that in all likelihood each of the mechanisms […] has played a significant role in human evolution, the importance of each depending on the forms of cooperation under consideration and the ecological and social conditions under which ancestral humans interacted. […] what can be known or reasonably conjectured from genetic, archaeological and other data about [the] ancestral human conditions suggests that neither helping close family members nor reciprocal altruism provides an adequate account of the emergence of [our] cooperative species. […] multi-level selection models based on gene culture coevolution [however] contribute substantially to a convincing explanation.

As mentioned, if you find this kind of stuff interesting you should strongly consider reading the book.

September 29, 2016

## The Emergence of Norms

“Put very crudely, the main thesis of this book is that certain types of norms are possible solutions to problems posed by certain types of social interaction situations. […] Three types of paradigmatic situations are dealt with. They are referred to as (1) Prisoner’s Dilemma-type situations; (2) Co-ordination situations; (3) Inequality (or Partiality) situations. Each of them, it is claimed, poses a basic difficulty, to some or all of the individuals involved in them. Three types of norms, respectively, are offered as solutions to these situational problems. It is shown how, and in what sense, the adoption of these norms of social behaviour can indeed resolve the specified problem.”

I should probably before moving on apologize for the infrequent updates – you should expect blogging to be light also in the months to come. With that out of the way, the book to which the title of this post refers and from which the above quote is taken is this Oxford University Press publication. Here’s what I wrote about the book on goodreads:

“The last chapter wasn’t in my opinion nearly as good as the others, presumably in part because I was unfamiliar with a lot of the literature to which she referred, but also because I could not really agree with all the distinctions and arguments made, and I was close to giving the book 3 stars as a result of this [I gave the book 4 stars on goodreads]. I think she overplays the ‘impersonal’ nature of norms in that chapter; if a norm based on sanctions is not enforced then it is irrelevant, and to the extent that it is enforced *someone* needs to impose the sanction on the transgressor. The fact that it’s actually in some contexts considered ‘a problem that needs explaining’ to figure out exactly how to support a model with sanctioning in a context where enforcement is costly to the individual (it’s a problem because of the free-riding issue – it’s always easier to let someone else do the sanctioning…) seems to have eluded Margalit (for details on this topic, see e.g. Boyd and Richerson).

It’s probably helpful to be familiar with basic game theoretic concepts if you’re planning on reading this book (it has a lot of game theory, though most of it is quite simple stuff), as well as perhaps having some familiarity with basic economics (rationality assumptions, utility functions, etc.) but I’m not sure it’s strictly necessary – I think the author does cover most of the basic things you need to know to be able to follow the arguments. The first three chapters are quite good.”

I should point out here that when I was writing the review above I had been completely unaware of how long ago the book was written; the book is pretty self-contained and I hadn’t really noticed when I picked up the book that it’s actually a rather old book. If I had been aware of this I would not have been nearly as vocal in my criticism of the content of the last chapter in my review as was the case, given that some of the insights I blame the author for being unaware of were only discussed in the literature after the publication of this book; the unaddressed problems do remain unaddressed and they are problematic, but it’s probably unfair to blame the author for not thinking about stuff which probably nobody really had given any thought at the time of publication.

Some quotes and a few more comments:

“[One] angle from which it may be illuminating to view the account of norms offered here is that of evolutionary explanations. […] I propose to regard the argument underlying this book as, in a borrowed and somewhat metaphorical sense, a natural selection theory of the development of norms.”

“Norms do not as a rule come into existence at a definite point in time, nor are they the result of a manageable number of identifiable acts. The are, rather, the resultant of complex patterns of behaviour of a large number of people over a protracted period of time.”

“it is proposed that the main elements in the characterization of norms of obligation be: a significant social pressure for conformity to them and against deviation – actual or potential – from them; the belief by the people concerned in their indispensability for the proper functioning of society; and the expected clashes between their dictates on the one hand and personal interests and desires on the other.”

It should be noted here that far from all norms qualify as norms of obligation; this is but one norm subgroup, though it’s an important one. The author notes explicitly that norms encountered in the context of coordination problems are not norms of obligation.

“A situation of the generalized PD variety poses a problem to the participants involved. The problem is that of protecting an unstable yet jointly beneficial state of affairs from deteriorating, so to speak, into a stable yet jointly destructive one. My contention concerning such a situation is that a norm, backed by appropriate sanctions, could solve this problem. In this sense it can be said that such situations ‘call for’ norms. It can further be said that a norm solving the problem inherent in a situation of this type is generated by it. Such norms I shall call PD norms. […] the smaller and the more determinate the class of participants in a generalized PD-structured situation, and the more isolated the occurrence of the dilemma among them, the more likely it is that there might be solutions other than (PD) norms to the pertinent problem […] And conversely, the larger and the more indeterminate the class of participants, and the more frequent the occurrence of the dilemma among them, the more likely it is that a solution, if any, would be in the form of a PD norm. […] the more difficult (or costly) it is to ensure […] personal contact, […] the more acute the need for some impersonal device, such as social norms, which would induce the desired co-operation.”

You can easily add more details to the conceptual framework underlying the analysis in order to refine it in various ways, and the author does talk a little bit about how you might go about doing that; for example it might not be realistic that nobody ever deviates, and so you might decide to replace an unrealistic stability condition that nobody deviates with another one which might be that at most some percentage, say X, of the population deviates. Such refined theoretical models can incidentally yield very interesting and non-trivial theoretical results – Boyd and Richerson cover such models in The Origin and Evolution of Cultures. It should perhaps be noted that even relatively simple models dealing with these sorts of topics may easily end up nevertheless being sufficiently complicated for analytical solutions to not be forthcoming.

“there are norms whose function is to maintain social control on certain groups of people through preventing them from solving the problem inherent in the PD-structured situation in which they are placed. That is, these norms are designed to help keep these people in a state of affairs which, while disadvantageous to them […] is considered beneficial to society as a whole. A conspicuous example of norms of this type are anti-trust laws.”

In the context of coordination problems, the author distinguishes between two solution mechanisms/norms; conventions and decrees. Broadly speaking conventions can be thought of as established solutions to coordination problems encountered in the past, whereas decrees are solutions to novel problems where no equilibrium has yet been established – see also the more detailed quotes below. In the context of sanctions an important difference between coordination norms and PD norms is that sanctions can be said to play a primary role in the context of PD norms but only a secondary role in the context of coordination norms; nobody has a unilateral incentive to deviate in the context of coordination-type situations/problems and so defection so to speak carries its own punishment independent of the potential level of an associated sanction. If everybody else drive in the right side of the road, you don’t gain anything from driving in the left side of the road – and it’s unlikely to be the size of the fine which is the primary reason why you don’t drive in the left side of the road in such a context.

“It is worth noting that within the large class of problems of strategy (i.e. problems of interdependent decision), the problems of co-ordination stand in opposition to problems of conflict, the contrast being particularly acute between the extreme cases of pure co-ordination on the one hand and of pure conflict (the so-called zero-sum problems) on the other. Whereas in the pure co-ordination case the parties’ interests converge completely, and the agents win or lose together, in the pure conflict case the parties’ interests diverge completely, and one person’s gain is the other’s loss. […] [Shelling argues] that games of strategy range over a continuum with games of pure conflict […] and games of pure co-ordination as opposite limits. All other games […] involve mixtures in varying proportions of conflict and co-ordination, of competition and partnership, and are referred to as mixed-motive games.”

One thing to add here, which is of course not mentioned in the book, is that whereas the situation does play a sometimes major role in terms of which setting you find yourself in, there’s also a relevant mental/psychological aspect to consider here; in the context of bargaining, it’s a very well-established result that bargainers who conceive of the bargaining situation as a zero-sum (‘conflict’) game do worse than bargainers who do not.

“Very generally, where communities which have their own ways of going about things – their own arrangements, regularities, conventions – come into contact, and where the situation demands that barriers between them be dropped, or that one – any one – of them absorb the other, various co-ordination problems are likely to crop up and to call for […] decree-type co-ordination norms to solve them.”

“Conventions are, typically:

(1) Non-statutory norms, which need not be enacted, formulated, or promulgated.
(2) They are neither issued nor promulgated by any identifiable authority, and are hence what is usually called impersonal, or anonymous norms.
(3) They involve in the main non-institutionalized, non-organized, and informal sanctions (i.e. punishments or rewards).

Decrees, in contrast, are, typically:
(1) Statutory;
(2) Issued and promulgated by some appropriately endowed authority (not necessarily at the level of the state);
(3) The sanctions they involve might be organized, institutionalized, and formal, even physical.”

Conventions and decrees are quite different, but in terms of what they do they solve similar problems:

“Since a co-ordination problem is a situation such that any of its co-ordination equilibria is preferred, by all involved, to any combination of actions which is not a co-ordination equlibrium, each of those involved is interested in there being something which will point – in a way conspicuous to all and perceived to be conspicuous to all – to one particular co-ordination equilibrum as the solution. This precisely is what our co-ordination norms, whether conventions or decrees, do.”

“Thibaut and Kelley note that norms ‘will develop more rapidly and more surely in highly cohesive groups than in less cohesive groups’ – assuming that the majority of the members have about the same degree of dependence on the group […] To the extent that norms reduce interference, cut communication costs, heighten value similarity and insure the interaction sequence necessary for task performance, norms improve the reward-cost positions attained by the members of a dyad and thus increase the cohesiveness of the dyad”

“[I]n so far as conformity to a co-ordination norm ensures the achievement of some co-ordination equilibrium, which for everyone involved in the corresponding co-ordination problem belongs of necessity to the group of preferred outcomes, it is rational for everyone to conform to it. Are we to conclude from this, however, that the social choice to which the co-ordination norm is instrumental is itself rational? My answer to this question is that although it is rational to conform to a prevailing co-ordination norm, the social choice resulting from it is not necessarily rational. […] it may not be optimal, for some or for all involved. It can in principle be changed into a better one, only this involves an explicit process which is not always feasible. […] The changing of an existing convention in favour of a ‘better’, more rational one, has to be explicit. It can be achieved through an explicit agreement of all concerned, or through a regulation (decree) issued and properly promulgated by some appropriately endowed authority. Where communication, or promulgation, is impossible, it is difficult to see how an existing convention (which is a co-ordination norm) might be changed. It is of some interest to note that whereas an ‘act of convening’ is not necessary for a convention to form, it might be necessary for an existing convention to be exchanged for an alternative one.”

“The difference in the role played by the two types of norms might now be formulated thus: a co-ordination norm helps those involved ‘meet’ each other; a PD norm helps those involved protect themselves from damaging, even ruining, each other.”

“[T]here are states of inequality which appear on the surface to be stable but which are, in a somewhat subtle and complicated way, strategically unstable. They may be in equilibrium, but it is a rather flimsy one; far from being self-perpetuating, they are susceptible to threats. Now the assumption that the party discriminated in favour of is interested in the preservation of such a status quo leads reasonably to the assumption that he will seek to fortify it against its potential undermining. […] it is the central thesis of this chapter that [a] significant device to render the status quo stable [is] to fortify it by norms. The idea is that once it is in some sense normatively required that the status quo endure, the nature of the possible calculations and considerations of deviance fundamentally changes: it is no longer evaluated only in terms of being ‘costly’ or ‘risky’, but as being ‘wrong‘ or ‘subversive‘. […] the methods of norms and force as possible fortifiers of the status quo in question are functionally equivalent […] provided the norms are effective, they both amount to making deviance from the status quo more costly through the impositions of sanctions.”

“Once norms are internalized, one abides by them not out of fear of the pending sanctions associated with them, but out of some inner conviction. And when this is so, one is likely to conform to the norms even in one’s thoughts, intentions, and in what one does in private.”

“The function of norms, generally speaking, is to put restraints on possible courses of conduct, to restrict the number of alternatives open for action. When a certain course of conduct is normatively denounced (is considered ‘wrong’), it becomes a less eligible course of conduct than it might otherwise have been: although through lying, for example, one might quite conveniently get away with some misdeed, its being recognized and acknowledged as normatively (morally) prohibited normally makes it a less attractive way out, or even precludes its having been considered an alternative in the first place. In this sense, then, norms might be said to be coercive, to the extent that they function as constraints on actions; that is, to the extent that they prevent one for doing an ation one might have done had there been no norm denouncing it, or at least to the extent that they render a certain course of action less eligible than it might otherwise have been.”

