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Reading The Essential Talmud about ten years ago I vaguely recall the author stating that it was common for working class males to devote each day to one page of one a tractate from the commentaries on the oral law of the Jewish religion. As I am not religious, and look dimly on excessive orthopraxy, it struck me as a depressing thought.
But I am not entirely different. I often will relax at some point in the day and open up a random page of a population genetics textbook. Just as those Jewish men attempted to gain insight into the divine intent for how they should live their life, so with population genetics I am attempting to refine the theory which allows me to interpret the world around me.
It would probably help anyone who reads many of my posts as well, as it develops particular habits of mind. Though I often recommend Principles of Population Genetics, Elements of Evolutionary Genetics is also excellent. So in the future I’ll try to write up short insights which are pretty banal to most population geneticists, but which might be interesting to a motivated public, if my modest readership can be considered the “public.”
Page 100 has a section, “Selection in inbreeding populations.” The most important formal relationship on this page is:
Δq ≈ qs[h(1 –f) + f]
q = minor allele frequency on a biallelic locus, that is, the remainder from 1 – p
h = dominane coefficient , so that h = 0 means q is totally recessive and h = 0.5 means that the locus is additive in regards to allelic effect.
f = inbreeding coefficient, a basic measure of two alleles at the same locus sharing recent common ancestry (and therefore, rendering the genotype likely homozygous). From 0 to 1, with 1 meaning totally inbred and homozygous.
s = selection coefficient against the population mean fitness. Usually the value is near zero, though not exactly zero. A positive selection coefficient of 0.01 is considered very favorable for a new mutant.
What you see here is that in an instance where q is entirely recessive, inbreeding increases the selection on the locus. In a normal population with lots of random mating homozygous recessive genotypes are rare. When f ≈ 0 the change in the frequency of q is just a function of the selection coefficient and the dominance. As inbreeding increases, the importance of alleles (or lack thereof) in heterozygote genotypes decreases. For recessive traits inbreeding is another way to expose the novel alleles to selection.
This is one reason that unscrupulous breeders of animals sometimes utilize very close relatives in programs to change traits. The problem is that inbreeding has an effect across the whole genome, even if you are interested in particular loci. And that effect on the whole genome is often very bad, as lots of deleterious alleles with recessive expression are present in populations which are normally outbred. Of course in plants this also results in purging of genetic load, as alleles get flushed out of the system. Unfortunately for mammals, and complex metazoans in general, this doesn’t seem to work to well for out lineage. If it did work well zoological veterinarians, who I’ve talked to, would be a lot more hopeful about what they’re trying to do by mating near relations in the hopes that they can get a large enough population to maintain a viable breeding program.
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Hey Razib,
I know many Muslim societies get criticized for this – and often times it is warranted. What is interesting is that they are overlooking an ancient wisdom imparted by Umar ibn al-Khattab (ra) to avoid negative traits in progeny, when they appear, by telling one of the Companions, “Your offspring are becoming so thin and weak. Marry outside your close of kin.”
http://www.zawaj.com/marriage-in-islam-questions-and-answers/
Sage advice…
Peace
http://www.zawaj.com/marriage-in-islam-questions-and-answers/Sage advice...PeaceReplies: @Razib Khan
the variance in this is high though. not very common in bengal. very common in pakistan.
Sure, remember our discussion about tribes? You’ll likely find this to be rarer among people like Malays, etc. who haven’t been tribal for a while. And even in other countries, the more tribal ethnicities (and rural) tend toward this.
Definitely time to dampen it down for while though until some of the negative effects are corrected for.
Peace.
Hopefully this helps some people: I was staring at the formula trying to intuit *why* the terms were where they were, and getting kinda confused, when I re-read Razib’s writing and noticed that it applies only to the *minor* allele at the locus, so once the allele under consideration reaches some threshold due to selective advantage, the formula switches to describe the behaviour of *another* allele and no longer applies to the current one under consideration.
