Previously: 2011; 2012-2013; 2013-2014; 2014-2015

"When I was one-and-twenty / I heard a wise man say, / 'Give crowns and pounds and guineas / But not your heart away; / Give pearls away and rubies / But keep your fancy free.' / But I was one-and-twenty, / No use to talk to me."

My past year of completed writings, sorted by topic:

Genetics:

• Embryo selection for intelligence cost-benefit analysis
  • meta-analysis of intelligence GCTAs, limits set by measurement error, current polygenic scores, possible gains with current IVF procedures, the benefits of selection on multiple complex traits, the possible annual value in the USA of selection & value of larger GWASes, societal consequences of various embryo selection scenarios, embryo count versus polygenic scores as limiting factors, comparison with iterated embryo selection, limits to total gains from iterated embryo selection etc.
• Wikipedia article on Genome-wide complex trait analysis (GCTA)

AI:

• Computational Complexity vs the Singularity
• Adding metadata to an RNN for mimicking individual author style
• Armstrong’s AI control problem: Reinforce.js demo

Biology:

• vitamin D & metformin for life-extension: cost-benefit analysis

Statistics:

• Candy Japan new packaging decision analysis
• “The Power of Twins: Revisiting Student’s Scottish Milk Experiment Example”
• Genius Revisited: Critiquing the Value of High IQ Elementary Schools
• Inferring mean ethnic IQs from very high IQ samples like TIP/SMPY

Cryptography:

• shell scripts for easy cryptographic timestamping

Misc:

• Newton’s comet apocalypse system

gwern.net itself has remained largely stable (some CSS fixes and image size changes); I continue to use Patreon and send out my newsletters.

I'll admit it: I am confused about genetics and heritability. Not about the results of the various twin studies - Scott summarises them as "~50% of the variation is heritable and ~50% is due to non-shared environment", which seems generally correct.

But I am confused about what this means in practice, due to arguments like "contacts are very important for business success, rich people get much more contacts than poor people, yet business success is strongly correlated with genetic parent wealth" and such. Assuming that genetics strongly determines... most stuff... goes against so many things we know or think we know about how the world works. And by "we" I mean lots of different people with lots of different political views - genetic determinism means, for instance, that current variations in regulation and taxes are pretty unimportant for individual outcomes.

Now, there are many caveats about the genetic results, particularly that they measure the variance of a factor rather than its absolute importance (and hence you get results like variation in nutrition being almost invisible as an explanation for variation in height), but it's still hard to figure out what this all means.

Then we have Scott's latest post, which points out that "non-shared environment" is not the same as "nurture", since it includes, for instance, dumb luck.

However, "heritable" is not the same as as "nature", either. For instance, sexism and racial prejudices, if they are widespread, come under the "heritable" effects rather than the "environment" ones. And then it gets even more confusing.

Widespread prejudice is not "environment". Rarer prejudice is.

For instance, imagine that we lived in a very sexist society where women were not allowed to work at all. Then there would be an extremely high, almost perfect, correlation between "having a Y chromosome" and "having a job". But this would obviously be susceptible to a cultural fix.

Obviously racial effects can have the same effect. It covers anything visible. So a high heritability is compatible with genetics being a cause of competence, and/or prejudice against visible genetic characteristics being important ("Our results indicate that we either live in a meritocracy or a hive of prejudice!").

Note that as prejudices get less widespread, they move from showing up on the genetic variation, to showing up in the environmental variation side. So widespread prejudices create a "nature" effect, rarer ones create a "nurture" effect. Evenly reducing the magnitude of a prejudice, however, doesn't change the side it will show up on.

Positional genetic goods: Beauty... and IQ?

Let's zoom in on one of those visible genetic characteristics: beauty. As Robin Hanson is fond of pointing out, beautiful people are more successful, and are judged as more competent and cooperative than they actually are. Therefore if we have a gene that increases both beauty and IQ, we would expect it's impact on success to be high. In the presence of such a gene, the correlation between IQ and success would be higher than it should objectively be. This suggest a (small) note of caution on the "mutation load" hypotheses; if reducing mutation load increases factors such as beauty, then we would expect increased success without necessarily increased competence.