“[N]orms are rather easily accepted as part of the ‘natural order of things’. To be sure, one might be quite resentful of this natural order, or of one’s lot therein, and regard it as discriminating against one. But usually there is very little one is going to do about it unless – and until – the object of one’s resentment is personified: only few will start a revolution against an elusive oppressive ‘system’; many more might revolt against an identifiable oppressive ruler. […] These norms have to apply to the privileged as well as to the deprived, or else they lose much of their effectiveness as a disguise for the real exercise of power underlying them. […] The absence of any precedents in which someone privileged was spared the sanction, the absence of any loopholes which might facilitate a discriminatory application of the norms, contribute to their deterrence value”.

February 13, 2016

## A few lectures

The sound quality of this lecture is not completely optimal – there’s a recurring echo popping up now and then which I found slightly annoying – but this should not keep you from watching the lecture. It’s a quite good lecture, and very accessible – I don’t really think you even need to know anything about genetics to follow most of what he’s talking about here; as far as I can tell it’s a lecture intended for people who don’t really know much about population genetics. He introduces key concepts as they are needed and he does not go much into the technical details which might cause people trouble (this of course also makes the lecture somewhat superficial, but you can’t get everything). If you’re the sort of person who wants details not included in the lecture you’re probably already reading e.g. Razib Khan (who incidentally recently blogged/criticized a not too dissimilar paper from the one discussed in the lecture, dealing with South Asia)…

I must admit that I actually didn’t like this lecture very much, but I figured I might as well include it in this post anyway.

I found some questions included and some aspects of the coverage a bit ‘too basic’ for my taste, but other people interested in chess reading along here may like Anna’s approach better; like Krause’s lecture I think it’s an accessible lecture, despite the fact that it actually covers many lines in quite a bit of detail. It’s a long lecture but I don’t think you necessarily need to watch all of it in one go (…or at all?) – the analysis of the second game, the Kortschnoj-Gheorghiu game, starts around 45 minutes in so that might for example be a good place to include a break, if a break is required.

February 1, 2016

## The Origin of Species

I figured I ought to blog this book at some point, and today I decided to take out the time to do it. This is the second book by Darwin I’ve read – for blog content dealing with Darwin’s book The Voyage of the Beagle, see these posts. The two books are somewhat different; Beagle is sort of a travel book written by a scientist who decided to write down his observations during his travels, whereas Origin is a sort of popular-science research treatise – for more details on Beagle, see the posts linked above. If you plan on reading both the way I did I think you should aim to read them in the order they are written.

Darwin was not right about everything and there’s a lot of stuff that modern biologists know which he had no idea about, so naturally some mistaken ideas made their way into Origin as well; for example the idea of the inheritance of acquired characteristics (Lamarckian inheritance) occasionally pops up and is implicitly defended in the book as a credible complement to natural selection, as also noted in Oliver Francis’ afterword to the book. On a general note it seems that Darwin did a better job convincing people about the importance of the concept of evolution than he did convincing people that the relevant mechanism behind evolution was natural selection; at least that’s what’s argued in wiki’s featured article on the history of evolutionary thought (to which I have linked before here on the blog).

Darwin emphasizes more than once in the book that evolution is a very slow process which takes a lot of time (for example: “I do believe that natural selection will always act very slowly, often only at long intervals of time, and generally on only a very few of the inhabitants of the same region at the same time”, p.123), and arguably this is also something about which he is part right/part wrong because the speed with which natural selection ‘makes itself felt’ depends upon a variety of factors, and it can be really quite fast in some contexts (see e.g. this and some of the topics covered in books like this one); though you can appreciate why he held the views he did on that topic.

A big problem confronted by Darwin was that he didn’t know how genes work, so in a sense the whole topic of the ‘mechanics of the whole thing’ – the ‘nuts and bolts’ – was more or less a black box to him (I have included a few quotes which indirectly relate to this problem in my coverage of the book below; as can be inferred from those quotes Darwin wasn’t completely clueless, but he might have benefited greatly from a chat with Gregor Mendel…) – in a way a really interesting thing about the book is how plausible the theory of natural selection is made out to be despite this blatantly obvious (at least to the modern reader) problem. Darwin was incidentally well aware there was a problem; just 6 pages into the first chapter of the book he observes frankly that: “The laws governing inheritance are quite unknown”. Some of the quotes below, e.g. on reciprocal crosses, illustrate that he was sort of scratching the surface, but in the book he never does more than that.

Below I have added some quotes from the book.

“Certainly no clear line of demarcation has as yet been drawn between species and sub-species […]; or, again, between sub-species and well-marked varieties, or between lesser varieties and individual differences. These differences blend into each other in an insensible series; and a series impresses the mind with the idea of an actual passage. […] I look at individual differences, though of small interest to the systematist, as of high importance […], as being the first step towards such slight varieties as are barely thought worth recording in works on natural history. And I look at varieties which are in any degree more distinct and permanent, as steps leading to more strongly marked and more permanent varieties; and at these latter, as leading to sub-species, and to species. […] I attribute the passage of a variety, from a state in which it differs very slightly from its parent to one in which it differs more, to the action of natural selection in accumulating […] differences of structure in certain definite directions. Hence I believe a well-marked variety may be justly called an incipient species […] I look at the term species as one arbitrarily given, for the sake of convenience, to a set of individuals closely resembling each other, and that it does not essentially differ from the term variety, which is given to less distinct and more fluctuating forms. The term variety, again, in comparison with mere individual differences, is also applied arbitrarily, and for mere convenience’ sake. […] the species of large genera present a strong analogy with varieties. And we can clearly understand these analogies, if species have once existed as varieties, and have thus originated: whereas, these analogies are utterly inexplicable if each species has been independently created.”

“Owing to [the] struggle for life, any variation, however slight and from whatever cause proceeding, if it be in any degree profitable to an individual of any species, in its infinitely complex relations to other organic beings and to external nature, will tend to the preservation of that individual, and will generally be inherited by its offspring. The offspring, also, will thus have a better chance of surviving, for, of the many individuals of any species which are periodically born, but a small number can survive. I have called this principle, by which each slight variation, if useful, is preserved, by the term of Natural Selection, in order to mark its relation to man’s power of selection. We have seen that man by selection can certainly produce great results, and can adapt organic beings to his own uses, through the accumulation of slight but useful variations, given to him by the hand of Nature. But Natural Selection, as we shall hereafter see, is a power incessantly ready for action, and is as immeasurably superior to man’s feeble efforts, as the works of Nature are to those of Art. […] In looking at Nature, it is most necessary to keep the foregoing considerations always in mind – never to forget that every single organic being around us may be said to be striving to the utmost to increase in numbers; that each lives by a struggle at some period of its life; that heavy destruction inevitably falls either on the young or old, during each generation or at recurrent intervals. Lighten any check, mitigate the destruction ever so little, and the number of the species will almost instantaneously increase to any amount. The face of Nature may be compared to a yielding surface, with ten thousand sharp wedges packed close together and driven inwards by incessant blows, sometimes one wedge being struck, and then another with greater force. […] A corollary of the highest importance may be deduced from the foregoing remarks, namely, that the structure of every organic being is related, in the most essential yet often hidden manner, to that of all other organic beings, with which it comes into competition for food or residence, or from which it has to escape, or on which it preys.”

“Under nature, the slightest difference of structure or constitution may well turn the nicely-balanced scale in the struggle for life, and so be preserved. How fleeting are the wishes and efforts of man! how short his time! And consequently how poor will his products be, compared with those accumulated by nature during whole geological periods. […] It may be said that natural selection is daily and hourly scrutinising, throughout the world, every variation, even the slightest; rejecting that which is bad, preserving and adding up all that is good; silently and insensibly working, whenever and wherever opportunity offers, at the improvement of each organic being in relation to its organic and inorganic conditions of life. We see nothing of these slow changes in progress, until the hand of time has marked the long lapses of ages, and then so imperfect is our view into long past geological ages, that we only see that the forms of life are now different from what they formerly were.”

“I have collected so large a body of facts, showing, in accordance with the almost universal belief of breeders, that with animals and plants a cross between different varieties, or between individuals of the same variety but of another strain, gives vigour and fertility to the offspring; and on the other hand, that close interbreeding diminishes vigour and fertility; that these facts alone incline me to believe that it is a general law of nature (utterly ignorant though we be of the meaning of the law) that no organic being self-fertilises itself for an eternity of generations; but that a cross with another individual is occasionally perhaps at very long intervals — indispensable. […] in many organic beings, a cross between two individuals is an obvious necessity for each birth; in many others it occurs perhaps only at long intervals; but in none, as I suspect, can self-fertilisation go on for perpetuity.”

“as new species in the course of time are formed through natural selection, others will become rarer and rarer, and finally extinct. The forms which stand in closest competition with those undergoing modification and improvement, will naturally suffer most. […] Whatever the cause may be of each slight difference in the offspring from their parents – and a cause for each must exist – it is the steady accumulation, through natural selection, of such differences, when beneficial to the individual, which gives rise to all the more important modifications of structure, by which the innumerable beings on the face of this earth are enabled to struggle with each other, and the best adapted to survive.”

“Natural selection, as has just been remarked, leads to divergence of character and to much extinction of the less improved and intermediate forms of life. On these principles, I believe, the nature of the affinities of all organic beings may be explained. It is a truly wonderful fact – the wonder of which we are apt to overlook from familiarity – that all animals and all plants throughout all time and space should be related to each other in group subordinate to group, in the manner which we everywhere behold – namely, varieties of the same species most closely related together, species of the same genus less closely and unequally related together, forming sections and sub-genera, species of distinct genera much less closely related, and genera related in different degrees, forming sub-families, families, orders, sub-classes, and classes. The several subordinate groups in any class cannot be ranked in a single file, but seem rather to be clustered round points, and these round other points, and so on in almost endless cycles. On the view that each species has been independently created, I can see no explanation of this great fact in the classification of all organic beings; but, to the best of my judgment, it is explained through inheritance and the complex action of natural selection, entailing extinction and divergence of character […] The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.”

“No one has been able to point out what kind, or what amount, of difference in any recognisable character is sufficient to prevent two species crossing. It can be shown that plants most widely different in habit and general appearance, and having strongly marked differences in every part of the flower, even in the pollen, in the fruit, and in the cotyledons, can be crossed. […] By a reciprocal cross between two species, I mean the case, for instance, of a stallion-horse being first crossed with a female-ass, and then a male-ass with a mare: these two species may then be said to have been reciprocally crossed. There is often the widest possible difference in the facility of making reciprocal crosses. Such cases are highly important, for they prove that the capacity in any two species to cross is often completely independent of their systematic affinity, or of any recognisable difference in their whole organisation. On the other hand, these cases clearly show that the capacity for crossing is connected with constitutional differences imperceptible by us, and confined to the reproductive system. […] fertility in the hybrid is independent of its external resemblance to either pure parent. […] The foregoing rules and facts […] appear to me clearly to indicate that the sterility both of first crosses and of hybrids is simply incidental or dependent on unknown differences, chiefly in the reproductive systems, of the species which are crossed. […] Laying aside the question of fertility and sterility, in all other respects there seems to be a general and close similarity in the offspring of crossed species, and of crossed varieties. If we look at species as having been specially created, and at varieties as having been produced by secondary laws, this similarity would be an astonishing fact. But it harmonizes perfectly with the view that there is no essential distinction between species and varieties. […] the facts briefly given in this chapter do not seem to me opposed to, but even rather to support the view, that there is no fundamental distinction between species and varieties.”

“Believing, from reasons before alluded to, that our continents have long remained in nearly the same relative position, though subjected to large, but partial oscillations of level, I am strongly inclined to…” (…’probably get some things wrong…’, US)

“In considering the distribution of organic beings over the face of the globe, the first great fact which strikes us is, that neither the similarity nor the dissimilarity of the inhabitants of various regions can be accounted for by their climatal and other physical conditions. Of late, almost every author who has studied the subject has come to this conclusion. […] A second great fact which strikes us in our general review is, that barriers of any kind, or obstacles to free migration, are related in a close and important manner to the differences between the productions of various regions. […] A third great fact, partly included in the foregoing statements, is the affinity of the productions of the same continent or sea, though the species themselves are distinct at different points and stations. It is a law of the widest generality, and every continent offers innumerable instances. Nevertheless the naturalist in travelling, for instance, from north to south never fails to be struck by the manner in which successive groups of beings, specifically distinct, yet clearly related, replace each other. […] We see in these facts some deep organic bond, prevailing throughout space and time, over the same areas of land and water, and independent of their physical conditions. The naturalist must feel little curiosity, who is not led to inquire what this bond is.  This bond, on my theory, is simply inheritance […] The dissimilarity of the inhabitants of different regions may be attributed to modification through natural selection, and in a quite subordinate degree to the direct influence of different physical conditions. The degree of dissimilarity will depend on the migration of the more dominant forms of life from one region into another having been effected with more or less ease, at periods more or less remote; on the nature and number of the former immigrants; and on their action and reaction, in their mutual struggles for life; the relation of organism to organism being, as I have already often remarked, the most important of all relations. Thus the high importance of barriers comes into play by checking migration; as does time for the slow process of modification through natural selection. […] On this principle of inheritance with modification, we can understand how it is that sections of genera, whole genera, and even families are confined to the same areas, as is so commonly and notoriously the case.”

