The Atlantic: How Eugenic Breeding Transformed the Dairy Industry

The Perfect Milk Machine: How Big Data Transformed the Dairy Industry:
There is a reason, of course, that the semen that Badger-Bluff Fanny Freddie produces has become such a hot commodity in what one artificial-insemination company calls "today's fast paced cattle semen market." In January of 2009, before he had a single daughter producing milk, the United States Department of Agriculture took a look at his lineage and more than 50,000 markers on his genome and declared him the best bull in the land. And, three years and 346 milk- and data-providing daughters later, it turns out that they were right. [. . .]

No matter how you apportion the praise or blame, the net effect is the same. Thousands of years of qualitative breeding on family-run farms begat cows producing a few thousand pounds of milk in their lifetimes; a mere 70 years of quantitative breeding optimized to suit corporate imperatives quadrupled what all previous civilization had accomplished. And the crazy thing is, we're at the cusp of a new era in which genomic data starts to compress the cycle of trait improvement, accelerating our path towards the perfect milk-production machine, also known as the Holstein dairy cow. [. . .]

"Animal breeders for many decades have used models that assume most traits are influenced by thousands of genes with very small effects. Some [individual] genes do have detectable effects, but many studies of plant and animal traits conclude that most of the genetic variation is from many little effects."

For dairy cows -- or humans, for that matter -- it's just not as simple as the dominant-recessive single-gene paradigm that Mendel created. In fact, Mendel picked his model organism well. Its simplicity allowed him to focus in on the simplest possible genetic model and figure it out. He could easily manipulate the plant breeding; he could observe key traits of the plant; and these traits happened to be controlled by a single gene, so the math lay within human computational range. Pea plants were perfect for studying the basics of genetics.

With that in mind, allow me to suggest, then, that the dairy farmers of America, and the geneticists who work with them, are the Mendels of the genomic age. That makes the dairy cow the pea plant of this exciting new time in biology. Last week in the Proceedings of the National Academy of Science, two of the most successful bulls of all time had their genomes published.

This is a landmark in dairy herd genomics, but it's most significant as a sign that while genomics remains mostly a curiosity for humans, it's already coming of age when it comes to cattle. It's telling that the cutting-edge genomics company Illumina has precisely one applied market: animal science. They make a chip that measures 50,000 markers on the cow genome for attributes that control the economically important functions of those animals. [. . .]

Mendel may have worked with plants, the rules he revealed turned out to be universal for all living things. The same could be true of the statistical rules that dairy scientists are learning about how to match up genomic data with the physical attributes they generate. The statistical rules that reflect the way dozens or hundreds of genes come together to make a cow likely to develop mastitis, say, may be formally similar to the rules that govern what makes people susceptible to schizophrenia or prone to living for a long time. Researchers like the University of Queensland's Peter Visscher are bringing the lessons of animal science to bear on our favorite animal, ourselves.

Want to live for a very long time? Well, we hope to discover the group of genes that are responsible for longevity. The problem is that you have genomic data over here and you have phenotypic data, i.e. how things actually are, over there. What you need, then, is some way of translating between these two realms. And it's that matrix, that series of transformations, that animal scientists have been working on for the past decade.

And this is as deep as the author of this piece, Alexis Madrigal, gets into the "lessons of animal science" for humans. Predict lifespan and disease risk. But don't allow yourself to imagine this sort of information might have any more direct uses or implications for humans. Breathlessly promoting genetic betterment of cows in one article; mouthing sentiments like this in another:
Ever since humans deduced the powerful nature of DNA and all the associated molecules that do work in our cells, people have wondered: how long before we can simply change our own genes? On the one hand, all kinds of genetic diseases could be cured. On the dark side, if genetics sets the limits of human action, how long before we create genetically enhanced humans? And, like many things in bioethics, these thoughts are never very far away from the long shadow of the Nazis' eugenics program.


Lemniscate said...

I've been working on Visscher's method, among others, for heritability estimation.

It really is just a matter of sample size. Visscher's group has already used his 'realized relatedness matrix' to predict IQ in humans with non-negligible accuracy. This is using GWAS data in a relatively small sample, and GWAS data necessarily only captures a small subset of genetic variation, especially at rare variants. When we have large samples of sequence data with IQ phenotypes, it will be easy to predict someone's IQ 'breeding value'.

If we had a free market in human sperm banks, I bet it wouldn't be long before they started advertising prime human sperm based on its breeding value for traits such as IQ, height, longevity, etc.

Of course, such a beneficial, voluntary thing will not be allowed to happen.

Anonymous said...

"Visscher's group has already used his 'realized relatedness matrix' to predict IQ in humans with non-negligible accuracy."

Can you give a reference for this? Calculation of heritability is not the same thing as phenotype prediction from genotype.

Anonymous said...

Here's the Visscher paper on intelligence:

Anonymous said...

That just calculates heritabiity. He can't predict IQ from just the genotype very well. No one can yet.

Silver said...

Of course, such a beneficial, voluntary thing will not be allowed to happen.

Your pessimism is unwarranted (but apparently a staple postscript when it comes to eugenicist genes-talk). This gang is going straight for the jugular: looks. (Look are for many an even more frightening prospect than intelligence.) Equalitarian reactionaries will not be able to hold back the tide of eugenic progress indefinitely, even if they did manage to win some impressive victories in the interim.

Lemniscate said...

If you look at table 2 of the IQ paper, he predicts IQ phenotypes for a subsample left out of the prediction model with a correlation to the true value of around 0.1 for fluid intelligence.

His method of estimating heritability is based on the animal breeding model, which fits a linear mixed model to all the variants simultaneously. This allows one to construct a best-linear-unbiased-predictor from the fittted SNP effects, even if each SNP effect itself is not found to be significantly different from zero.

It is certainly not accurate yet, but it has only been tried in a small GWAS sample. If you had a large sample with sequence data (or at least sequence imputed data), then you would be able to capture all of the genetic variability influencing intelligence thereby allowing for an accurate prediction of phenotype from genotype for a highly heritable trait like IQ.

Re Silver, I'm sure it'll happen eventually, but probably not before the Chinese have bred a race of super-geniuses. Surely there's going to be strong challenges to any genetic selection method for IQ in humans in the west?