But is it possible that IQ itself is in part a positional good? Consider that success doesn't just depend on competence, but on social skills, ability to present yourself well in an interview, and how managers and peers judge you. If IQ affects or covaries with one or another of those skills, then we would be overemphasising the importance of IQ in competence. Thus attempts to genetically boost IQ could give less impact than expected. The person whose genome was changed would benefit, but at the (partial) expense of everyone else.

Do people know of experiments (or planned experiments) that disentangle these issues?

http://blog.23andme.com/23andme-and-you/a-new-23andme-experience/

Looks like they were finally able to work out something with the FDA, and are back up and running. On the one hand, I'm very excited about the return of personalized genetic testing, but on the other hand I'm disappointed that their price doubled to $199. I was going to get kits for my 4-member family for Christmas, but that won't be feasible now.

Another interesting release from 23andme that came out at the same time is their [transparency report](https://www.23andme.com/transparency-report/), which shows how many requests from law enforcement they have gotten for customer DNA access, and what percentage they have gone through with.

Epistemic status: Wild guesswork based on half-understood studies from way outside my field. More food for thought than trustworthy information.

tl/dr: Estimates of familial relatedness between people should help promote empathy, so here's how to make them - and might this be useful for Effective Altruism?

The why

I don't know how it is for you, but for me, knowing I'm related to someone makes a specific emotional difference. Scenario: I'm at a big family-and-friends get-together, I meet a guy, we get along. (For clarity, let's assume no sexual tension.) And then we're told we're third cousins via some weird aunt. From the moment I'm told, I feel different towards him. Firm, forthcoming, obliging. Some kind of basic kinship emotion, I guess, noticeable when it shifts on these rare occasions but basically going on, deep down in System 1, every time that emailing a remote uncle feels different from emailing a similarly remote associate.

Meanwhile, my System 2 has heard that all humans are at least 50th degree cousins and likes to point out everyone I've ever had sex with was a cousin of some degree. That similarly remote associate where I don't have that kinship feeling - he's a relative too, just a more distant one. And when I notice that, I get a bit of that kinship feeling too...

With me so far? Here's my thesis: the two human feelings of kinship and empathy are closely connected, and to make one of them more salient is to increase the salience of the other.

I don't think this has been tested properly. A. J. Jacobs, who is running a huge family reunion event in New York this summer, said "some ambitious psychology professor needs to conduct a study about whether we deliver lower electrical shocks to people if we know we’re related" and I think he's exactly right.

Has anybody here not heard of circles of empathy? They're a concept invented by the very cool 19th century rationalist William Edward Hartpole Lecky in his "History of European Morals From Augustus to Charlemagne". Peter Singer summarizes it as follows:

Lecky wrote of human concern as an expanding circle which begins with the individual, then embraces the family and ‘soon the circle... includes first a class, then a nation, then a coalition of nations, then all humanity, and finally, its influence is felt in the dealings of man [sic] with the animal world’.

There's more to read about this in Peter Singer's "The Expanding Circle" or Steven Pinker's "The Better Angels of Our Nature", but what strikes me about it is contained in that single sentence: The expansion that is described tracks actual genetic relatedness, or Consanguinity. The list goes down a gradient of (expected) genetic relatedness. This makes the size of the circle of empathy seem to depend on a threshold of how related you need to be to someone in order to care about them.

(Note that Becky published his "History of European Morals" - with this inclusion of concern about animals - in 1869, i.e. only ten years after the publication of "On the Origin of Species". There was some animal rights legislation before Darwin, but animal rights as a movement only arose after we knew animals to be our relatives.)

On the other hand, those who would promote empathy have always relied on familial vocabulary, chiefly "brother" and "sister", to refer to people who evidently weren't actual brothers or sisters. Martin Luther King, Jesus, the Buddha, Mandela, Gandhi, they all do this. So maybe it works a bit. Maybe it helps trigger that emotional kinship response and that somehow helps people get along.

Now to see how these emotional responses would arise, we could discuss reciprocal altruism and gene-centered Darwinism and whatnot, but "The Selfish Gene" is required reading anyway and I assume you've done your homework. I'd like to instead go to the second part of my thesis, the one about increasing salience.