“the natural system is founded on descent with modification […] and […] all true classification is genealogical; […] community of descent is the hidden bond which naturalists have been unconsciously seeking, […] not some unknown plan or creation, or the enunciation of general propositions, and the mere putting together and separating objects more or less alike.”

September 27, 2015

## Photosynthesis in the Marine Environment (III)

This will be my last post about the book. After having spent a few hours on the post I started to realize the post would become very long if I were to cover all the remaining chapters, and so in the end I decided not to discuss material from chapter 12 (‘How some marine plants modify the environment for other organisms’) here, even though I actually thought some of that stuff was quite interesting. I may decide to talk briefly about some of the stuff in that chapter in another blogpost later on (but most likely I won’t). For a few general remarks about the book, see my second post about it.

Some stuff from the last half of the book below:

“The light reactions of marine plants are similar to those of terrestrial plants […], except that pigments other than chlorophylls a and b and carotenoids may be involved in the capturing of light […] and that special arrangements between the two photosystems may be different […]. Similarly, the CO2-fixation and -reduction reactions are also basically the same in terrestrial and marine plants. Perhaps one should put this the other way around: Terrestrial-plant photosynthesis is similar to marine-plant photosynthesis, which is not surprising since plants have evolved in the oceans for 3.4 billion years and their descendants on land for only 350–400 million years. […] In underwater marine environments, the accessibility to CO2 is low mainly because of the low diffusivity of solutes in liquid media, and for CO2 this is exacerbated by today’s low […] ambient CO2 concentrations. Therefore, there is a need for a CCM also in marine plants […] CCMs in cyanobacteria are highly active and accumulation factors (the internal vs. external CO2 concentrations ratio) can be of the order of 800–900 […] CCMs in eukaryotic microalgae are not as effective at raising internal CO2 concentrations as are those in cyanobacteria, but […] microalgal CCMs result in CO2 accumulation factors as high as 180 […] CCMs are present in almost all marine plants. These CCMs are based mainly on various forms of HCO3 [bicarbonate] utilisation, and may raise the intrachloroplast (or, in cyanobacteria, intracellular or intra-carboxysome) CO2 to several-fold that of seawater. Thus, Rubisco is in effect often saturated by CO2, and photorespiration is therefore often absent or limited in marine plants.”

“we view the main difference in photosynthesis between marine and terrestrial plants as the latter’s ability to acquire Ci [inorganic carbon] (in most cases HCO3) from the external medium and concentrate it intracellularly in order to optimise their photosynthetic rates or, in some cases, to be able to photosynthesise at all. […] CO2 dissolved in seawater is, under air-equilibrated conditions and given today’s seawater pH, in equilibrium with a >100 times higher concentration of HCO3, and it is therefore not surprising that most marine plants utilise the latter Ci form for their photosynthetic needs. […] any plant that utilises bulk HCO3 from seawater must convert it to CO2 somewhere along its path to Rubisco. This can be done in different ways by different plants and under different conditions”

“The conclusion that macroalgae use HCO3 stems largely from results of experiments in which concentrations of CO2 and HCO3 were altered (chiefly by altering the pH of the seawater) while measuring photosynthetic rates, or where the plants themselves withdrew these Ci forms as they photosynthesised in a closed system as manifested by a pH increase (so-called pH-drift experiments) […] The reason that the pH in the surrounding seawater increases as plants photosynthesise is first that CO2 is in equilibrium with carbonic acid (H2CO3), and so the acidity decreases (i.e. pH rises) as CO2 is used up. At higher pH values (above ∼9), when all the CO2 is used up, then a decrease in HCO3 concentrations will also result in increased pH since the alkalinity is maintained by the formation of OH […] some algae can also give off OH to the seawater medium in exchange for HCO3 uptake, bringing the pH up even further (to >10).”

Carbonic anhydrase (CA) is a ubiquitous enzyme, found in all organisms investigated so far (from bacteria, through plants, to mammals such as ourselves). This may be seen as remarkable, since its only function is to catalyse the inter-conversion between CO2 and HCO3 in the reaction CO2 + H2O ↔ H2CO3; we can exchange the latter Ci form to HCO3 since this is spontaneously formed by H2CO3 and is present at a much higher equilibrium concentration than the latter. Without CA, the equilibrium between CO2 and HCO3 is a slow process […], but in the presence of CA the reaction becomes virtually instantaneous. Since CO2 and HCO3 generate different pH values of a solution, one of the roles of CA is to regulate intracellular pH […] another […] function is to convert HCO3 to CO2 somewhere en route towards the latter’s final fixation by Rubisco.”

“with very few […] exceptions, marine macrophytes are not C 4 plants. Also, while a CAM-like [Crassulacean acid metabolism-like, see my previous post about the book for details] feature of nightly uptake of Ci may complement that of the day in some brown algal kelps, this is an exception […] rather than a rule for macroalgae in general. Thus, virtually no marine macroalgae are C 4 or CAM plants, and instead their CCMs are dependent on HCO3 utilization, which brings about high concentrations of CO2 in the vicinity of Rubisco. In Ulva, this type of CCM causes the intra-cellular CO2 concentration to be some 200 μM, i.e. ∼15 times higher than that in seawater.“

“deposition of calcium carbonate (CaCO3) as either calcite or aragonite in marine organisms […] can occur within the cells, but for macroalgae it usually occurs outside of the cell membranes, i.e. in the cell walls or other intercellular spaces. The calcification (i.e. CaCO3 formation) can sometimes continue in darkness, but is normally greatly stimulated in light and follows the rate of photosynthesis. During photosynthesis, the uptake of CO2 will lower the total amount of dissolved inorganic carbon (Ci) and, thus, increase the pH in the seawater surrounding the cells, thereby increasing the saturation state of CaCO3. This, in turn, favours calcification […]. Conversely, it has been suggested that calcification might enhance the photosynthetic rate by increasing the rate of conversion of HCO3 to CO2 by lowering the pH. Respiration will reduce calcification rates when released CO2 increases Ci and/but lowers intercellular pH.”

“In general, photoinhibition can be defined as the lowering of photosynthetic rates at high irradiances. This is mainly due to the rapid (sometimes within minutes) degradation of […] the D1 protein. […] there are defense mechanisms [in plants] that divert excess light energy to processes different from photosynthesis; these processes thus cause a downregulation of the entire photosynthetic process while protecting the photosynthetic machinery from excess photons that could cause damage. One such process is the xanthophyll cycle. […] It has […] been suggested that the activity of the CCM in marine plants […] can be a source of energy dissipation. If CO2 levels are raised inside the cells to improve Rubisco activity, some of that CO2 can potentially leak out of the cells, and so raising the net energy cost of CO2 accumulation and, thus, using up large amounts of energy […]. Indirect evidence for this comes from experiments in which CCM activity is down-regulated by elevated CO2

“Photoinhibition is often divided into dynamic and chronic types, i.e. the former is quickly remedied (e.g. during the day[…]) while the latter is more persistent (e.g. over seasons […] the mechanisms for down-regulating photosynthesis by diverting photon energies and the reducing power of electrons away from the photosynthetic systems, including the possibility of detoxifying oxygen radicals, is important in high-light plants (that experience high irradiances during midday) as well as in those plants that do see significant fluctuations in irradiance throughout the day (e.g. intertidal benthic plants). While low-light plants may lack those systems of down-regulation, one must remember that they do not live in environments of high irradiances, and so seldom or never experience high irradiances. […] If plants had a mind, one could say that it was worth it for them to invest in pigments, but unnecessary to invest in high amounts of Rubisco, when growing under low-light conditions, and necessary for high-light growing plants to invest in Rubisco, but not in pigments. Evolution has, of course, shaped these responses”.

“shallow-growing corals […] show two types of photoinhibition: a dynamic type that remedies itself at the end of each day and a more chronic type that persists over longer time periods. […] Bleaching of corals occurs when they expel their zooxanthellae to the surrounding water, after which they either die or acquire new zooxanthellae of other types (or clades) that are better adapted to the changes in the environment that caused the bleaching. […] Active Ci acquisition mechanisms, whether based on localised active H+ extrusion and acidification and enhanced CO2 supply, or on active transport of HCO3, are all energy requiring. As a consequence it is not surprising that the CCM activity is decreased at lower light levels […] a whole spectrum of light-responses can be found in seagrasses, and those are often in co-ordinance with the average daily irradiances where they grow. […] The function of chloroplast clumping in Halophila stipulacea appears to be protection of the chloroplasts from high irradiances. Thus, a few peripheral chloroplasts ‘sacrifice’ themselves for the good of many others within the clump that will be exposed to lower irradiances. […] While water is an effective filter of UV radiation (UVR)2, many marine organisms are sensitive to UVR and have devised ways to protect themselves against this harmful radiation. These ways include the production of UV-filtering compounds called mycosporine-like amino acids (MAAs), which is common also in seagrasses”.

“Many algae and seagrasses grow in the intertidal and are, accordingly, exposed to air during various parts of the day. On the one hand, this makes them amenable to using atmospheric CO2, the diffusion rate of which is some 10 000 times higher in air than in water. […] desiccation is […] the big drawback when growing in the intertidal, and excessive desiccation will lead to death. When some of the green macroalgae left the seas and formed terrestrial plants some 400 million years ago (the latter of which then ‘invaded’ Earth), there was a need for measures to evolve that on the one side ensured a water supply to the above-ground parts of the plants (i.e. roots1) and, on the other, hindered the water entering the plants to evaporate (i.e. a water-impermeable cuticle). Macroalgae lack those barriers against losing intracellular water, and are thus more prone to desiccation, the rate of which depends on external factors such as heat and humidity and internal factors such as thallus thickness. […] the mechanisms of desiccation tolerance in macroalgae is not well understood on the cellular level […] there seems to be a general correlation between the sensitivity of the photosynthetic apparatus (more than the respiratory one) to desiccation and the occurrence of macroalgae along a vertical gradient in the intertidal: the less sensitive (i.e. the more tolerant), the higher up the algae can grow. This is especially true if the sensitivity to desiccation is measured as a function of the ability to regain photosynthetic rates following rehydration during re-submergence. While this correlation exists, the mechanism of protecting the photosynthetic system against desiccation is largely unknown”.

July 28, 2015

## Photosynthesis in the Marine Environment (I)

I’m currently reading this book. Below some observations from part 1.

“The term autotroph is usually associated with the photosynthesising plants (including algae and cyanobacteria) and heterotroph with animals and some other groups of organisms that need to be provided high-energy containing organic foods (e.g. the fungi and many bacteria). However, many exceptions exist: Some plants are parasitic and may be devoid of chlorophyll and, thus, lack photosynthesis altogether6, and some animals contain chloroplasts or photosynthesising algae or
cyanobacteria and may function, in part, autotrophically; some corals rely on the photosynthetic algae within their bodies to the extent that they don’t have to eat at all […] If some plants are heterotrophic and some animals autotrophic, what then differentiates plants from animals? It is usually said that what differs the two groups is the absence (animals) or presence (plants) of a cell wall. The cell wall is deposited outside the cell membrane in plants, and forms a type of exo-skeleton made of polysaccharides (e.g. cellulose or agar in some red algae, or silica in the case of diatoms) that renders rigidity to plant cells and to the whole plant.”

“For the autotrophs, […] there was an advantage if they could live close to the shores where inorganic nutrient concentrations were higher (because of mineral-rich runoffs from land) than in the upper water layer of off-shore locations. However, living closer to shore also meant greater effects of wave action, which would alter, e.g. the light availability […]. Under such conditions, there would be an advantage to be able to stay put in the seawater, and under those conditions it is thought that filamentous photosynthetic organisms were formed from autotrophic cells (ca. 650 million years ago), which eventually resulted in macroalgae (some 450 million years ago) featuring holdfast tissues that could adhere them to rocky substrates. […] Very briefly now, the green macroalgae were the ancestors of terrestrial plants, which started to invade land ca. 400 million years ago (followed by the animals).”