Razib, what do you make of those who posit inbreeding as some cultural background under which genetic traits for nepotism have undergone selection? Shouldn’t this be much more difficult and require longer stretches of time than is commonly assumed? Judging from the power of fictive kinship in organising human affairs across many societies, perhaps the large differences in nepotistic tendencies are really culturally mediated due to different social and familial organisation?
There’s a recent paper using simulations showing that slight preexisting genetic tendencies towards nepotism for distant kin can nevertheless translate over time into high levels of actual nepotism within large and rigidly defined kinship units, due to game theoretic interactions and cultural selection between groups, I’ll try to find the reference.
pretty much my thought.
Isn’t this the way new dog breeds have been developed in the past, even to the point of mating pups with their parents? I guess a lot of selection goes into separating the desirable traits from the undesirable? Yet it doesn’t seem to require too many generations (can be done in the lifetime of a single breeder). Would like to hear your comment.
it's a quick way of getting a 'breed.' but most dog breeds aren't that inbred, the more inbred ones might have say 10 founding individuals. and there are lots of older 'working dog' breeds which are pretty genetically OK because they were bred 'organically.'Replies: @Luke Lea, @Twinkie
https://en.wikipedia.org/wiki/Fumarase_deficiency
And here it is!
A perfect example of inbreeding depression in so many ways.
Most of the town is a bit sloooow.
Huge founder effects now apparent after 5 or 6 effective generations.
Razib, what do you make of those who posit inbreeding as some cultural background under which genetic traits for nepotism have undergone selection? Shouldn't this be much more difficult and require longer stretches of time than is commonly assumed? Judging from the power of fictive kinship in organising human affairs across many societies, perhaps the large differences in nepotistic tendencies are really culturally mediated due to different social and familial organisation?
There's a recent paper using simulations showing that slight preexisting genetic tendencies towards nepotism for distant kin can nevertheless translate over time into high levels of actual nepotism within large and rigidly defined kinship units, due to game theoretic interactions and cultural selection between groups, I'll try to find the reference.Replies: @Razib Khan
Shouldn’t this be much more difficult and require longer stretches of time than is commonly assumed? Judging from the power of fictive kinship in organising human affairs across many societies, perhaps the large differences in nepotistic tendencies are really culturally mediated due to different social and familial organisation?
pretty much my thought.
Razib writes:
“This is one reason that unscrupulous breeders of animals sometimes utilize very close relatives in programs to change traits.”
I would remove “unscrupulous” from that sentence. ALL animal breeds were created from highly inbred populations to RETAIN traits. By definition a breed is a group of animals sharing a common ancestor/ancestry with a uniform phenotype.
By definition a breed is a group of animals sharing a common ancestor/ancestry with a uniform phenotype.
no, that's false too. a breed is what breeders and organizations say is a breed, and if you look at the genetics of some 'breeds' they are what we in the genetics community call 'phenotypic' breeds. they may have common traits which make them look related, but they aren't too closely related. e.g., the manx cat is a phenotype cat type. i can give you a list of many more dogs like this...but i don't want breeders getting mad at me, because genetic relatedness is something that really want for some reason.
anyway, you're talking to someone who actually knows more about this than the vast majority of geneticists because this is my bailiwick. you can breed for traits and selective for parents without them being closely related, though with dogs in particular inbreeding is now baked into the cake for many breeds (all individual are basically like half-siblings). but this is not true for all breeds and breed types, so close relative mating need not happen, even if u like one particular trait.Replies: @Twinkie
"This is one reason that unscrupulous breeders of animals sometimes utilize very close relatives in programs to change traits."
I would remove "unscrupulous" from that sentence. ALL animal breeds were created from highly inbred populations to RETAIN traits. By definition a breed is a group of animals sharing a common ancestor/ancestry with a uniform phenotype.Replies: @Razib Khan
this is false. e.g., some dog breeds for example have OK effective population sizes, because they were selected over a longer time scale. i can give you one example: the chihuahua.