Recognizing you're related to somebody does something. (Especially if you have an incest fetish, of course.) I propose that whatever it does increases empathy. And empathy might not be a categorically good thing, but it comes pretty close, at least until you extend it to all food groups. So maybe we could increase empathy among people by pointing out their relatedness. And maybe we can do this more vividly, more strikingly than by simply saying "we're all descended from apes, so we're all related, duh" or by boring the non-nerd majority to death with talk of human genetic clustering and fixation indexes.

So I'd like to revisit that "brothers and sisters" thing from MLK and those other guys. Maybe they shouldn't have used figurative language. Maybe a more lasting feeling of kinship can be created by literal language: By telling people how related they are. Detailed ancestry information is being collected at various Wiki-like sites, but even assuming they'll grow and become less US-centric, they don't go back very far (except around very famous people) and what came before remains guesswork. So let's do some Fermi-ish estimates.

The how

The drop dead amazing Nature Article Modelling the recent common ancestry of all living humans is way too careful and scientific to put an exact number on how long ago the last common ancestor lived, unfortunately. But the mean date their simulations come up with is 1415 BC, which will be approximately 120 generations ago, so let's say really remote people like the Karitiana tribe are, at most, something like 125th degree cousins of all of us. So that's a useful upper bound for the degree of cousinhood between any two arbitrary humans, such as you and me.

The lower bound could be something like 3 - if you and I were that closely related, we'd share a great-great-grandparent and could probably ascertain rather than guess that. With fairly extensive genealogy, the lower bound might go up to around 5 - which is the level where you need to look at 64 ancestors for each of us who lived in the middle of the 19th century and failed to use Facebook. We'd find it hard to ascertain whether your great-great-great-great-grandmother Mary was identical to mine.

There are a lot of special cases where the lower bound can be higher. If both people involved know their family more than 3 generations were deep-rooted peasant folks from two distinct populations, the history books might tell them how many centuries further back are very unlikely to contain a common ancestor. (This will of course be much rarer among descendants of immigrants, like Americans, than it is for citizens of older or more rural countries.) If they're of different ethnicities, castes or classes that wouldn't normally date each other 80 years ago, the lower bound should probably go up a few more generations. If both people involved are Icelanders, they can just look up their last common ancestor in the comprehensive Icelandic family tree. But let's assume you and I don't have any of these special cases, and we're stuck with a lower bound of 3. Now between that and 125, how do we narrow it down?

Turns out the authors of that gorgeous Nature paper don't hand out access to their simulations to random dudes who just email them. So lets see how far we get on the hard way.

In a completely random mating model (where people do not tend to mate with people who happen to live near them, i.e. happen to be descendants of the same people), your number of ancestors doubles with every generation you go back, in a sort of ancestor tree that grows backwards. We're looking for the point where the two ancestor trees first meet. If we assume generations have homogenous lengths (which implies further simplifying assumptions like moms and dads are the same age) and further assume only people from within the same generation have kids with each other, cousins of the Nth degree have a common ancestor N+1 generations ago, and each has 2^N+1 ancestors belonging to that generation.

This means that for you and me to be, say, 15th degree cousins, our two sets of 2¹⁵⁺¹=65536 ancestors have to have one person in common, some 480 years ago, assuming 30 years as mean parenthood age. Of course we each probably have less than 65536 unique ancestors due to... um... "reticulations".

But empirically, it seems that "a pair of modern Europeans living in neighboring populations share around 2–12 genetic common ancestors from the last 1,500 years" and even individuals from opposite ends of Europe will normally have common ancestors if you search back 3000 years (source). That isn't what you get from the simplistic model above - the numbers of ancestors it calculates exceed the world population less than 32 generations (about 800 years) ago. The empirical genetic data from this paper would indicate that it is likely the median first common ancestor between me and anybody in central Europe is somewhere like 1200 years (or 40 generations) ago and any two people anywhere in Europe would probably be at most 100th degree cousins.

Around 600 years ago is a good time to look at, because that's shortly before intercontinental travel started to intricately connect all regions of the world, including genetically. If most of your 600-years-ago ancestors lived outside Europe, you and I might still be <25 degrees cousins - maybe you have some ancestor who left for Europe 300 years ago, leaving siblings behind (your ancestors) and having kids in Europe (mine). Or vice versa. But that kind of thing is unlikely and since we're doing rough estimates I suggest we round that probability down to zero.