“Marine ‘plants’ (= all photoautotrophic organisms of the seas) can be divided into phytoplankton (‘drifters’, mostly unicellular) and phytobenthos (connected to the bottom, mostly multicellular/macroscopic).
The phytoplankton can be divided into cyanobacteria (prokaryotic) and microalgae (eukaryotic) […]. The phytobenthos can be divided into macroalgae and seagrasses (marine angiosperms, which invaded the shallow seas some 90 million years ago). The micro- and macro-algae are divided into larger groups as based largely on their pigment composition [e.g. ‘red algae‘, ‘brown algae‘, …]

There are some 150 currently recognised species of marine cyanobacteria, ∼20 000 species of eukaryotic microalgae, several thousand species of macroalgae and 50(!) species of seagrasses. Altogether these marine plants are accountable for approximately half of Earth’s photosynthetic (or primary) production.

The abiotic factors that are conducive to photosynthesis and plant growth in the marine environment differ from those of terrestrial environments mainly with regard to light and inorganic carbon (Ci) sources. Light is strongly attenuated in the marine environment by absorption and scatter […] While terrestrial plants rely of atmospheric CO2 for their photosynthesis, marine plants utilise largely the >100 times higher concentration of HCO3 as the main Ci source for their photosynthetic needs. Nutrients other than CO2, that may limit plant growth in the marine environment include nitrogen (N), phosphorus (P), iron (Fe) and, for the diatoms, silica (Si).”

“The conversion of the plentiful atmospheric N2 gas (∼78% in air) into bio-available N-rich cellular constituents is a fundamental process that sustains life on Earth. For unknown reasons this process is restricted to selected representatives among the prokaryotes: archaea and bacteria. N2 fixing organisms, also termed diazotrophs (dia = two; azo = nitrogen), are globally wide-spread in terrestrial and aquatic environments, from polar regions to hot deserts, although their abundance varies widely. [Why is nitrogen important, I hear you ask? Well, when you hear the word ‘nitrogen’ in biology texts, think ‘protein’ – “Because nitrogen is relatively easy to measure and protein is not, protein content is often estimated by assaying organic nitrogen, which comprises from 15 to 18% of plant proteins” (Herrera et al.see this post]. […] . Cyanobacteria dominate marine diazotrophs and occupy large segments of marine open waters […]  sustained N2 fixation […] is a highly energy-demanding process. […] in all diazotrophs, the nitrogenase enzyme complex […] of marine cyanobacteria requires high Fe levels […] Another key nutrient is phosphorus […] which has a great impact on growth and N2 fixation in marine cyanobacteria. […] Recent model-based estimates of N2 fixation suggest that unicellular cyanobacteria contribute significantly to global ocean N budgets.”

“For convenience, we often divide the phytoplankton into different size classes, the pico-phytoplankton (0.2–2 μm effective cell diameter, ECD4); the nanophytoplankton (2–20 μm ECD) and the microphytoplankton (20–200 μm ECD). […] most of the major marine microalgal groups are found in all three size classes […] a 2010 paper estimate that these plants utilise 46 Gt carbon yearly, which can be divided into 15 Gt for the microphytoplankton, 20 Gt for the nanophytoplankton and 11 Gt for the picophytoplankton. Thus, the very small (nano- + pico-forms) of phytoplankton (including cyanobacterial forms) contribute 2/3 of the overall planktonic production (which, again, constitutes about half of the global production”).

“Many primarily non-photosynthetic organisms have developed symbioses with microalgae and cyanobacteria; these photosynthetic intruders are here referred to as photosymbionts. […] Most photosymbionts are endosymbiotic (living within the host) […] In almost all cases, these micro-algae are in symbiosis with invertebrates. Here the alga provides the animal with organic products of photosynthesis, while the invertebrate host can supply CO2 and other inorganic nutrients including nitrogen and phosphorus to the alga […]. In cases where cyanobacteria form the photosymbiont, their ‘caloric’ nutritional value is more questionable, and they may instead produce toxins that deter other animals from eating the host […] Many reef-building […] corals contain symbiotic zooxanthellae within the digestive cavity of their polyps, and in general corals that have symbiotic algae grow much faster than those without them. […] The loss of zooxanthellae from the host is known as coral bleaching […] Certain sea slugs contain functional chloroplasts that were ingested (but not digested) as part of larger algae […]. After digesting the rest of the alga, these chloroplasts are imbedded within the slugs’ digestive tract in a process called kleptoplasty (the ‘stealing’ of plastids). Even though this is not a true symbiosis (the chloroplasts are not organisms and do not gain anything from the association), the photosynthetic activity aids in the nutrition of the slugs for up to several months, thus either complementing their nutrition or carrying them through periods when food is scarce or absent.”

“90–100 million years ago, when there was a rise in seawater levels, some of the grasses that grew close to the seashores found themselves submerged in seawater. One piece of evidence that supports [the] terrestrial origin [of marine angiosperms] can be seen in the fact that residues of stomata can be found at the base of the leaves. In terrestrial plants, the stomata restrict water loss from the leaves, but since seagrasses are principally submerged in a liquid medium, the stomata became absent in the bulk parts of the leaves. These marine angiosperms, or seagrasses, thus evolved from those coastal grasses that successfully managed to adapt to being submerged in saline waters. Another theory has it that the ancestors of seagrasses were freshwater plants that, therefore, only had to adapt to water of a higher salinity. In both cases, the seagrasses exemplify a successful readaptation to marine life […] While there may exist some 20 000 or more species of macroalgae […], there are only some 50 species of seagrasses, most of which are found in tropical seas. […] the ability to extract nutrients from the sediment renders the seagrasses at an advantage over (the root-less) macroalgae in nutrient-poor waters. […] one of the basic differences in habitat utilisation between macroalgae and seagrasses is that the former usually grow on rocky substrates where they are held in place by their holdfasts, while seagrasses inhabit softer sediments where they are held in place by their root systems. Unlike macroalgae, where the whole plant surface is photosynthetically active, large proportions of seagrass plants are comprised of the non-photosynthetic roots and rhizomes. […] This means […] that seagrasses need more light in order to survive than do many algae […] marine plants usually contain less structural tissues than their terrestrial counterparts”.

“if we define ‘visible light’ as the electromagnetic wave upon which those energy-containing particles called quanta ‘ride’ that cause vision in higher animals (those quanta are also called photons) and compare it with light that causes photosynthesis, we find, interestingly, that the two processes use approximately the same wavelengths: While mammals largely use the 380–750 nm (nm = 10-9 m) wavelength band for vision, plants use the 400–700-nm band for photosynthesis; the latter is therefore also termed photosynthetically active radiation (PAR […] If a student
asks “but how come that animals and plants use almost identical wavelengths of radiation for so very different purposes?”, my answer is “sorry, but we don’t have the time to discuss that now”, meaning that while I think it has to do with too high and too low quantum energies below and above those wavelengths, I really don’t know.”

“energy (E) of a photon is inversely proportional to its wavelength […] a blue photon of 400 nm wavelength contains almost double the energy of a red one of 700 nm, while the photons of PAR between those two extremes carry decreasing energies as wavelengths increase. Accordingly, low-energy photons (i.e. of high wavelengths, e.g. those of reddish light) are absorbed to a greater extent by water molecules along a depth gradient than are photons of higher energy (i.e. lower wavelengths, e.g. bluish light), and so the latter penetrate deeper down in clear oceanic waters […] In water, the spectral distribution of PAR reaching a plant is different from that on land. This is because water not only attenuates the light intensity (or, more correctly, the photon flux, or irradiance […]), but, as mentioned above and detailed below, the attenuation with depth is wavelength dependent; therefore, plants living in the oceans will receive different spectra of light dependent on depth […] The two main characteristics of seawater that determine the quantity and quality of the irradiance penetrating to a certain depth are absorption and scatter. […] Light absorption in the oceans is a property of the water molecules, which absorb photons according to their energy […] Thus, red photons of low energy are more readily absorbed than, e.g. blue ones; only <1% of the incident red photons (calculated for 650 nm) penetrate to 20 m depth in clear waters while some 60% of the blue photons (450 nm) remain at that depth. […] Scatter […] is mainly caused by particles suspended in the water column (rather than by the water molecules themselves, although they too scatter light a little). Unlike absorption, scatter affects short-wavelength photons more than long-wavelength ones […] in turbid waters, photons of decreasing wavelengths are increasingly scattered. Since water molecules are naturally also present, they absorb the higher wavelengths, and the colours penetrating deepest in turbid waters are those between the highly scattered blue and highly absorbed red, e.g. green. The greenish colour of many coastal waters is therefore often due not only to the presence of chlorophyll-containing phytoplankton, but because, again, reddish photons are absorbed, bluish photons are scattered, and the midspectrum (i.e. green) fills the bulk part of the water column.”

“the open ocean, several kilometres or miles from the shore, almost always appears as blue. The reason for this is that in unpolluted, particle-free, waters, the preferential absorption of long-wavelength (low-energy) photons is what mainly determines the spectral distribution of light attenuation. Thus, short-wavelength (high-energy) bluish photons penetrate deepest and ‘fill up’ the bulk of the water column with their colour. Since water molecules also scatter a small proportion of those photons […], it follows that these largely water-penetrating photons are eventually also reflected back to our eyes. Or, in other words, out of the very low scattering in clear oceanic waters, the photons available to be scattered and, thus, reflected to our eyes, are mainly the bluish ones, and that is why the clear deep oceans look blue. (It is often said that the oceans are blue because the blue sky is reflected by the water surface. However, sailors will testify to the truism that the oceans are also deep blue in heavily overcast weathers, and so that explanation of the general blueness of the oceans is not valid.)”

“Although marine plants can be found in a wide range of temperature regimes, from the tropics to polar regions, the large bodies of water that are the environment for most marine plants have relatively constant temperatures, at least on a day-to-day basis. […] For marine plants that are found in intertidal regions, however, temperature variation during a single day can be very high as the plants find themselves alternately exposed to air […] Marine plants from tropical and temperate regions tend to have distinct temperature ranges for growth […] and growth optima. […] among most temperate species of microalgae, temperature optima for growth are in the range 18–25 ◦C, while some Antarctic diatoms show optima at 4–6 ◦C with no growth above a critical temperature of 7–12 ◦C. By contrast, some tropical diatoms will not grow below 15–17 ◦C. Similar responses are found in macroalgae and seagrasses. However, although some marine plants have a restricted temperature range for growth (so-called stenothermal species; steno = narrow and thermal relates to temperature), most show some growth over a broad range of temperatures and can be considered eurythermal (eury = wide).”

June 4, 2015

## Mammoths, Sabertooths, and Hominids: 65 Million Years of Mammalian Evolution in Europe (3)

Here’s a previous post in the series. In this post I’ll pick up roughly where I left off in my last post, around the time of the ‘Grande Coupure‘ roughly 34 million years ago.

“The extinction of the arboreal primates and the reduction or extinction of several browsing groups […] are strong evidence for the retreat of the forests during the early Oligocene and their replacement by open woodlands or even drier biotopes. […] Among the most distinctive species to enter Europe after the “Grande Coupure” were the first true rhinoceroses [which] achieved a high diversity and were going to characterize the mammalian faunas of Europe for millions of years, until the extinction of the last woolly rhinos during the late Pleistocene. […] the evolution of this group produced the largest terrestrial mammals of any time. The giant Paraceratherium […] was 6 m tall at the shoulders and had a 1.5-m-long skull […]. The males of this animal weighed around 15 tons, while the females were somewhat smaller, about 10 tons.” [Wikipedia has a featured article about these things here].

“One of the most significant features of the early Oligocene small-mammal communities was the first entry of lagomorphs into Europe. The lagomorphs — that is, the order of mammals that includes today’s hares and rabbits — originated very early on the Asian continent and from there colonized North America. The presence of the Turgai Strait prevented this group from entering Europe during the Eocene. […] the most characteristic immigrants during the early Oligocene were the cricetids of the genus Atavocricetodon. The cricetids are today represented in Europe by hamsters, reduced to three or four species […] These cricetids are typical inhabitants of the cold steppes of eastern Europe and Central Asia, and their limited representation in today’s European ecosystems does not reflect their importance in the history of the Cenozoic mammalian faunas of Eurasia. After its first entry following the “Grande Coupure,” this group experienced extraordinary success, diversifying into several genera and species. Even more significantly, the cricetids gave rise to the rodent groups that were going to be dominant during the Pliocene and Pleistocene — that is, the murids (the family of mice and rats) and arvicolids (the family of voles). […] In addition, new carnivore families, like the nimravids, appeared […]. The nimravids were once regarded as true felids (the family that includes today’s big and small cats) because of their similar dental and cranial adaptations. […] one of the more distinctive attributes of the nimravids was their long, laterally flattened upper canines, which were similar to those of the Miocene and Pliocene saber-toothed cats […]. However, most of these features have proved to be the result of a similar adaptation to hypercarnivorism, and the nimravids are now placed in a separate family of early carnivores whose evolution paralleled that of the large saber-toothed felids.” [Actually some of the nimravids were in some sense ‘even more sabertoothed’ than the (‘true’) saber-toothed cats which came later: “Although [the nimravid] Eusmilus bidentatus was no larger than a modern lynx, the adaptations for gape seen on its skull and mandible are more advanced than in any of the felid sabertooths of the European Pliocene and Pleistocene.”]

