Wednesday, February 1, 2023

Chapter 4: Why Don't Mutations Kill Us?

Gregor Mendel and mutations. Spontaneous mutations. Rate of mutation. (pp. 82-83)
[Mutation, Randomness, & Evolution]
Why aren’t we extinct? - a 100-year old problem
History of mutation load (genetic load). Prediction of 30,000 genes. (pp. 83-84)
[What Is a Mutation?] [Genetic Load, Neutral Theory, and Junk DNA]
Biochemical mutation rate
Knowing the overall error rate of DNA replication (10-10 mutations per base pair) and the number of cell divisions in the germ line gives an average of 138 new mutations per generation. (pp. 84-85)
[Parental age and the human mutation rate ] [Estimating the Human Mutation Rate: Biochemical Method] [Human Y Chromosome Mutation Rates] [Mutation Rates]
Phylogenetic mutation rate
If you know the number of generations since the time of a common ancestor then you can calculate a mutation rate by looking at sequences that are evolving at the neutral rate. (pp. 85-86)
[Estimating the Human Mutation Rate: Phylogenetic Method] [Calculating time of divergence using genome sequences and mutation rates (humans vs other apes)]
   Box: Tick, tock, the molecular clock (p. 87)
   [The Modern Molecular Clock] [Can some genomes evolve more slowly than others?]
   [Reading the Entrails of Chickens] [Calibrating the Molecular Clock]
The direct method of calculating mutation rate
Comparing the sequences of a child and both parents gives you the number of new mutations per generation. (p. 88)
[Direct Measurement of Human Mutation Rate] [Parental age and the human mutation rate] [Estimating the Human Mutation Rate: Direct Method] [Human Mutation Rates] [Human mutation rates - what's the right number?] [Somatic cell mutation rate in humans]
You are not Craig Venter
Craig Venter's genome sequence was the first one to include all 46 chromosomes separately. The amount of heterogeneity in human genomes means that no two individuals are alike. (pp. 89-90)
[What happens when twins get their DNA tested?] [Genetic variation in the human population] [Genetic variation and the complete human genome sequence] [Sequencing both copies of your diploid genome] [Sequencing human diploid genomes] [All about Craig]
Revisiting the genetic load argument
Given the mutation rate and the probability of deleterious mutations, only a small percenage of the human genome can be susceptible to mutation or our species would go extinct. (pp. 90-94)
[Revisiting the genetic load argument with Dan Graur]
   Box: Human gene knockouts (pp. 92-93)
How much of our genome is conserved?
About 8-10% of the DNA sequences in the human genome are conserved in other species. (pp. 94-95)
Defining function
The best definition of function is the maintenance definition that relies on purifying selection. Functional DNA is any stretch of DNA whose deletion from the genome would reduce the fitness of the individual. (pp. 96-98)
[Identifying functional DNA (and junk) by purifying selection] [On the Meaning of the Word "Function"] [The Function Wars: Part I] [The Function Wars: Part II] [The Function Wars: Part III] [The Function Wars: Part IV] [Restarting the function wars (The Function Wars Part V)] [The Function Wars Part VI: The problem with selected effect function] [The Function Wars Part VII: Function monism vs function pluralism] [The Function Wars Part VIII: Selected effect function and de novo genes] [The Function Wars Part IX: Stefan Linquist on Causal Role vs Selected Effect] [The Function Wars Part X: "Spam DNA"?]
   Box: Levels of selection (pp. 99-101)
   [The Function Wars Part XIII: Ford Doolittle writes about transposons and levels of selection]
Why is the evidence of sequence conservation so hard to accept?
There are several arguments against sequence conservation as an indicator of function. (pp. 101-103)
   Box: Deleting DNA to prove that it is junk (pp. 104-105)
Bulk DNA hypotheses
Skeletal DNA hypotheses. The bodyguard hypothesis. Genetic diversity. (pp. 105-110)
[Teaching about genomes using Nessa Carey's book: Junk DNA]
Medical relevance
Medical relevance is a weak argument for function because mutations in junk DNA can cause genetic diseases. (pp. 110-112)
[Junk DNA vs noncoding]
Ignoring history
Opponents of junk DNA have propagated a false narrative about the history of junk DNA by claiming that scientists in the late 1960s and early 1970s thought that all noncoding DNA was junk. (pp. 112-115)
[The "standard" view of junk DNA is completely wrong] [Junk DNA vs noncoding DNA] [The surprising (?) conservation of noncoding DNA] [More misconceptions about junk DNA - what are we doing wrong?] [Alan McHughen defends his views on junk DNA] [A University of Chicago history graduate student's perspective on junk DNA] [Nature journalist is confused about noncoding RNAs and junk] [What is the dominant view of junk DNA?]
Notes for Chapter 4 (pp. 321-324)

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