nhaliday + trees   22

Sacred text as cultural genome: an inheritance mechanism and method for studying cultural evolution: Religion, Brain & Behavior: Vol 7, No 3
Yasha M. Hartberg & David Sloan Wilson

Any process of evolution requires a mechanism of inheritance for the transmission of information across generations and the expression of phenotypes during each generation. Genetic inheritance mechanisms have been studied for over a century but mechanisms of inheritance for human cultural evolution are far less well understood. Sacred religious texts have the properties required for an inheritance system. They are replicated across generations with high fidelity and are transcribed into action every generation by the invocation and interpretation of selected passages. In this article we borrow concepts and methods from genetics and epigenetics to study the “expressed phenotypes” of six Christian churches that differ along a conservative–progressive axis. Their phenotypic differences, despite drawing upon the same sacred text, can be explained in part by differential expression of the sacred text. Since the invocation and interpretation of sacred texts are often well preserved, our methods allow the expressed phenotypes of religious groups to be studied at any time and place in history.
study  interdisciplinary  bio  sociology  cultural-dynamics  anthropology  religion  christianity  theos  protestant-catholic  politics  ideology  correlation  organizing  institutions  analogy  genetics  genomics  epigenetics  comparison  culture  pdf  piracy  density  flexibility  noble-lie  deep-materialism  new-religion  universalism-particularism  homo-hetero  hypocrisy  group-selection  models  coordination  info-dynamics  evolution  impact  left-wing  right-wing  time  tradition  spreading  sanctity-degradation  coalitions  trees  usa  social-capital  hari-seldon  wisdom  the-basilisk  frequency 
10 weeks ago by nhaliday
Sequence Modeling with CTC
A visual guide to Connectionist Temporal Classification, an algorithm used to train deep neural networks in speech recognition, handwriting recognition and other sequence problems.
acmtariat  techtariat  org:bleg  nibble  better-explained  machine-learning  deep-learning  visual-understanding  visualization  analysis  let-me-see  research  sequential  audio  classification  model-class  exposition  language  acm  approximation  comparison  markov  iteration-recursion  concept  atoms  distribution  orders  DP  heuristic  optimization  trees  greedy  matching  gradient-descent 
december 2017 by nhaliday
Ancient Admixture in Human History
- Patterson, Reich et al., 2012
Population mixture is an important process in biology. We present a suite of methods for learning about population mixtures, implemented in a software package called ADMIXTOOLS, that support formal tests for whether mixture occurred and make it possible to infer proportions and dates of mixture. We also describe the development of a new single nucleotide polymorphism (SNP) array consisting of 629,433 sites with clearly documented ascertainment that was specifically designed for population genetic analyses and that we genotyped in 934 individuals from 53 diverse populations. To illustrate the methods, we give a number of examples that provide new insights about the history of human admixture. The most striking finding is a clear signal of admixture into northern Europe, with one ancestral population related to present-day Basques and Sardinians and the other related to present-day populations of northeast Asia and the Americas. This likely reflects a history of admixture between Neolithic migrants and the indigenous Mesolithic population of Europe, consistent with recent analyses of ancient bones from Sweden and the sequencing of the genome of the Tyrolean “Iceman.”
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november 2017 by nhaliday
Biopolitics | West Hunter
I have said before that no currently popular ideology acknowledges well-established results of behavioral genetics, quantitative genetics, or psychometrics. Or evolutionary psychology.

What if some ideology or political tradition did? what could they do? What problems could they solve, what capabilities would they have?

Various past societies knew a few things along these lines. They knew that there were significant physical and behavioral differences between the sexes, which is forbidden knowledge in modern academia. Some knew that close inbreeding had negative consequences, which knowledge is on its way to the forbidden zone as I speak. Some cultures with wide enough geographical experience had realistic notions of average cognitive differences between populations. Some people had a rough idea about regression to the mean [ in dynasties], and the Ottomans came up with a highly unpleasant solution – the law of fratricide. The Romans, during the Principate, dealt with the same problem through imperial adoption. The Chinese exam system is in part aimed at the same problem.


At least some past societies avoided the social patterns leading to the nasty dysgenic trends we are experiencing today, but for the most part that is due to the anthropic principle: if they’d done something else you wouldn’t be reading this. Also to between-group competition: if you fuck your self up when others don’t, you may be well be replaced. Which is still the case.