“About 30 million years ago, a new glacial phase began, and for 4 million years Antarctica was subjected to multiple glaciation episodes. The global sea level experienced the largest lowering in the whole Cenozoic, dropping by about 150 m […]. A possible explanation for this new glacial event lies in the final opening of the Drake Passage between Antarctica and South America, which led to the completion of a fully circumpolar circulation and impeded any heat exchange between Antarctic waters and the warmer equatorial waters. A second, perhaps complementary cause for this glacial pulse is probably related to the final opening of the seaway between Greenland and Norway. The cold Arctic waters, largely isolated since the Mesozoic, spread at this time into the North Atlantic. The main effect of this cooling was a new extension of the dry landscapes on the European and western Asian lands. For instance, we know from pollen evidence that a desert vegetation was dominant in the Levant during the late Oligocene and earliest Miocene […] This glacial event led to the extinction of several forms that had persisted from the Eocene”.

“Among the carnivores, the late Oligocene saw the decline and local extinction of the large nimravids [Key word: local. They came back to Europe later during the early Miocene, and “the nimravids maintained a remarkable stability throughout the Miocene, probably in relation to a low speciation rate”]. In contrast, the group of archaic feloids that had arisen during the early Oligocene […] continued its evolution into the late Oligocene and diversified into a number of genera […] The other group of large carnivores that spread during the late Oligocene were the “bear-dog” amphicyonids, which from that time on became quite diverse, with many different ecological adaptations. […] The late Oligocene saw, in addition to the bearlike amphicyonids, the spread of the first true ursids […]. The members of this genus did not have the massive body dimensions of today’s bears but were medium-size omnivores […] Another group of carnivores that spread successfully during the late Oligocene were the mustelids, the family that includes today’s martens, badgers, skunks, and otters. […] In contrast to these successes, the creodonts of the genus Hyaenodon, which had survived all periods of crisis since the Eocene, declined during the late Oligocene. The last Hyaenodon in Europe was recorded at the end of the Oligocene […], and did not survive into the Miocene. This was the end in Europe of a long-lived group of successful carnivorans that had filled the large-predator guild for millions of years. However, as with other Oligocene groups, […] the hyaenodonts persisted in Africa and, from there, made a short incursion into Europe during the early Miocene”.

“After a gradual warming during the late Oligocene, global temperatures reached a climatic optimum during the early Miocene […] Shallow seas covered several nearshore areas in Europe […] as a consequence of a general sea-level rise. A broad connection was established between the Indian Ocean and both the Mediterranean and Paratethys Seas […] Widespread warm-water faunas including tropical fishes and nautiloids have been found, indicating conditions similar to those of the present-day Guinea Gulf, with mean surface-water temperatures around 25 to 27°C. Important reef formations bounded most of the shallow-water Mediterranean basins. […] Reef-building corals that today inhabit the Great Barrier Reef within a temperature range of 19 to 28°C became well established on North Island, New Zealand […] The early Miocene climate was warm and humid, indicating tropical conditions […]. Rich, extensive woodlands with varied kinds of plants developed in different parts of southern Europe […] The climatic optimum of the early Miocene also led to a maximum development of mangroves. These subtropical floras extended as far north as eastern Siberia and Kamchatka”.

“Despite the climatic stability of the early Miocene, an important tectonic event disrupted the evolution of the Eurasian faunas during this epoch. About 19 million years ago, the graben system along the Red Sea Fault, active in the south since the late Oligocene, opened further […] Consequently, the Arabian plate rotated counterclockwise and collided with the Anatolian plate. The marine gateway from the Mediterranean toward the Indo-Pacific closed, and a continental migration bridge (known as the Gomphothere Bridge) between Eurasia and Africa came into existence. This event had enormous consequences for the further evolution of the terrestrial faunas of Eurasia and Africa. Since the late Eocene, Africa had evolved in isolation, developing its own autochthonous fauna. Part of this fauna consisted of a number of endemic Oligocene survivors, such as anthracotheres, hyaenodonts, and primates, for which Africa had acted as a refuge […] The first evidence of an African–Eurasian exchange was the presence of the anthracothere Brachyodus in a number of early Miocene sites in Europe […] a second dispersal event from Africa, that of the gomphothere and deinothere proboscideans, had much more lasting effects. […] Today we can easily identify any proboscidean by its long proboscis and tusks. However, the primitive proboscideans from the African Eocene had a completely different appearance and are hardly recognizable as the ancestors of today’s elephants. Instead, they were hippolike semiamphibious ungulates with massive, elongated bodies supported by rather short legs. […] The first proboscideans entering Europe were the so-called gomphotheres […] which dispersed worldwide during the early Miocene from Africa to Europe, Asia, and North America […]. Gomphotherium was the size of an Indian elephant, about 2.5 m high at the withers. Its skull and dentition, however, were different from those of modern elephants. Gomphotherium’s skull was long […] and displayed not two but four tusks, one pair in the upper jaw and the other pair at the end of the lower jaw. […] Shortly after the entry of Gomphotherium and Zygolophodon [a second group of mastodons], a third proboscidean group, the deinotheres, successfully settled in Eurasia. Unlike the previous genera, the deinotheres were not elephantoids but represented a different, now totally extinct kind of proboscidean.”

“The dispersal of not only the African proboscideans but also many eastern immigrants contributed to a significant increase in the diversity of the impoverished early Miocene terrestrial biotas. The entry of this set of immigrants probably led to the extinction of a number of late Oligocene and early Miocene survivors, such as tapirids, anthracotherids, and primitive suids [pigs] and moschoids. In addition to the events that affected the Middle East area, sea-level fluctuations enabled short-lived mammal exchanges across the Bering Strait between Eurasia and North America, permitting the arrival of the browsing horse Anchitherium in Eurasia […] Widely used for biostragraphic purposes, the dispersal of Anchitherium was the first of a number of similar isolated events undergone by North American equids that entered Eurasia and rapidly spread on this continental area.”

“A new marine transgression, known as the Langhian Transgression, characterized the beginning of the middle Miocene, affecting the circum-Mediterranean area. Consequently, the seaway to the Indo-Pacific reopened for a short time, restoring the circum-equatorial warm-water circulation. […] tropical conditions became established as far north as Poland in marine coastal and open-sea waters. After the optimal conditions of the early Miocene, the middle Miocene was a period of global oceanic reorganization, representing a major change in the climatic evolution of the Cenozoic. Before this process began, high-latitude paleoclimatic conditions were generally warm although oscillating, but they rapidly cooled thereafter, leading to an abrupt high-latitude cooling event at about 14.5 million years ago […] Increased production of cold, deep Antarctic waters caused the extinction of several oceanic benthic foraminifers that had persisted from the late Oligocene–early Miocene and promoted a significant evolutionary turnover of the oceanic assemblages from about 16 to 14 million years ago […] This middle Miocene cooling was associated with a major growth of the Eastern Antarctic Ice Sheets (EAIS) […] Middle Miocene polar cooling and east Antarctic ice growth had severe effects on middle- to low-latitude terrestrial environments. There was a climatic trend to cooler winters and decreased summer rainfall. Seasonal, summer-drought-adapted schlerophyllous vegetation progressively evolved and spread geographically during the Miocene, replacing the laurophyllous evergreen forests that were adapted to moist, subtropical and tropical conditions with temperate winters and abundant summer rainfalls […] These effects were clearly seen in a wide area to the south of the Paratethys Sea, extending from eastern Europe to western Asia. According to the ideas of the American paleontologist Ray Bernor, this region, known as the Greek-Iranian (or sub-Paratethyan) Province, acted as a woodland environmental “hub” for a corridor of open habitats that extended from northwestern Africa eastward across Arabia into Afghanistan, north into the eastern Mediterranean area, and northeast into northern China. The Greek-Iranian Province records the first evidence of open woodlands in which a number of large, progressive open-country mammals—such as hyaenids, thick-enameled hominoids, bovids, and giraffids — diversified and dispersed into eastern Africa and southwestern Asia […] the peculiar biotope developed in the Greek-Iranian Province acted as the background from which the African savannas evolved during the Pliocene and Pleistocene.”

“The most outstanding effect of the Middle Miocene Event is seen among the herbivorous community, which showed a trend toward developing larger body sizes, more-hypsodont teeth, and more-elongated distal limb segments […]. Increasing body size in herbivores is related to a higher ingestion of fibrous and low-quality vegetation. Browsers and grazers have to be large because they need long stomachs and intestines to process a large quantity of low-energy food (this is why they have to eat almost continuously). Because of the mechanism of rumination, ruminants are the only herbivores that can escape this rule and subsist at small sizes. Increasing hypsodonty and high-crowned teeth are directly related to the ingestion of more-abrasive vegetation […] Finally, the elongation of the distal limb segments is related to increasing cursoriality. The origin of cursoriality can be linked to the expansion of the home range in open, low-productive habitats. […] At the taxonomic level, this habitat change in the low latitudes involved the rapid adaptive radiation of woodland ruminants (bovids and giraffids). […] Gazelles dispersed into Europe at this time from their possible Afro-Arabian origins […] Not only gazelles but also the giraffids experienced a wide adaptive radiation into Africa after their dispersal from Asia. […] Among the suids [pigs], the listriodontines evolved in a peculiar way in northern Africa, leading to giant forms such as Kubanochoerus, with a weight of about 500 kg, which in some species may have reached 800 kg.”

March 8, 2015

## Wikipedia articles of interest

i. Invasion of Poland. I recently realized I had no idea e.g. how long it took for the Germans and Soviets to defeat Poland during WW2 (the answer is 1 month and five days). The Germans attacked more than two weeks before the Soviets did. The article has lots of links, like most articles about such topics on wikipedia. Incidentally the question of why France and Britain applied a double standard and only declared war on Germany, and not the Soviet Union, is discussed in much detail in the links provided by u/OldWorldGlory here.

ii. Huaynaputina. From the article:

“A few days before the eruption, someone reported booming noise from the volcano and fog-like gas being emitted from its crater. The locals scrambled to appease the volcano, preparing girls, pets, and flowers for sacrifice.”

This makes sense – what else would one do in a situation like that? Finding a few virgins, dogs and flowers seems like the sensible approach – yes, you have to love humans and how they always react in sensible ways to such crises.

I’m not really sure the rest of the article is really all that interesting, but I found the above sentence both amusing and depressing enough to link to it here.

iii. Albert Pierrepoint. This guy killed hundreds of people.

On the other hand people were fine with it – it was his job. Well, sort of, this is actually slightly complicated. (“Pierrepoint was often dubbed the Official Executioner, despite there being no such job or title”).

Anyway this article is clearly the story of a guy who achieved his childhood dream – though unlike other children, he did not dream of becoming a fireman or a pilot, but rather of becoming the Official Executioner of the country. I’m currently thinking of using Pierrepoint as the main character in the motivational story I plan to tell my nephew when he’s a bit older.

iv. Second Crusade (featured). Considering how many different ‘states’ and ‘kingdoms’ were involved, a surprisingly small amount of people were actually fighting; the article notes that “[t]here were perhaps 50,000 troops in total” on the Christian side when the attack on Damascus was initiated. It wasn’t enough, as the outcome of the crusade was a decisive Muslim victory in the ‘Holy Land’ (Middle East).

v. 0.999… (featured). This thing is equal to one, but it can sometimes be really hard to get even very smart people to accept this fact. Lots of details and some proofs presented in the article.

vi. Shapley–Folkman lemma (‘good article’ – but also a somewhat technical article).

vii. Multituberculata. This article is not that special, but I add it here also because I think it ought to be and I’m actually sort of angry that it’s not; sometimes the coverage provided on wikipedia simply strikes me as grossly unfair, even if this is perhaps a slightly odd way to think about stuff. As pointed out in the article (Agustí points this out in his book as well), “The multituberculates existed for about 120 million years, and are often considered the most successful, diversified, and long-lasting mammals in natural history.” Yet notice how much (/little) coverage the article provides. Now compare the article with this article, or this.