In genetic studies, no other continent is anywhere near as well-studied as Europe, so I guess we'll just have to roll with it and assume that other places are about the same as this paper found and the nice exponential drop-off with geographic distance that's the case in Europe is also the case elsewhere. America and Australia as continents of immigrants continue to be a special cases. But for two people with families from, say, West Africa, I'd be comfortable assuming that if they're from roughly the same large region (say around the Bight of Benin) they're probably something like 40th degree cousins and if not, they're still something like 100 degree cousins at least.

It gets only slightly more complicated if the set of ancestors you know - say your four grandparents - are a mix of descendants from different regions or continents. Just add the number of generations between you and them to your expected degree of cousinhood to everybody from that region or continent.

Needless to say these are all wild guesses. I'm basically hoping someone more qualified than me will see this and be horrified enough to go do the job properly.

Now I'm not an American but statistically you probably are, and you might be more interested in know how closely you're related to other Americans - your boss, your sexual partners, or Mel Gibson. The bad news is that as a member of a nation of relatively recent immigrants, and particularly if your ancestors didn't all come from different continents, you have a harder time estimating most recent common ancestors with people than most other people on Earth. The good news, however, is that the data collected at the large ancestry sites ancestry.com, FamilySearch.org, Geni.com and WikiTree.com are all growing fastest in the US-centric part of their "world trees".

For cousinhood between people whose ancestors seem to have lived on entirely seperate continents as far as anyone knows, I think we can only fall back on our upper bound of 125 degrees of cousinhood. Things get fuzzy so far back, the world population was much smaller, and the population of those who have descendants living today is smaller still. Shared ancestry within any particular generation remains unlikely, but over the centuries and millenia, between trade (particularly in slaves), the various empires and the mass rapes of warfare, genes did get mixed around. Again, see that spectacular Nature paper if you still haven't.

Side note: The most recent common ancestor of two arbitrarily chosen people on different continents is likely to be someone who had kids on different continents. So it is probably a very rich person, a sailor or a soldier, i.e. a male. In general, the number of unique males in anybody's ancestor tree will likely be much smaller than the number of unique females. I expect the difference will be sharper in most recent common ancestors of humans from different continents, because women have shorter fertility windows inside which to travel intercontinentally and don't seem to have moved nearly as much as men except as slaves.

The point of all this is simple. Now you can look at somebody and figure she's not only your cousin, you even have a guess as to the degree of cousin she is. I like to do that when I'm angry with people, because for me, it makes a distinct emotional difference. Maybe try if that works for you too.

Relation to the care allocation problem

I suspect this cousinhood thing could be a fairly principled solution to the problem of how to allocate caring between humans and animals, which Yvain/Scott laid out in a recent SSC post. Why not go by actual (known or estimated) blood relations, and privilege closer relatives over more distant ones?

Our last common ancestor with chimps was something like 5 to 6 million years ago, so our ancestor trees merge about 250000 (human) generations ago, making chimps something like quarter-million-degrees-cousins of all of us. Generations get a lot shorter further back, so our last common ancestor with cattle and dogs, about 92 million years ago, may be 30 million generations ago. Birds would be much more distant, our last common ancestor with them was around 310 million years ago, and so forth. (Richard Dawkins The Ancestor's Tale has much more on this.) For me, this maps rather nicely onto my intuitive prejudices as to how much I should care about which creatures. It fails to map my caring for plants far more than I care for bacteria, but EA has nothing to improve on in that department.

If EA has to have impartiality in the sense that your neighbor can't be more important to you than a tribesman in Mongolia, this isn't EA. Quoth Yvain:

allowing starving Third World people into the circle of concern totally pushes out most First World charities like art museums and school music programs and holiday food drives. This is a scary discovery and most people shy away from it. Effective altruists are the people who are selected for not having shied away from it.

So anybody trying to grow EA might want to make that step easier. Maybe a "closeness multiplier" on units of caring works better than a series of unprincipled exceptions, and still gets across the idea that units of caring are to be distributed between everybody (or everybody's QALYs), if unevenly. And then to become more impartial would be to have that multiplier approach 1.

And if that were the case, my personal preference for how to design that multiplier would be that it shouldn't rely on arbitrary constructs like citizenships. Maybe if EAs want to find a principled solution to the care allocation problem, consanguinity should be one of the options.