If you were designing an ideology from scratch you could make use of all of these facts – not that thinking about genetics and selection hands you the solution to every problem, but you’d have more strings to your bow. And, off the top of your head, you’d understand certain trends that are behind the mountains of Estcarp, for our current ruling classes : invisible and unthinkable, That Which Must Not Be Named. .

“The closest…s the sort of libertarianism promulgated by Charles Murray”
Not very close..
A government that was fully aware of the implications and possibilities of human genetics, one that had the usual kind of state goals [ like persistence and increased power] , would not necessarily be particularly libertarian.

And giving tax breaks to college-educated liberals to have babies wouldn’t appeal much to Trump voters, methinks.

It might be worth making a reasonably comprehensive of the facts and preferences that a good liberal is supposed to embrace and seem to believe. You would have to be fairly quick about it, before it changes. Then you could evaluate about the social impact of having more of them.

Rise and Fall: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/
Every society selects for something: generally it looks as if the direction of selection pressue is more or less an accident. Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this. I mean, they would have known how, if they’d wanted to, just as they knew how to select for destriers, coursers, and palfreys. It was still possible to know such things in the Middle Ages, because Harvard did not yet exist.

A rising empire needs quality human capital, which implies that at minimum that budding imperial society must not have been strongly dysgenic. At least not in the beginning. But winning changes many things, possibly including selective pressures. Imagine an empire with substantial urbanization, one in which talented guys routinely end up living in cities – cities that were demographic sinks. That might change things. Or try to imagine an empire in which survival challenges are greatly reduced, at least for elites, so that people have nothing to keep their minds off their minds and up worshiping Magna Mater. Imagine that an empire that conquers a rival with interesting local pathogens and brings some of them home. Or one that uses up a lot of its manpower conquering less-talented subjects and importing masses of those losers into the imperial heartland.

If any of those scenarios happened valid, they might eventually result in imperial decline – decline due to decreased biological capital.

Right now this is speculation. If we knew enough about the GWAS hits for intelligence, and had enough ancient DNA, we might be able to observe that rise and fall, just as we see dysgenic trends in contemporary populations. But that won’t happen for a long time. Say, a year.

hmm: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100350
“Although nations and empires in the past could have decided to select men for bravery or intelligence, there’s not much sign that anyone actually did this.”

Maybe the Chinese imperial examination could effectively have been a selection for intelligence.
Nope. I’ve modelled it: the fraction of winners is far too small to have much effect, while there were likely fitness costs from the arduous preparation. Moreover, there’s a recent
paper [Detecting polygenic adaptation in admixture graphs] that looks for indications of when selection for IQ hit northeast Asia: quite a while ago. Obvious though, since Japan has similar scores without ever having had that kind of examination system.

decline of British Empire and utility of different components: https://westhunt.wordpress.com/2018/01/18/rise-and-fall/#comment-100390
Once upon a time, India was a money maker for the British, mainly because they appropriate Bengali tax revenue, rather than trade. The rest of the Empire was not worth much: it didn’t materially boost British per-capita income or military potential. Silesia was worth more to Germany, conferred more war-making power, than Africa was to Britain.
If you get even a little local opposition, a colony won’t pay for itself. I seem to remember that there was some, in Palestine.
Angels from on high paid for the Boer War.

You know, someone in the 50’s asked for the numbers – how much various colonies cost and how much they paid.

Turned out that no one had ever asked. The Colonial Office had no idea.
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october 2017 by nhaliday
Anatomy of an SQL Index: What is an SQL Index
“An index makes the query fast” is the most basic explanation of an index I have ever seen. Although it describes the most important aspect of an index very well, it is—unfortunately—not sufficient for this book. This chapter describes the index structure in a less superficial way but doesn't dive too deeply into details. It provides just enough insight for one to understand the SQL performance aspects discussed throughout the book.

B-trees, etc.
techtariat  tutorial  explanation  performance  programming  engineering  dbs  trees  data-structures  nibble 
september 2017 by nhaliday
Fundamental Theorems of Evolution: The American Naturalist: Vol 0, No 0
I suggest that the most fundamental theorem of evolution is the Price equation, both because of its simplicity and broad scope and because it can be used to derive four other familiar results that are similarly fundamental: Fisher’s average-excess equation, Robertson’s secondary theorem of natural selection, the breeder’s equation, and Fisher’s fundamental theorem. These derivations clarify both the relationships behind these results and their assumptions. Slightly less fundamental results include those for multivariate evolution and social selection. A key feature of fundamental theorems is that they have great simplicity and scope, which are often achieved by sacrificing perfect accuracy. Quantitative genetics has been more productive of fundamental theorems than population genetics, probably because its empirical focus on unknown genotypes freed it from the tyranny of detail and allowed it to focus on general issues.
study  essay  bio  evolution  population-genetics  fisher  selection  EGT  dynamical  exposition  methodology  🌞  big-picture  levers  list  nibble  article  chart  explanation  clarity  trees  ground-up  ideas 
march 2017 by nhaliday
Information Processing: Evidence for (very) recent natural selection in humans
height (+), infant head circumference (+), some biomolecular stuff, female hip size (+), male BMI (-), age of menarche (+, !!), and birth weight (+)