February 25, 2015

## Mammoths, Sabertooths, and Hominids: 65 Million Years of Mammalian Evolution in Europe (2)

Here’s my first post about the book.

I’ve added a few sample quotes and observations from the book below.

“Europe, although just an appendage of the Eurasian supercontinent, acted during most of its history as a crossroad where Asian, African, and American faunas passed one another, throughout successive dispersal and extinction events. But these events did not happen in an isolated context, since they were the response to climatic and environmental events of a higher order. Thus this book pays special attention to the abundant literature that for the past few decades has dedicated itself to the climatic evolution of our planet.”

“A common scenario tends to posit the early evolutionary radiation of placental mammals as occurring only after the extinction of the dinosaurs at the end of the Cretaceous period. The same scenario assumes a sudden explosion of forms immediately after the End Cretaceous Mass Extinction, filling the vacancies left by the vanished reptilian faunas. But a close inspection of the first epoch of the Cenozoic provides quite a different picture: the “explosion” began well before the end of the Cretaceous period and was not sudden, but lasted millions of years throughout the first division of the Cenozoic era, the Paleocene epoch. […] our knowledge of this remote time of mammalian evolution is much more obscure and incomplete than our understanding of the other periods of the Cenozoic. […] compared with our present world, and in contrast to the succeeding epochs, the Paleocene appears to us as a strange time, in which the present orders of mammals were absent or can hardly be distinguished: no rodents, no perissodactyls, no artiodactyls, bizarre noncarnivorous carnivorans. […] although the Paleocene was mammalian in character, we do not recognize it as a clear part of our own world; it looks more like an impoverished extension of the late Cretaceous world than the seed of the present Age of Mammals.”

“The diatrymas were human-size — up to 2 m tall — ground-running birds that inhabited the terrestrial ecosystems of Europe and North America in the Paleocene and the early to middle Eocene […] Besides the large diatrymas, a large variety of crocodiles — mainly terrestrial and amphibious eusuchian crocodiles — populated the marshes of the Paleocene rainforests. […] The high diversification of the crocodile fauna throughout the Paleocene and Eocene represents a significant ecological datum, since crocodiles do not tolerate temperatures below 10 to 15°C (exceptionally, they could survive in temperatures of about 5 or 6°C). Their existence in Europe indicates that during the first part of the Cenozoic the average temperature of the coldest month never fell below these values and that these mild conditions persisted at least until the middle Miocene.”

“At the end of the Paleocene, approximately 55.5 million years ago, there was a sudden, short-term warming known as the Latest Paleocene Thermal Maximum. Over a period of tens of thousands of years or less, the temperature of all the oceans increased by around 4°C. This was the highest warming during the entire Cenozoic, reaching global mean temperatures of around 20°C. There is some evidence that the Latest Paleocene Thermal Maximum resulted from a sudden increase in atmospheric CO2. Intense volcanic activity developed at the Paleocene–Eocene boundary, associated with the rifting process in the North Atlantic and the opening of the Norwegian-Greenland Sea. […] According to some analyses, atmospheric CO2 during the early Eocene may have been eight times its present concentration. […] The high temperatures and increasing humidity favored the extension of tropical rainforests over the middle and higher latitudes, as far north as Ellesmere Island, now in the Canadian arctic north. There, an abundant fauna — including crocodiles, monitor lizards, primates, rodents, multituberculates, early perissodactyls, and the pantodont Coryphodon — and a flora composed of tropical elements indicates the extension of the forests as far north as 78 degrees north latitude. […] The global oceanic level at the beginning of the Eocene was high, and extensive areas of Eurasia were still under the sea. In this context, Europe consisted of a number of emerged islands forming a kind of archipelago. A central European island consisted of parts of present-day England, France, and Germany, although it was placed in a much more southerly position, approximately at the present latitude of Naples. […] To the east, the growing Mediterranean opened into a wide sea, since the landmasses of Turkey, Iraq, and Iran were still below sea level. To the east of the Urals, the Turgai Strait still connected the warm waters of the Tethys Sea with the Polar Sea. […] Despite the opening of the Greenland-Norwegian Sea, Europe and North America were still connected during most of the early and middle Eocene across two main land bridges […] the De Geer Corridor [and] the Thule Bridge […] these corridors must have been effective, since the European fossil record shows a massive entry of American elements […] The ischyromyid and ailuravid rodents, as well as the miacid carnivores, were among the oldest representatives of the modern orders of mammals to appear in Europe during the early Eocene. However, they were not the only ones, since the “modernization” of the mammalian communities at this time went even further, and groups such as the first true primates, bats (Chiroptera), flying lemurs (Dermoptera), and oddtoed (Perissodactyla) and even-toed (Artiodactyla) ungulates entered onto the scene, in both Europe and North America.”

“Although it was the first member of the horse lineage, Pliolophus certainly did not look like a horse. As classically stated, it had the dimensions of a medium dog (“a fox-terrier”), bearing four hooves on the front legs and three on the hind legs. […] the first rhino-related forms included Hyrachius, a small rhino about the size of a wolf that during the Eocene inhabited a wide geographic range, from North America to Europe and Asia.” (Yep, in case you didn’t know Europe had rhinos for millions and millions of years…) “The artiodactyls are among the most successful orders of mammals, having diversified in the past 10 million years into a wide array of families, subfamilies, tribes, and genera all around the world, including pigs, peccaries, hippos, chevrotains, camels, giraffes, deer, antelopes, gazelles, goats, and cattle. They are easily distinguished from the perissodactyls because each extremity is supported on the two central toes, instead of on the middle strengthened toe. […] The oldest member of the order is Diacodexis, […] a rabbit-size ungulate”

“Although the number of middle Eocene localities in Europe is quite restricted, we have excellent knowledge of the terrestrial communities of this time thanks to the extraordinary fossiliferous site of Messel, Germany. […] several specimens from Messel retain in their gut their last meal, providing a rare opportunity for testing the teeth-inferred dietary requirements of a number of extinct mammalian groups. […] A dense canopy forest surrounded Messel lake, formed of several tropical and paratropical taxa that today live in Southeast Asia”.

“At the end of the middle Eocene, things began to change in the European archipelago. Several late Paleocene and early Eocene survivors had become extinct […] The last part of the middle Eocene saw a clear change in the structure of the herbivore community as specialized browsing herbivores […] replaced the small to medium-size omnivorous/ frugivorous archaic ungulates of the early Eocene and became the dominant species. […] These changes among the mammalian faunas were most probably a response to the major tectonic transformations occurring at that time and the associated environmental changes. During the middle Eocene, the Indian plate collided with Asia, closing the Tethys Sea north of India. The collision of India and the compression between Africa and Europe formed an active alpine mountain belt along the southern border of Eurasia. In the western Mediterranean, strong compression occurred during the late Eocene, […] leading to the final emergence of the Pyrenees. To the south of the Pyrenees, the sea branch between the Iberian plate and Europe retreated”

“The European terrestrial ecosystems at the end of the Eocene were quite different from those inherited from the Paleocene, which were dominated by archaic, unspecialized groups. In contrast, a diversified fauna of specialized small and large browsing herbivores […] characterized the late Eocene. From our perspective, they looked much more “modern” than those of the early and early-middle Eocene and perfectly adapted to the new late Eocene environmental conditions characterized by the spread of more open habitats.”

“during the Eocene […] Australia and South America were still attached to Antarctica, as the last remnants of the ancient Gondwanan supercontinent. Today’s circumpolar current did not yet exist, and the equatorial South Atlantic and South Pacific waters went closer to the Antarctic coasts, thus transporting heat from the low latitudes to the high southern latitudes. However, this changed during the late Eocene, when a rifting process began to separate Australia from Antarctica. At the beginning of the Oligocene, between 34 and 33 million years ago, the spread between the two continents was large enough to allow a first phase of circumpolar circulation, which restricted the thermal exchange between the low-latitude equatorial waters and the Antarctic waters. A sudden and massive cooling took place, and mean global temperatures fell by about 5°C. […] During a few hundred thousand years (the estimated duration of this early Oligocene glacial episode), the ice sheets expanded and covered extensive areas of Antarctica, particularly in its western regions. […] The onset of Antarctic glaciation and the growing of the ice sheets in western Antarctica provoked an important global sea-level lowering of about 30 m. Several shallow epicontinental seas became continental areas, including those that surrounded the European Archipelago. The Turgai Strait, which during millions of years had isolated the European lands from Asia, vanished and opened a migration pathway for Asian and American mammals to the west. […] The tectonic movements led to the final split of the Tethys Sea into two main seas, the Mediterranean Sea to the south and the Paratethys Sea, the latter covering the formerly open ocean areas of central and eastern Europe. […] After the retreat of the Turgai Strait and the emergence of the Paratethys province, the European Archipelago ceased to exist, and Europe approached its present configuration. The ancient barriers that had prevented Asian faunas from settling in this continental area no longer existed, and a wave of new immigrants entered from the east. This coincided with the trend toward more temperate conditions and the spread of open environments initiated during the late Eocene. Consequently, most of the species that had characterized the middle and late Eocene declined or became completely extinct, replaced by herds of Asian newcomers.”

February 23, 2015

## Mammoths, Sabertooths, and Hominids: 65 Million Years of Mammalian Evolution in Europe

The book frequently has more information about a given species/genus than does wikipedia’s corresponding article (and there’s stuff in here which wikipedia does not have articles about at all…), and/but I’ve tried to avoid linking to stubs below. Some articles below have decent coverage, but these are in general topics not well covered on wikipedia – I don’t think there’s a single featured article among the articles included. Even so, it’s probably worth having a look at some of the articles below if you’re curious to know which kind of stuff’s covered in this book. Aside from the links, I decided to also include a few pictures from the articles.

February 13, 2015

## The Voyage of the Beagle (III)

This will be my last post about the book.

What all of above stuff means is of course that for quite a while I didn’t really read very much in this book because I’d settled on not reading it while I was at home, but I also usually had a different book on my e-reader which it was easier and more convenient to bring on my walks. At the end I decided that I should really read the rest of this book because it’s quite good (before I started rereading the book it was on my list of favourites on goodreads, and it still is), and so I decided to read it at home.

The book is really nice. If you liked the quotes I included either in my previous posts about the book and/or in this post, it’s worth considering taking the time to read the book. I may be wrong, but I could easily imagine this being the sort of book that many people might think to themselves that they’ll read when they get old, but then when they reach the pension age they’ll never get around to actually doing it; if this impression is correct, that’s just a damn shame. Reading books like this one or perhaps something like Mark Twain’s The Innocents Abroad (available for free here) will, aside from giving you some enjoyable experiences in the company of good writers, probably make it easier for you to think about the world in a slightly different manner than the one you’re used to.

The book is full of good stuff and so I had to leave out a lot of good stuff in my posts. Below I have added a few more illustrative quotes from the book.

“I heard also of an old lady who, at a dinner at Coquimbo, remarked how wonderfully strange it was that she should have lived to dine in the same room with an Englishman; for she remembered as a girl, that twice, at the mere cry of “Los Ingleses,” every soul, carrying what valuables they could, had taken to the mountains.”

“The connection between earthquakes and the weather has been often disputed: it appears to me to be a point of great interest, which is little understood.”

“My geological examination of the country generally created a good deal of surprise amongst the Chilenos: it was long before they could be convinced that I was not hunting for mines. This was sometimes troublesome: I found the most ready way of explaining my employment, was to ask them how it was that they themselves were not curious concerning earthquakes and volcanos? – why some springs were hot and others cold? – why there were mountains in Chile, and not a hill in La Plata? These bare questions at once satisfied and silenced the greater number; some, however (like a few in England who are a century behind hand), thought that all such inquiries were useless and impious; and that it was quite sufficient that God had thus made the mountains.”

“Our arrival in the offing caused some little apprehension. Peru was in a state of anarchy; and each party having demanded a contribution, the poor town of Iquique was in tribulation, thinking the evil hour was come. The people had also their domestic troubles; a short time before, three French carpenters had broken open, during the same night, the two churches, and stolen all the plate: one of the robbers, however, subsequently confessed, and the plate was recovered. The convicts were sent to Arequipa, which though the capital of this province, is two hundred leagues distant, the government there thought it a pity to punish such useful workmen, who could make all sorts of furniture; and accordingly liberated them. Things being in this state, the churches were again broken open, but this time the plate was not recovered. The inhabitants became dreadfully enraged, and declaring that none but heretics would thus “eat God Almighty,” proceeded to torture some Englishmen, with the intention of afterwards shooting them. At last the authorities interfered, and peace was established.”