Adoption and twin studies are very important for determining the impact of genes versus environment in the modern world (and hence the likely impact of various interventions). Other types of studies tend to show larger effects for some types of latter interventions, but these studies are seen as dubious, as they may fail to adjust for various confounders (eg families with more books also have more educated parents).

But adoption studies have their own confounders. The biggest ones are that in many countries, the genetic parents have a role in choosing the adoptive parents. Add the fact that adoptive parents also choose their adopted children, and that various social workers and others have great influence over the process, this would seem a huge confounder interfering with the results.

This paper also mentions a confounder for some types of twin studies, such as identical versus fraternal twins. They point out that identical twins in the same family will typically get a much greater shared environment than fraternal twins, because people will treat them much more similarly. This is to my mind quite a weak point, but it is an issue nonetheless.

Since I have very little expertise in these areas, I was just wondering if anyone knew about efforts to estimate the impact of these confounders and adjust for them.

The paper is called DNA methylation age and human tissues and cell types and it's from Genome Biology. Here is a Nature article based on the paper.

I have submitted this to LW because of its relevance to the measurement of aging and, hence, to life extension. Here is a bit from the Nature piece:

"Ageing is a major health problem, and interestingly there are really no objective measures of aging, other than a verified birth date," says Darryl Shibata, a pathologist at the University of Southern California in Los Angeles. "Studies like this one provide important new efforts to increase the rigour of human aging studies."

Note: The discrepancy in spelling ("ageing" vs. "aging") is in the original.

It's been reduced to 99$ and it seems like it is a permanent reduction. I was thinking of buying it at 299$ because it had not been on sale for a while, so I'm very pleased this happened.

Their press release on it:

http://blog.23andme.com/news/one-million-strong-a-note-from-23andmes-anne-wojcicki/

Your daily dose of science knowledge will once more be provided by Gregory Cochran, clearing up some misconceptions you may have heard about Epigenetics.

As I understand it, in some circles,  there is a burgeoning hope that practice in this generation will somehow improve performance in the next – based on a word they have heard but do not understand. That word is epigenetics.

Genes can certainly be modified in ways that persist.   For example, the cells in your skin produce more skin cells when they divide, rather than muscle cells or neurons.  Most of your cells have a copy of the entire human genome, but only certain elements are expressed in a particular type of cell, and that pattern persists  when that  kind of cell divides. We understand, to a degree, some of the chemical changes that cause these lasting changes in gene expression patterns.   One is methylation,  a method of suppressing gene activity.  It involves attaching a methyl group to a cytosine base. This methylation pattern is copied when somatic cells divide.

The question is whether A. such changes can persist into the next generation and B. if they do, is this some sort of adaptive process, rather than an occasional screwup?  We’re  interested in whether this happens in humans,  so we’ll only consider mammals.

It’s rare, but sometimes it happens.  It has only been found to happen at a few sites in the genome, and when it does happen,  only a fraction of the offspring are affected. Probably the best known example is the agouti yellow allele in mice.  Mice that carry this allele are fat, yellow, and prone to cancer and diabetes – some of them. Yellow mothers tend to have yellow babies,  while genetically identical brown mothers mostly have brown babies.  The agouti yellow allele is the product of a recent insertion in the genome, about 50 years ago.  For the overwhelming majority of genes, the epigenetic markers are reset in a new embryo, which means that epigenetic changes induced by the parent’s experiences disappear.  The embryo is back at square one.   This agouti yellow allele is screwed up – somehow the reset isn’t happening correctly.

In mice, the mammalian species in which most such investigations have been done,  the few other locations in the genome where anything like this happens are mainly retroposons and other repeated elements.

There is another way that you can get transmission across generations without genetic change.  Rats that are nurtured by stressed mothers are more likely to be stressed.  This isn’t transmitted perfectly, but it happens.  Presumably the uterine environment,  or maybe maternal behavior, is different in stressed mice in a way that stresses their offspring.   This reminds me of a science fiction story that abused this principle.  The  idea was that alligators (or maybe it was crocodiles) almost have a four-chambered heart, which is generally associated with higher metabolism and friskiness. Our protagonist operates on an alligator and soups up its heart: the now-more-vigorous animal has better blood circulation and lays healthier eggs that develop into babies that also have a working four-chambered heart. So ‘normal’ alligators were like stressed mice: fix the problem and you get to see what they’re really capable of. The problem was that the most interesting consequence was growing wings, flying around and eating people. Alligators turned out to be stunted dragons. Not so good.

