Wednesday, August 21, 2024

The Acolyte was cancelled

Apparently, Season 2 of the outstanding Star Wars series "The Acolyte" was cancelled by Disney. In a previous post, I described why I liked Season 1. 

Was the show too "woke"? And by "woke" I mean trying to appeal to an educated and enlightened audience by moving beyond traditional tropes.

The auteur Leslye Headland conjured up a distinctive take on the Star Wars universe that you may like or not like, but it was not cookie-cutter.

Thursday, August 15, 2024

The Fundamental Law of Genetics

In the first lecture of my genetics course, I introduce the following as The Fundamental Law of Genetics

Phenotype = Genotype + Environment    (1)

The phenotype (observed traits) of an organism depends on genetic factors and environmental factors. One example of a phenotype is blood pressure. Your blood pressure (and whether or not you have high blood pressure) depends on genetic factors (alleles) you inherit from your parents as well as environmental factors (the world we live in influences traits) such as diet and exercise. 

The concept of genotype is central to genetics and is defined as the identity of alleles for genes in an individual i.e. which “version” (allele) for each gene. The gene is the basic unit of heredity, and at a molecular level, encompasses a region of DNA that is transcribed into RNA and then (typically) translated into protein. The DNA sequence of a gene can be altered by mutation to give rise to different versions or alleles which may possess different functional properties (after being transcribed/translated into protein) that influence the phenotype. Your genotype is basically the specification of what allele you have at each gene, e.g. mutant or wild-type allele and if mutant, which mutation(s). 

Humans are diploid and thus carry two sets of genes, each set contributed by one of two parents. Genes are positioned on chromosomes, each a single molecule of DNA, and we receive one set of 23 chromosomes from Mom and one set of 23 chromosomes from Dad. The human genome contains ~20,000 gene pairs, and the complete genotype of an individual is the identity of alleles at all of these genes.

That is a lot of information to process but if you understand the above (i.e. bold terms) then you are well on your way to understanding genetics including human genetics.

At the end of the course, in the human genetics section, I introduce the quantitative version of The Fundamental Law of Human Genetics:

VP = VG + VE    (2)

The variable V represents variance, and the subscript P is phenotype, G is genotype, and E is environment. In other words, phenotypic variance equals genotypic variance plus environmental variance. Genotypic variance is the variation in phenotype caused by differences in genotype among individuals. VG = 0 in the case of identical twins who possess identical genotypes. Environmental variance is the variation in phenotype caused by differences in environment among individuals. VE = 0, when two individuals share the exact same environment such as two plants growing next to each other.

Most traits are continuous, taking on a range of values rather than a few discrete possibilities. For example, we can measure the (systolic) blood pressure in a population, and then plot the distribution of values. Most likely, the result will be a Gaussian (normal) distribution whose parameters are the mean (center) and variance (width) of the bell-shaped curve. For a healthy population, the mean systolic blood pressure may be around 120 mmHg with a standard deviation (square root of variance) of roughly 15 mmHg. Thus in this example, the phenotypic variance is 15 15 = 225 (mmHg)2. According to eq. (2), we should be able to decompose the blood pressure phenotypic variance into genotypic variance and environmental variance (see Figure below).

Figure 25.4(c) from Genetics: From Genes to Genomes. This figure represents a distribution of plant stem lengths, but for the example, the x-axis is systolic blood pressure, and the y-axis is number of people.

In a thought experiment, for the trait of blood pressure in a large population, I can clone myself and send one clone to live with each member of the population fully sharing the environment (e.g. diet) of that person. I can then measure the blood pressure of the clones (all with identical genotypes) after a period of time, and the phenotypic variance among the clones would be VE (due to environmental differences). Alternatively, each member of the population could all come and live with me and share my environment. After a period of time we could measure the blood pressure of the population and that would be VG (due to genotypic differences). According to eq. (2), the phenotypic variance of the original population should equal VG + VE.

Of course the thought experiment is not practical, but of even greater importance is that eq. (2) is an approximation of the more complete equation:

VP = VG + VGEVE        (3)

where VGE represents the phenotypic variance from Gene-Environment interaction (GxE). Intuitively, VGE describes how certain genotypes may have a bigger (or smaller) than expected impact on a trait in certain environmental settings. For example, an allele that promotes increased excretion of excess sodium by the kidneys would have a bigger impact reducing blood pressure for a high-salt diet compared to a low-salt diet. Mathematically, VGE represents the residual from the simple linear model of additive genetic factors plus additive environmental factors in eq. (2). In other words in the thought experiment, most likely VP would not equal VG + VE because VGE does not equal 0.

Finally, according to the Lynch and Walsh textbook (Genetics and Analysis of Quantitative Traits), VGE can be decomposed into a genotype-environment interaction term (as described above) and a genotype-environment covariance term which measures how certain genotypes are physically associated with certain environments, i.e. not randomly distributed across environments. For example, immigrants from India tend to be associated with wealthier environments in America.

My next genetics post will be on the concept of heritability. 


Wednesday, August 7, 2024

Eligibility for women's Olympic events should be based in part on a genetic test

By all accounts Imane Khelif is a woman, but the fact she is a woman is not sufficient to guarantee participation in women's Olympic events. In my opinion, eligibility should also be based in part on a genetic test, namely whether the athlete is XX or XY.

As you know from high school biology, human biological sex is typically determined by the absence or presence of the Y chromosome.  Females possess 2 X chromosomes (XX) and males possess an X chromosome and a Y chromosome (XY). The Y chromosome contains the SRY gene (Wikipedia) that is a master transcriptional regulator responsible for the development of the testes: "SRY initiates testis differentiation by activating male-specific transcription factors that allow these bipotential cells to differentiate and proliferate." The testes in turn produce testosterone which stimulates protein production in muscle cells leading to increased muscle mass especially in combination with intensive training. This is why doping with anabolic steroids (testosterone analogs) is such a big deal in competitive athletics.

In a simple world, based on the genetic test, anyone who is XY would not be allowed to compete in women's Olympic events. But life is more complicated. For example, one can be XY but phenotypically female if the SRY gene has been inactivated by mutation. 

Imane Khelif and Lin Yu-ting were not allowed to compete in the IBA Women’s World Boxing Championships 2023 based on a genetic test. We do not know the results of this test, and so it is impossible to ascertain whether this ruling was justified. Plus, as mentioned above, there are a lot of subtleties with respect to interpreting the genetic test.

Overall, I view this controversy as being vastly overblown by conservative culture warriors, and a red herring compared to the real problem in sports which has been and still is doping. At the highest levels of athletic competition, a tiny sliver of an advantage can be the difference between winning and losing (e.g. 100M men's sprint final), and doping can literally have an oversized impact (e.g. Mark McGwire, Sammy Sosa, and Barry Bonds) which is why athletes continue to dope.

In summary I would say that gender is not based on a genetic test, but eligibility for women's Olympic events should be based in part on a genetic test.

ChatGPT identified 142 statistical "issues" in problematic paper

Today the Bayesian statistician Andrew Gelman posted a rather pointed critique of a paper on his blog stating: "Wow! This paper is an ...