“We did not reach the saltpetre-works till after sunset, having ridden all day across an undulating country, a complete and utter desert. The road was strewed with the bones and dried skins of many beasts of burden which had perished on it from fatigue. Excepting the Vultur aura, which preys on the carcasses, I saw neither bird, quadruped, reptile, nor insect. […] I cannot say I liked the very little I saw of Peru: in summer, however, it is said that the climate is much pleasanter. In all seasons, both inhabitants and foreigners suffer from severe attacks of ague. This disease is common on the whole coast of Peru, but is unknown in the interior. The attacks of illness which arise from miasma never fail to appear most mysterious. […] Callao is a filthy, ill-built, small seaport. The inhabitants, both here and at Lima, present every imaginable shade of mixture, between European, Negro, and Indian blood. They appear a depraved, drunken set of people.”

“Of land-birds I obtained twenty-six kinds, all peculiar to the group and found nowhere else, with the exception of one lark-like finch from North America […] The remaining land-birds form a most singular group of finches, related to each other in the structure of their beaks, short tails, form of body and plumage […] The most curious fact is the perfect gradation in the size of the beaks in the different species […] Seeing this gradation and diversity of structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this archipelago, one species had been taken and modified for different ends. […] With the exception of a wren with a fine yellow breast, and of a tyrant-flycatcher with a scarlet tuft and breast, none of the birds are brilliantly coloured, as might have been expected in an equatorial district. Hence it would appear probable, that the same causes which here make the immigrants of some peculiar species smaller, make most of the peculiar Galapageian species also smaller, as well as very generally more dusky coloured.” [For more on related topics, see incidentally this previous post of mine].

“As I at first observed, these islands are not so remarkable for the number of the species of reptiles, as for that of the [number of] individuals […] we must admit that there is no other quarter of the world where this Order replaces the herbivorous mammalia in so extraordinary a manner. […] by far the most remarkable feature in the natural history of this archipelago [is] that the different islands to a considerable extent are inhabited by a different set of beings. […] The inhabitants […] state that they can distinguish the tortoises from the different islands; and that they differ not only in size, but in other characters. […] I have strong reasons to suspect that some of the [finch] species of the sub-group Geospiza are confined to separate islands. If the different islands have their representatives of Geospiza, it may help to explain the singularly large number of the species of this sub-group in this one small archipelago, and as a probable consequence of their numbers, the perfectly graduated series in the size of their beaks. […] The distribution of the tenants of this archipelago would not be nearly so wonderful, if, for instance, one island had a mocking-thrush, and a second island some other quite distinct genus,- if one island had its genus of lizard, and a second island another distinct genus, or none whatever; -or if the different islands were inhabited, not by representative species of the same genera of plants, but by totally different genera […]. But it is the circumstance, that several of the islands possess their own species of the tortoise, mocking-thrush, finches, and numerous plants, these species having the same general habits, occupying analogous situations, and obviously filling the same place in the natural economy of this archipelago, that strikes me with wonder. It may be suspected that some of these representative species, at least in the case of the tortoise and of some of the birds, may hereafter prove to be only well-marked races; but this would be of equally great interest to the philosophical naturalist.”

“I was much disappointed in the personal appearance of the [Tahiti] women; they are far inferior in every respect to the men.” [Good luck writing anything like that today and getting it published…] […] After the main discussion was ended, several of the chiefs took the opportunity of asking Captain Fitz Roy many intelligent questions on international customs and laws, relating to the treatment of ships and foreigners. […] This Tahitian parliament lasted for several hours; and when it was over Captain Fitz Roy invited Queen Pomarre to pay the Beagle a visit. […] In the evening four boats were sent for her majesty; the ship was dressed with flags, and the yards manned on her coming on board. She was accompanied by most of the chiefs. The behaviour of all was very proper: they begged for nothing, and seemed much pleased with Captain Fitz Roy’s presents.”

“When I showed the chief a very small bundle, which I wanted carried, it became absolutely necessary for him to take a slave. These feelings of pride are beginning to wear away; but formerly a leading man would sooner have died, than undergone the indignity of carrying the smallest burden.”

“Some time ago, Mr. Bushby suffered a […] serious attack. A chief and a party of men tried to break into his house in the middle of the night, and not finding this so easy, commenced a brisk firing with their muskets. Mr. Bushby was slightly wounded, but the party was at length driven away. Shortly afterwards it was discovered who was the aggressor; and a general meeting of the chiefs was convened to consider the case. It was considered by the New Zealanders as very atrocious, inasmuch as it was a night attack, and that Mrs. Bushby was lying ill in the house: this latter circumstance, much to their honour, being considered in all cases as a protection. The chiefs agreed to confiscate the land of the aggressor to the King of England. The whole proceeding, however, in thus trying and punishing a chief was entirely without precedent. The aggressor, moreover, lost caste in the estimation of his equals and this was considered by the British as of more consequence than the confiscation of his land. […] a chief and a party of men volunteered to walk with us to Waiomio, a distance of four miles. The chief was at this time rather notorious from having lately hung one of his wives and a slave for adultery. When one of the missionaries remonstrated with him he seemed surprised, and said he thought he was exactly following the English method.”

“It is impossible to behold these waves without feeling a conviction that an island, though built of the hardest rock, let it be porphyry, granite, or quartz, would ultimately yield and be demolished by such an irresistible power. Yet these low, insignificant coral-islets stand and are victorious: for here another power, as an antagonist, takes part in the contest. The organic forces separate the atoms of carbonate of lime, one by one, from the foaming breakers, and unite them into a symmetrical structure. Let the hurricane tear up its thousand huge fragments; yet what will that tell against the accumulated labour of myriads of architects at work night and day, month after month? […] We feel surprise when travellers tell us of the vast dimensions of the Pyramids and other great ruins, but how utterly insignificant are the greatest of these, when compared to these mountains of stone accumulated by the agency of various minute and tender animals! This is a wonder which does not at first strike the eye of the body, but, after reflection, the eye of reason.”

“Those who look tenderly at the slave owner, and with a cold heart at the slave, never seem to put themselves into the position of the latter”

December 14, 2014

## Female Infidelity and Paternal Uncertainty – Evolutionary Perspectives on Male Anti-Cuckoldry Tactics

I finished this book yesterday. Below I have posted my goodreads review:

“A couple of chapters were really nice, but the authors repeat themselves *a lot* throughout the book and some chapters are really weak. I was probably at three stars after approximately 100 pages, but the book in my opinion lost steam after that. A couple of chapters are in my opinion really poor – basically they’re just a jumble of data-poor theorizing which is most likely just plain wrong. A main hypothesis presented in one of the chapters is frankly blatantly at odds with a lot of other evidence, some of which is even covered earlier in the same work, but the authors don’t even mention this in the coverage.

I don’t regret reading the book, but it’s not that great.”

Let’s say you have a book where Hrdy’s idea that it’s long been in the interest of human females to confuse paternity by various means, e.g. through extra-pair copulations, because such behaviour reduces the risk of infanticide (I’ve talked about these things before here on the blog, if you’re unfamiliar with this work and haven’t read my posts on the topics see for example this post) is covered, and where various other reasons why females may choose to engage in extra-pair copulations (e.g. ‘genetic benefits’) are also covered. Let’s say that in another, problematic, chapter of said book, a theory is proposed that ‘unfamiliar sperm’ (sperm from an individual the female has not had regular sex with before) leading to pregnancy is more likely to lead to preeclampsia in a female, a pregnancy complication which untreated will often lead to the abortion of the fetus. Let’s say the authors claim in that problematic chapter that the reason why females are more likely to develop preeclampsia in case of a pregnancy involving unfamiliar sperm is that such a pregnancy is likely to be a result of rape, and that the physiological mechanism leading to the pregnancy complication is an evolved strategy on part of the female, aimed at enabling her to exercise (post-copulatory) mate choice and reduce the negative fitness consequences of the rape. Let’s say the authors of the preeclampsia chapter/theory don’t talk at all about e.g. genetic benefits derived from extra-pair copulations which are not caused by rape but are engaged in willingly by the female because it’s in her reproductive interests to engage in them, and that the presumably common evolutionary female strategy of finding a semi-decent provider male as a long-term partner while also occasionally sleeping around with high-quality males (and low quality males – but only when not fertile (e.g. when pregnant…)) and have their children without the provider male knowing about it is not even mentioned. Assume the authors of the chapter seem to assume that getting a child by a male with unfamiliar sperm is always a bad idea.

Yeah, the above is what happened in this book, and it’s part of why it only gets two stars. These people are way too busy theorizing, and that specific theory is really poor – or at least the coverage of it was, as they don’t address the obvious issues which people reading the other chapters wouldn’t even have a hard time spotting. Kappeler et al. is a much better book, and it turns out that there was much less new stuff in this book than I’d thought – a lot of ‘the good stuff’ is also covered there.

It doesn’t help that many of the authors are systematically overestimating the extra-pair paternity rate by relying on samples/studies which are obviously deeply suspect due to selection bias. Not all of them goes overboard and claim the number is 10% or something like that, but many of them do – ‘the number is between 1-30%, with best estimates around 10%’ is a conclusion drawn in at least a couple of chapters. This is wrong. Only one contributor talking about these numbers come to the conclusion that the average number is likely to have been less than 5% in an evolutionary context (“Only very tentative conclusions about typical EPP [extra-pair paternity] rates throughout recent human history (e.g. in the past 50 000 years) can be drawn […] It seems reasonable to suggest that rates have typically been less than 10% and perhaps in most cases less than 5%. It also seems reasonable to suggest that they have probably also been variable across time and place, with some populations characterized by rates of 10% or higher.”). An idea worth mentioning in this context is that human behaviour can easily have been dramatically impacted by things which rarely happen now, because the reason why those things may be rare may well be that a lot of behaviour is aimed towards making sure it is rare and stays rare – this idea should be well known to people familiar with Hrdy’s thesis, and it also to me seems to apply to cuckoldry; cuckoldry may happen relatively infrequently, but perhaps the reason for this is that human males with female partners are really careful not to allow their partners to sleep around quite as much as their genetic code might like them to do. I mentioned in the coverage of Kappeler et al. that female sexual preferences change over the course of her menstrual cycle – they also talk about this in this book, but a related observation also made in the book is that males seem to be more vigilant and seem to intensify their level of mate guarding when their partner is ovulating. There’s probably a lot of stuff which goes on ‘behind the scenes’ which we humans are not aware of. Human behaviour is really complicated.

All these things said, there’s some really nice stuff in the book as well. The basic idea behind much of the coverage is that whereas females always know that their children are their children, males can never know for sure – and in a context where males may derive a fitness benefit from contributing to their offspring and a fitness loss by contributing to another male’s child, this uncertainty is highly relevant for how they might choose to behave in many contexts related to partnership dynamics. Many different aspects of the behaviour of human males is to some extent directed towards minimizing the risk of getting cuckolded and/or the risk of a partner in whom they have invested leaving him. They may choose to hide the female partner from competitors e.g. by monopolizing her time or by using violence to keep her from interacting with male competitors, they may signal to competitors that she is taken and/or perhaps that it may be costly to try to have sex with her (threats to other males, violence directed towards the competitor rather than the partner), they may try to isolate her socially by badmouthing her to potential competitors (e.g. male friends and acquaintances). On a more positive note males may also choose to do ‘nice things’ to keep the partner from leaving him, like ‘giving in to sexual requests’ and ‘performing sexual favors to keep her around’ (in at least one study, “men partnered to women who [were] more likely to be sexually unfaithful [were] also more likely to perform sexual inducements to retain their partners” – but before women reading this conclude that their incentives may look rather different from what they thought they did, it’s probably worth noting that the risk of abuse also goes up when the male thinks the partner might be unfaithful (see below)). If the first anti-cuckold approach, the mate-guarding strategy of trying to keep her from having sex with others, fails, then the male has additional options – one conceptualization in the book splits the strategy choices up into three groups; mate-guarding strategies, intra-vaginal strategies and post-partum strategies (in another chapter they distinguish among “preventative tactics, designed to minimize female infidelity; sperm-competition tactics, designed to minimize conception in the event of female infidelity; and differential paternal investment” – but the overall picture is reasonably similar). Intra-vaginal strategies relate to sperm competition and for example more specifically relate to e.g. the observation that a male may try to minimize the risk of being cuckolded after having been separated from the partner by having sex with the partner soon after they meet up again. A male may also increase the amount of sperm deposited during intercourse in such a context, compared to normal, and ‘sexual mechanics’ may also change as a function of cuckoldry risk (deeper thrusts and longer duration of sex if they’ve been separated for a while). There are five chapters on this stuff in the book, but I’ve limited coverage of this stuff because I don’t think it’s particularly interesting. Post-partum strategies naturally relate to strategies employed after the child has been born. Here the father may observe the child after it’s been born and then try to figure out if it looks like him/his family, and then adjust investment in the child based on how certain he is that he’s actually the father:

“There is growing evidence that human males are […] affected by […] evolutionary pressures to invest in offspring as a function of paternal certainty”, and “Burch and Gallup (2000) have shown that males spend less time with, invest fewer resources in, and are more likely to abuse ostensibly unrelated children than children they assume to be their genetic offspring. They also found that the less a male thinks a child (unrelated or genetic) looks like him, the worse he treats the child and the worse he views the relationship with that child.”