Anyhow, what reason is there to believe that reading Gradshteyn and Ryzhik until your eyes bleed will plant the seeds of math to come in your descendants?  None. Oh, I can come up with a scenario, if you want: but it requires that civilization (in particular, the key part of civilization, heavy use of weird definite and indefinite integrals and vast reproductive rewards for those skilled in such things) has risen and fallen over and over again at fairly short (but irregular)  intervals, so that humans have faced this adaptive problem over and over and over again.  A little like the way in which generations of aphids do different things in the summer (parthenogenesis) than in the late fall (sexual reproduction) – although that probably depends on direct cues like length of day rather than epigenetic changes.  Something like Motie history, maybe. But  I don’t believe it.  Not even a little bit.

Nature hasn’t even figured out how to have Jewish boys be born circumcised yet.

So why are people talking about this? Why do people like Tyler Cowen invoke it to ward off evil facts?

Because they’re chuckleheads, what else?

I think we can be a bit more specific that that so lets take it as an exercise. Motivated cognition for starters.

If you want to learn why the Conan the Barbarian was generated by better priors than modern history books, what the blind idiot god may have in store for you or how to solve thick problems check out other articles from the blog shared under the tag: westhunter 

I recently read (in Dawkins' The Ancestor's Tale) about the Alu sequence, and went on to read about transposons generally.  Having as I do a rather broad definition of life, I concluded that Alu (and others like it) are lifeforms in their own right, although parasitic ones.  I found the potential ethical implications somewhat staggering, especially given the need to shut up and multiply those implications by the rather large number of transposon instances in a typical multicellular organism.

I have written out my thoughts on the subject, at http://jttlov.no-ip.org/writings/alulife.htm.  I don't claim to have a well-worked out position, just a series of ideas and questions I feel to be worthy of discussion.

ETA: I have started editing the article based on the discussion below.  For reference with the existing discussion, I have preserved a copy of the original article as well, linked from the current version.

I've just watched this talk about Genetics and Intelligence by Steve Hsu₁, a theoretical physicist and Scientific Advisor to the Cognitive Genomics Lab of BGI (formerly the Beijing Genomics Institute), probably the leading genomics research center in the world.

Apparently, the main reason he gave this talk was to recruit volunteers for a study from the Cognitive Genomics Lab with the goal of investigating the genetics of human cognition.

From their homepage:

We currently seek participants with high cognitive ability. You can qualify for the study if you have obtained a high SAT/ACT/GRE score, or have performed well in academic competitions such as the Math, Physics, or Informatics Olympiads, the William Lowell Putnam Mathematical Competition, TopCoder, etc.

Automatic qualifying criteria include:

• An SAT score of at least 760V/800M post-recentering or 700V/780M pre-recentering; ACT score of 35-36; or GRE score of at least 700V/800Q.
• A PhD from a top US program in physics, math, EE, or theoretical computer science.
• Honorable mention or better in the Putnam competition.

If you qualify as a participant, we may send you a DNA saliva kit. After you return this kit, we will genotype your DNA, and the data will eventually be available to you on this website, in a format compatible with many 3rd party interpretational tools.

I guess there are quite a few Lesswrongers smart enough to qualify for this study. If you want to advance Science and get genotyped for free check out their website for further information.

1: Steve Hsu has an awesome blog called "Information Processing". He writes about the genetics of intelligence, economics, psychometry, career advice for geeks, physics, etc.

I wrote an article for h+ predicting that the rapid fall in the cost of gene sequencing will allow U.S. voters to learn much about presidential candidates' DNA.  The candidates won't be able to stop this because:

humans shed so much DNA that unless a politician lived in a plastic bubble he couldn’t shield his DNA from prying eyes. Politicians will probably pass laws making it a crime to involuntarily disclose a politician’s genetic traits. But since it would take only one person to leak the information onto the Internet, and given that any serious candidate for President will have many enemies, candidates’ genomes will undoubtedly become public.

DNA analysis has a decent chance of reducing political bias by providing objective information about candidates.  If, for example, 70% of the variation in human intelligence is determined by identified genes then DNA analysis would reduce disagreements among informed voters over a candidate's intelligence.