By definition a breed is a group of animals sharing a common ancestor/ancestry with a uniform phenotype.
no, that’s false too. a breed is what breeders and organizations say is a breed, and if you look at the genetics of some ‘breeds’ they are what we in the genetics community call ‘phenotypic’ breeds. they may have common traits which make them look related, but they aren’t too closely related. e.g., the manx cat is a phenotype cat type. i can give you a list of many more dogs like this…but i don’t want breeders getting mad at me, because genetic relatedness is something that really want for some reason.
anyway, you’re talking to someone who actually knows more about this than the vast majority of geneticists because this is my bailiwick. you can breed for traits and selective for parents without them being closely related, though with dogs in particular inbreeding is now baked into the cake for many breeds (all individual are basically like half-siblings). but this is not true for all breeds and breed types, so close relative mating need not happen, even if u like one particular trait.
Because of a series of disputes between the various national dog societies/kennel groups, we had a ridiculous situation in which fine examples of Akitas from their actual homeland were unrecognized by the kennel club in the United States, which continued to hold up a "bastardized" set of traits as THE standard for a dog originally from Japan.And the main reason the American Kennel Club continued to reject the resurrected and ostensibly more authentic standard from Japan for the Akita was fear driven by the breeders in the U.S. that they would lose money - under the new (Federation Cynologique Internationale) division the dogs that conformed to the Japanese standards would be called Akitas, but the American dogs would now be called "the Great Japanese Dogs" - a name without much cache and the attendant financial value.
Isn’t this the way new dog breeds have been developed in the past, even to the point of mating pups with their parents?
it’s a quick way of getting a ‘breed.’ but most dog breeds aren’t that inbred, the more inbred ones might have say 10 founding individuals. and there are lots of older ‘working dog’ breeds which are pretty genetically OK because they were bred ‘organically.’
On the one hand, we have dogs such as the Japanese Kai Ken that were the typical ancient village dogs that migrated and settled with people. Their breeding was probably quite "organic," especially in the beginning. These dogs were semi-feral and roamed about the villages, and were used to control rodents, serve as village watch dogs against intruders, bandits, and predators, and probably for hunting.
Over time, those that were relatively isolated probably developed a set of adaptations unique to the area (the Kai Ken, for example, are from the mountainous Yamanashi Prefecture of Japan). Of course, I have no doubt they were under continuous human selective pressures - I am sure dogs that were the most useful to the villagers enjoyed greater success in breeding, but it appears to me that the selection pressure from humans was probably relatively light if long-term, as such primitive village dogs seem to retain many of their phenotypical and behavioral similarities from others of the same broader type but from faraway regions (as is the case of the larger Northern Spitz-type dogs, a category of dogs that include Asian dogs such as the Japanese Kai and the Akita, the Korean Jindo as well as various Scandinavian Elk Hounds, and even the Israeli Canaan dog). Many such dogs still share some wolf-like behaviors such as extreme cleanliness.
The second broad category of dogs seems to be those that were "constructed" in more recent time with very specific human goals in mind. The classic example of this is the German Shepherd Dog, that was highly inbred from the beginning in order to build quickly "the perfect sheep-herding dog" breed. The rise of this kind of dogs was contemporaneous with the kennel club movements in Europe, in which there was a great deal of interest in "scientifically" categorizing and standardizing dog breeds. Initially, the goals of creating such breeds seem to have been functional in nature. Although Max von Stephanitz, the man behind the German Shepherd Dog and the first president of the German Shepherd Dog Union, insisted on building a superb working dog, eventually this obsession with physical conformations led to today's kennel club competition German Shepherd Dogs having the extreme sloping topline that are orthopedically unsound - obviously to the detriment of the working ability.