It’s worth mentioning that dividing the strategy set up into three, and exactly three, overall categories seem to me slightly artificial, also because some relevant behaviours may not fit very well into any of them; to take an example, “There is growing evidence that males who question their partner’s fidelity show an increase in spouse abuse during pregnancy, and the abuse is often directed toward the female’s abdomen” – this behavioural pattern relates to none of the three strategy categories mentioned, but also seems ‘relevant’. In general it’s important to observe that employment of a specific type of tactic does not necessarily preclude the employment of other tactics as well – as pointed out in the book:

“A male’s best strategy is to prevent female infidelity and, if he is unsuccessful in preventing female infidelity, he would benefit by attempting to prevent conception by a rival male. If he is unsuccessful in preventing conception by a rival male, he would benefit by adjusting paternal effort according to available paternity cues. The performance of one tactic does not necessitate the neglect of another tactic; indeed, a reproductively wise strategy would be to perform all three categories of anti-cuckoldry tactics”

There’s a lot of food for thought in the book. I’ve included some more detailed observations from the book below – in particular I’ve added some stuff closely related to what I believe people might normally term ‘red flags’ or similar in a relationship context. I’d say that enough research has been done on this kind of stuff for it to make a lot of sense for women to read some of it – in light of the evidence, there are certain types of male behaviours which should most definitely be considered strong warning signs that it may be a bad idea to engage with this individual. (I was annoyed that the book only dealt with male abuse, as there are quite a few female abusers as well, but I can’t really fault the authors for limiting coverage to male behaviours).

“Paternal investment in humans and many other species is facultatively expressed: it often benefits offspring but is not always necessary for their survival and thus the quantity and quality of human paternal investment often varies with proximate conditions […] The facultative expression of male parenting reflects the […] cost–benefit trade-offs as these relate to the current social and ecological contexts in which the male is situated. The degree of male investment (1) increases with increases in the likelihood that investment will be provided to his own offspring (i.e. paternity certainty), (2) increases when investment increases the survival and later reproductive prospects of offspring, and (3) decreases when there are opportunities to mate with multiple females. […] the conditional benefits of paternal investment in these species results in simultaneous cost–benefit trade-offs in females. Sometimes it is in the females’ best interest (e.g. when paired with an unhealthy male) to cuckold their partner and mate with higher-quality males […] As a result, women must balance the costs of reduced paternal investment or male retaliation against the benefits of cuckoldry; that is, having their children sired by a more fit man while having their social partner assist in the rearing of these children.”

“In several large but unrepresentative samples, 20–25% of adult women reported having had at least one extra-pair sexual relationship during their marriage […] Using a nationally representative sample in the USA, Wiederman (1997) found that 12% of adult women reported at least one extra-pair sexual relationship during their marriage, and about 2% reported such a relationship during the past 12 months; Treas and Giesen (2000) found similar percentages for another nationally representative sample. These may be underestimates, given that people are reluctant to admit to extra-pair relationships. In any case, the results indicate that some women develop simultaneous and multiple opposite-sex relationships, many of which become sexual and are unknown to their social partner […] The dynamics of these extra-pair relationships are likely to involve a mix of implicit (i.e. unconscious) and explicit (i.e. conscious) psychological processes (e.g. attention to symmetric facial features) and social strategies. […] the finding that attraction to extra-pair partners is influenced by hormonal fluctuations points to the importance of implicit mechanisms. […] The emerging picture is one in which women appear to have an evolved sensitivity to the proximate cues of men’s fitness, a sensitivity that largely operates automatically and implicitly and peaks around the time women ovulate. The implicit operation of these mechanisms enables women to assess the fitness of potential extra-pair partners without a full awareness that they are doing so. In this way, women are psychologically and socially attentive to the relationship with their primary partner and most of the time have no explicit motive to cuckold this partner. If their social partners monitor for indications of attraction to extra-pair men, which they often do […], then these cues are only emitted during a short time frame. Moreover, given that attraction to a potential extra-pair partner is influenced by hormonal mechanisms, often combined with some level of pre-existing and non-sexual emotional intimacy with the extra-pair male […], many of these women may have no intention of an extra-pair sexual relationship before it is initiated. Under these conditions, the dynamics of cuckoldry may involve some level of self deception on women’s part, a mechanism that facilitates their ability to keep the extra-pair relationship hidden from their social partners. […] As with women, men’s anti-cuckoldry biases almost certainly involve a mix of implicit processes and explicit behavioral strategies that can be directed toward their mates, toward potential rivals, and toward the evaluation of the likely paternity of children born to their partners”

“Males have evolved psychological adaptations that produce mate guarding and jealousy […] to reduce or to prevent a mate from being inseminated by another male. Recent evidence suggests that males maximize the utility of their mateguarding strategies by implementing them at ovulation, a key reproductive time in a female’s menstrual cycle […]. Further, jealousy appears to fluctuate with a man’s mate value and, hence, risk of cuckoldry. Brown and Moore (2003), for example, found that males who were less symmetrical were significantly more jealous. These and other data suggest that jealousy has evolved as a means by which males can attempt to deter extra-pair copulations […] When triggered, jealousy often results in a variety of behavioral responses, including male-on-female aggression […], divorce […], the monitoring and attempted control of the social and sexual behavior of their partners […], enhancement of their attractiveness as a mate […], and the monitoring of and aggression toward actual or perceived sexual rivals […]. In total, these behaviors encompass tactics that function to ensure, through coercion or enticement, that their reproductive investment and that of their mate is directed toward the man’s biological children. […] One of the more common behavioral responses to relationship jealousy is mate guarding. For men this involves reducing their partner’s opportunity to mate with other men.”

“Cuckoldry is a reproductive cost inflicted on a man by a woman’s sexual infidelity or temporary defection from her regular long-term relationship. Ancestral men also would have incurred reproductive costs by a long-term partner’s permanent defection from the relationship. These costs include loss of the time, effort, and resources the man has spent attracting his partner, the potential misdirection of his resources to a rival’s offspring, and the loss of his mate’s investment in offspring he may have had with her in the future […] Expressions of male sexual jealousy historically may have been functional in deterring rivals from mate poaching […] and deterring a mate from a sexual infidelity or outright departure from the relationship […] Buss (1988) categorized the behavioral output of jealousy into different ‘‘mate-retention’’ tactics, ranging from vigilance over a partner’s whereabouts to violence against rivals […] Performance of these tactics is assessed by the Mate Retention Inventory (MRI[)] […] Buss’s taxonomy (1988) partitioned the tactics into two general categories: intersexual manipulations and intrasexual manipulations. Intersexual manipulations include behaviors directed toward one’s partner, and intrasexual manipulations include behaviors directed toward same-sex rivals. Intersexual manipulations include direct guarding, negative inducements, and positive inducements. Intrasexual manipulations include public signals of possession. […] Unfortunately, little is known about which specific acts and tactics of men’s mate-retention efforts are linked with violence. The primary exception is the study by Wilson, Johnson, and Daly (1995), which identified several predictors of partner violence – notably, verbal derogation of the mate and attempts at sequestration such as limiting access to family, friends, and income.”

“Tactics within the direct guarding category of the MRI include vigilance, concealment of mate, and monopolization of time. An exemplary act for each tactic is, respectively, ‘‘He dropped by unexpectedly to see what she was doing,’’ ‘‘He refused to introduce her to his same-sex friends,’’ and ‘‘He monopolized her time at the social gathering.’’ Each of these tactics implicates what Wilson and Daly (1992) term ‘‘male sexual proprietariness,’’ which refers to the sense of entitlement men sometimes feel that they have over their partners […] Wilson et al. (1995) demonstrated that violence against women is linked closely to their partners’ autonomy-limiting behaviors. Women who affirmed items such as ‘‘He is jealous and doesn’t want you to talk to other men,’’ were more than twice as likely to have experienced serious violence by their partners.” [What was the base rate? I find myself asking. But it’s still relevant knowledge.] […] Not all mate-retention tactics are expected to predict positively violence toward partners. Some of these tactics include behaviors that are not in conflict with a romantic partner’s interests and, indeed, may be encouraged and welcomed by a partner […] Holding his partner’s hand in public, for example, may signal to a woman her partner’s commitment and devotion to her. […] Tactics within the public signals of possession category include verbal possession signals (e.g. ‘‘He mentioned to other males that she was taken’’), physical possession signals (e.g. ‘‘He held her hand when other guys were around’’), and possessive ornamentation (e.g. ‘‘He hung up a picture of her so others would know she was taken’’).”

“The current studies examined how mate-retention tactics are related to violence in romantic relationships, using the reports of independent samples of several hundred men and women in committed, romantic relationships […], and using the reports of 107 married men and women […] With few exceptions, we found the same pattern of results using three independent samples. Moreover, these samples were not just independent, but provided different perspectives (the male perpetrator’s, the female victim’s, and a combination of the two) on the same behaviors – men’s mate-retention behaviors and men’s violence against their partners. We identified overlap between the best predictors of violence across the studies. For example, men’s use of emotional manipulation, monopolization of time, and punish mate’s infidelity threat are among the best predictors of female-directed violence, according to independent reports provided by men and women, and according to reports provided by husbands and their wives. The three perspectives also converged on which tactics are the weakest predictors of relationship violence. For example, love and care and resource display are among the weakest predictors of female-directed violence. […] The tactic of emotional manipulation was the highest-ranking predictor of violence in romantic relationships in study 1, and the second highest-ranking predictor in studies 2 and 3. The items that comprise the emotional manipulation tactic include, ‘‘He told her he would ‘die’ if she ever left,’’ and ‘‘He pleaded that he could not live without her.’’ Such acts seem far removed from those that might presage violence. […] Monopolization of time also ranked as a strong predictor of violence across the three studies. Example acts included in this tactic are ‘‘He spent all his free time with her so that she could not meet anyone else’’ and ‘‘He would not let her go out without him.’’ […] The acts ‘‘Dropped by unexpectedly to see what my partner was doing’’ and ‘‘Called to make sure my partner was where she said she would be’’ are the third and fifth highest-ranking predictors of violence, respectively. These acts are included in the tactic of vigilance, which is the highest-ranking tactic-level predictor of violence in study 3. Given that (1) two of the top five actlevel predictors of violence are acts of vigilance, (2) the numerically best tactic-level predictor of violence is vigilance, and (3) seven of the nine acts included within the vigilance tactic are correlated significantly with violence […], a man’s vigilance over his partner’s whereabouts is likely to be a key signal of his partner-directed violence. […] Wilson et al. (1995) found that 40% of women who affirmed the statement ‘‘He insists on knowing who you are with and where you are at all times’’ reported experiencing serious violence at the hands of their husbands.”

“Relative to women’s reports of their partners’ behavior, men self-reported more frequent use of intersexual negative inducements, positive inducements, and controlling behavior. Although not anticipated, the sex difference in reported frequency of controlling behaviors is not surprising upon examination of the acts included in the CBI [Controlling Behavior Index]. More than half of the acts do not require the woman’s physical presence or knowledge, for example ‘‘Deliberately keep her short of money’’ and ‘‘Check her movements.’’ In addition, such acts might be more effective if the woman is not aware of their occurrence. […] Increased effort devoted to mate retention is predicted to occur when the adaptive problems it was designed to solve are most likely to be encountered – when a mate is particularly desirable, when there exist mate poachers, when there is a mate-value discrepancy, and when the partner displays cues to infidelity or defection”

“Although sometimes referred to as marital rape, spouse rape, or wife rape,we use the term forced in-pair copulation (FIPC) to refer to the forceful act of sexual intercourse by a man against his partner’s will. […] FIPC is not performed randomly […] FIPC reliably occurs immediately after extra-pair copulations, intrusions by rival males, and female absence in many species of waterfowl […] and other avian species […] FIPC in humans often follow[s] accusations of female infidelity”

November 16, 2014