Strong selection in the recent past can cause allele frequencies to change significantly. Consider two different SNPs, which today have equal minor allele frequency (for simplicity, let this be equal to one half). Assume that one SNP was subject to strong recent selection, and another (neutral) has had approximately zero effect on fitness. The advantageous version of the first SNP was less common in the far past, and rose in frequency recently (e.g., over the last 2k years). In contrast, the two versions of the neutral SNP have been present in roughly the same proportion (up to fluctuations) for a long time. Consequently, in the total past breeding population (i.e., going back tens of thousands of years) there have been many more copies of the neutral alleles (and the chunks of DNA surrounding them) than of the positively selected allele. Each of the chunks of DNA around the SNPs we are considering is subject to a roughly constant rate of mutation.

Looking at the current population, one would then expect a larger variety of mutations in the DNA region surrounding the neutral allele (both versions) than near the favored selected allele (which was rarer in the population until very recently, and whose surrounding region had fewer chances to accumulate mutations). By comparing the difference in local mutational diversity between the two versions of the neutral allele (should be zero modulo fluctuations, for the case MAF = 0.5), and between the (+) and (-) versions of the selected allele (nonzero, due to relative change in frequency), one obtains a sensitive signal for recent selection. See figure at bottom for more detail. In the paper what I call mutational diversity is measured by looking at distance distribution of singletons, which are rare variants found in only one individual in the sample under study.

The 2,000 year selection of the British: http://www.unz.com/gnxp/the-2000-year-selection-of-the-british/

Detection of human adaptation during the past 2,000 years: http://www.biorxiv.org/content/early/2016/05/07/052084

The key idea is that recent selection distorts the ancestral genealogy of sampled haplotypes at a selected site. In particular, the terminal (tip) branches of the genealogy tend to be shorter for the favored allele than for the disfavored allele, and hence, haplotypes carrying the favored allele will tend to carry fewer singleton mutations (Fig. 1A-C and SOM).

To capture this effect, we use the sum of distances to the nearest singleton in each direction from a test SNP as a summary statistic (Fig. 1D).

Figure 1. Illustration of the SDS method.

Figure 2. Properties of SDS.

Based on a recent model of European demography [25], we estimate that the mean tip length for a neutral sample of 3,000 individuals is 75 generations, or roughly 2,000 years (Fig. 2A). Since SDS aims to measure changes in tip lengths of the genealogy, we conjectured that it would be most likely to detect selection approximately within this timeframe.

Indeed, in simulated sweep models with samples of 3,000 individuals (Fig. 2B,C and fig. S2), we find that SDS focuses specifically on very recent time scales, and has equal power for hard and soft sweeps within this timeframe. At individual loci, SDS is powered to detect ~2% selection over 100 generations. Moreover, SDS has essentially no power to detect older selection events that stopped >100 generations before the present. In contrast, a commonly-used test for hard sweeps, iHS [12], integrates signal over much longer timescales (>1,000 generations), has no specificity to the more recent history, and has essentially no power for the soft sweep scenarios.

Catching evolution in the act with the Singleton Density Score: http://www.molecularecologist.com/2016/05/catching-evolution-in-the-act-with-the-singleton-density-score/
The Singleton Density Score (SDS) is a measure based on the idea that changes in allele frequencies induced by recent selection can be observed in a sample’s genealogy as differences in the branch length distribution.

You don’t need a weatherman: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/
You can do a million cool things with this method. Since the effective time scale goes inversely with sample size, you could look at evolution in England over the past 1000 years or the past 500. Differencing, over the period 1-1000 AD. Since you can look at polygenic traits, you can see whether the alleles favoring higher IQs have increased or decreased in frequency over various stretches of time. You can see if Greg Clark’s proposed mechanism really happened. You can (soon) tell if creeping Pinkerization is genetic, or partly genetic.