Again, these two categories are not discrete, and are more opposites on a broad spectrum, but that spectrum does exist. I would, of course, like to see confirmation (or falsification) of that through genetics studies on dogs.
it's a quick way of getting a 'breed.' but most dog breeds aren't that inbred, the more inbred ones might have say 10 founding individuals. and there are lots of older 'working dog' breeds which are pretty genetically OK because they were bred 'organically.'Replies: @Luke Lea, @Twinkie
My current dog breed, a Bernese Mountain Dog, was developed very quickly (over a couple of decades if I remember correctly) at the turn of the last century. I by luck happen to have a very beautiful example (a gift) whose father won best of breed at Westminster three years ago. The father was from California (Vinny Invincible) but the mother from Norway — those are the lengths you have to go to get a good example. Otherwise, many are quite runty, as I learned in a long search for a good one. [I should add that the original stock from which the breed was developed was already an established working farm “breed”, used to pull milk carts in the Alps.]
The Talmud study practice you refer to in the opening of your post is called Daf Yomi (“daily page”) and is fairly new in relative terms — less than 100 years old. There is a set worldwide schedule and everyone participating studies the same page on the same day. It takes about seven years to read through the entire Talmud at this pace.
One thing to note is that most of the Talmud is very mundane. There are some “theological” discussions but enormous sections of it have to do with civil law, damages, elements of ritual practice, etc. It is mostly a logical analysis, attempting to reconcile differences of opinion between Rabbis and attribute statements that are not clear based on other statements that are. There is some story-telling and folk medicine. There’s not a lot of talk about God.
In practice working-class males were expected to engage in some traditional learning, but usually lighter fare. A page of Talmud a day in the original is a pretty major commitment and not really do-able except for the highly educated.
One thing to note is that most of the Talmud is very mundane. There are some "theological" discussions but enormous sections of it have to do with civil law, damages, elements of ritual practice, etc. It is mostly a logical analysis, attempting to reconcile differences of opinion between Rabbis and attribute statements that are not clear based on other statements that are. There is some story-telling and folk medicine. There's not a lot of talk about God.
In practice working-class males were expected to engage in some traditional learning, but usually lighter fare. A page of Talmud a day in the original is a pretty major commitment and not really do-able except for the highly educated.Replies: @Moshe
Nah, lots of morons do daf yomi. In fact it helps to be a moron. What human interested in learning goes to a daf yomi shiur? I’ve met plenty of talmidei chachamim, from chareidi to heretic and if any of them did daf yomi it was as a minor part of their gemara study. I never met a “dafyominik” who was actually intelligent about anything.
As for God, yup, not much about God. These people worship Toirah, not God. Is all actually rather musty and robotic.
As for logical analysis, sure, but in laughably illogical ways.
Selah.
It’s logical within its four daled amos. You’ve got to give it credit. By modern rational standards, not so much.
Historically, the young Jewish man could marry early and get rich, if able to distinguish himself in Talmudic study, because they were given an examination by prospective fathers in law and after marriage, kest, a period of being supported while devoting them self to full time Talmudic study. Real achievements were demanded of the young husband, but on being recognized as a eminent scholar a Jewish man received a range of valuable emoluments in addition to a wealthy man’s daughter as wife, including :extremely high status in the community of a kind which brought economic benefits (a ruling granted business monopolies on trade with gentiles to eminent scholars) and gifts, even if a scholar was well-off. Finally, the brainy Talmudist got protection from anyone speaking against him, which was enforced by bans and fines. Historically, there was consanguinity in Jewish communities, including uncle-niece marriage.
Razib – can you recommend a genetics primer (or more than one, maybe a genetics primer then a population genetics primer like the two you mention above) for the intelligent layman, one that assumes zero starting knowledge of Mendel/Watson/DNA/RNA?
Ideally after reading your recommendation(s) one should be able to understand what your ‘genetic distance’ maps are saying , as well as comprehend “importance of alleles (or lack thereof) in heterozygote genotypes” or “biallelic locus”.
http://www.cam.ac.uk/research/news/female-butterflies-can-smell-if-a-male-butterfly-is-inbred
I suppose inbreeding in humans would not come naturally, and be the result of a society’s traditional marriage practices.
There is a butterfly species that has imitated the appearance of another species (one avoided by predators). I wonder if, in the interests of swifter results, instinctive aversion to inbreeding is weakened somehow during a rapid period of evolution.