You could probably find out if the Middle Easterners really have gotten slower, and when it happened.

Looking at IQ alleles, you could not only show whether the Ashkenazi Jews really are biologically smarter but if so, when it happened, which would give you strong hints as to how it happened.

We know that IQ-favoring alleles are going down (slowly) right now (not counting immigration, which of course drastically speeds it up). Soon we will know if this was true while Russia was under the Mongol yoke – we’ll know how smart Periclean Athenians were and when that boost occurred. And so on. And on!


“The pace has been so rapid that humans have changed significantly in body and mind over recorded history."

bicameral mind: https://westhunt.wordpress.com/2016/05/08/you-dont-need-a-weatherman/#comment-78934

Chinese, Koreans, Japanese and Ashkenazi Jews all have high levels of myopia. Australian Aborigines have almost none, I think.

I expect that the fall of all great empires is based on long term dysgenic trends. There is no logical reason why so many empires and civilizations throughout history could grow so big and then not simply keep growing, except for dysgenics.
I can think of about twenty other possible explanations off the top of my head, but dysgenics is a possible cause.
I agree with DataExplorer. The largest factor in the decay of civilizations is dysgenics. The discussion by R. A. Fisher 1930 p. 193 is very cogent on this matter. Soon we will know for sure.
Sometimes it can be rapid. Assume that the upper classes are mostly urban, and somewhat sharper than average. Then the Mongols arrive.
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august 2016 by nhaliday
soft question - How do you not forget old math? - MathOverflow
Terry Tao:
I find that blogging about material that I would otherwise forget eventually is extremely valuable in this regard. (I end up consulting my own blog posts on a regular basis.) EDIT: and now I remember I already wrote on this topic: terrytao.wordpress.com/career-advice/write-down-what-youve-d‌​one

The only way to cope with this loss of memory I know is to do some reading on systematic basis. Of course, if you read one paper in algebraic geometry (or whatever else) a month (or even two months), you may not remember the exact content of all of them by the end of the year but, since all mathematicians in one field use pretty much the same tricks and draw from pretty much the same general knowledge, you'll keep the core things in your memory no matter what you read (provided it is not patented junk, of course) and this is about as much as you can hope for.

Relating abstract things to "real life stuff" (and vice versa) is automatic when you work as a mathematician. For me, the proof of the Chacon-Ornstein ergodic theorem is just a sandpile moving over a pit with the sand falling down after every shift. I often tell my students that every individual term in the sequence doesn't matter at all for the limit but somehow together they determine it like no individual human is of any real importance while together they keep this civilization running, etc. No special effort is needed here and, moreover, if the analogy is not natural but contrived, it'll not be helpful or memorable. The standard mnemonic techniques are pretty useless in math. IMHO (the famous "foil" rule for the multiplication of sums of two terms is inferior to the natural "pair each term in the first sum with each term in the second sum" and to the picture of a rectangle tiled with smaller rectangles, though, of course, the foil rule sounds way more sexy).

One thing that I don't think the other respondents have emphasized enough is that you should work on prioritizing what you choose to study and remember.

Timothy Chow:
As others have said, forgetting lots of stuff is inevitable. But there are ways you can mitigate the damage of this information loss. I find that a useful technique is to try to organize your knowledge hierarchically. Start by coming up with a big picture, and make sure you understand and remember that picture thoroughly. Then drill down to the next level of detail, and work on remembering that. For example, if I were trying to remember everything in a particular book, I might start by memorizing the table of contents, and then I'd work on remembering the theorem statements, and then finally the proofs. (Don't take this illustration too literally; it's better to come up with your own conceptual hierarchy than to slavishly follow the formal hierarchy of a published text. But I do think that a hierarchical approach is valuable.)

Organizing your knowledge like this helps you prioritize. You can then consciously decide that certain large swaths of knowledge are not worth your time at the moment, and just keep a "stub" in memory to remind you that that body of knowledge exists, should you ever need to dive into it. In areas of higher priority, you can plunge more deeply. By making sure you thoroughly internalize the top levels of the hierarchy, you reduce the risk of losing sight of entire areas of important knowledge. Generally it's less catastrophic to forget the details than to forget about a whole region of the big picture, because you can often revisit the details as long as you know what details you need to dig up. (This is fortunate since the details are the most memory-intensive.)

Having a hierarchy also helps you accrue new knowledge. Often when you encounter something new, you can relate it to something you already know, and file it in the same branch of your mental tree.
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june 2016 by nhaliday

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