By definition a breed is a group of animals sharing a common ancestor/ancestry with a uniform phenotype.
no, that's false too. a breed is what breeders and organizations say is a breed, and if you look at the genetics of some 'breeds' they are what we in the genetics community call 'phenotypic' breeds. they may have common traits which make them look related, but they aren't too closely related. e.g., the manx cat is a phenotype cat type. i can give you a list of many more dogs like this...but i don't want breeders getting mad at me, because genetic relatedness is something that really want for some reason.
anyway, you're talking to someone who actually knows more about this than the vast majority of geneticists because this is my bailiwick. you can breed for traits and selective for parents without them being closely related, though with dogs in particular inbreeding is now baked into the cake for many breeds (all individual are basically like half-siblings). but this is not true for all breeds and breed types, so close relative mating need not happen, even if u like one particular trait.Replies: @Twinkie
For a recent example of this, I offer the Akita-inu: https://en.wikipedia.org/wiki/Akita_(dog)#American_history
Because of a series of disputes between the various national dog societies/kennel groups, we had a ridiculous situation in which fine examples of Akitas from their actual homeland were unrecognized by the kennel club in the United States, which continued to hold up a “bastardized” set of traits as THE standard for a dog originally from Japan.
And the main reason the American Kennel Club continued to reject the resurrected and ostensibly more authentic standard from Japan for the Akita was fear driven by the breeders in the U.S. that they would lose money – under the new (Federation Cynologique Internationale) division the dogs that conformed to the Japanese standards would be called Akitas, but the American dogs would now be called “the Great Japanese Dogs” – a name without much cache and the attendant financial value.
it's a quick way of getting a 'breed.' but most dog breeds aren't that inbred, the more inbred ones might have say 10 founding individuals. and there are lots of older 'working dog' breeds which are pretty genetically OK because they were bred 'organically.'Replies: @Luke Lea, @Twinkie
It seems to me that there are, broadly-speaking, two categories of dogs, neither of which is obviously discrete.
On the one hand, we have dogs such as the Japanese Kai Ken that were the typical ancient village dogs that migrated and settled with people. Their breeding was probably quite “organic,” especially in the beginning. These dogs were semi-feral and roamed about the villages, and were used to control rodents, serve as village watch dogs against intruders, bandits, and predators, and probably for hunting.
Over time, those that were relatively isolated probably developed a set of adaptations unique to the area (the Kai Ken, for example, are from the mountainous Yamanashi Prefecture of Japan). Of course, I have no doubt they were under continuous human selective pressures – I am sure dogs that were the most useful to the villagers enjoyed greater success in breeding, but it appears to me that the selection pressure from humans was probably relatively light if long-term, as such primitive village dogs seem to retain many of their phenotypical and behavioral similarities from others of the same broader type but from faraway regions (as is the case of the larger Northern Spitz-type dogs, a category of dogs that include Asian dogs such as the Japanese Kai and the Akita, the Korean Jindo as well as various Scandinavian Elk Hounds, and even the Israeli Canaan dog). Many such dogs still share some wolf-like behaviors such as extreme cleanliness.
The second broad category of dogs seems to be those that were “constructed” in more recent time with very specific human goals in mind. The classic example of this is the German Shepherd Dog, that was highly inbred from the beginning in order to build quickly “the perfect sheep-herding dog” breed. The rise of this kind of dogs was contemporaneous with the kennel club movements in Europe, in which there was a great deal of interest in “scientifically” categorizing and standardizing dog breeds. Initially, the goals of creating such breeds seem to have been functional in nature. Although Max von Stephanitz, the man behind the German Shepherd Dog and the first president of the German Shepherd Dog Union, insisted on building a superb working dog, eventually this obsession with physical conformations led to today’s kennel club competition German Shepherd Dogs having the extreme sloping topline that are orthopedically unsound – obviously to the detriment of the working ability.
Again, these two categories are not discrete, and are more opposites on a broad spectrum, but that spectrum does exist. I would, of course, like to see confirmation (or falsification) of that through genetics studies on dogs.