Resources
Great popular science and popular science-adjacent books
I’m a huge fan of ‘popular science’ books. These books, when written well, provide a great overview of a topic for the non-specialist, and can be a window into further reading. I am using popular science rather broadly here, to mean any books which do not require more than a high-school (or at most early undergraduate) background in the subject. As such, I may include books that may not, strictly speaking, be intended for a non-scientific audience. Below are some such books that I particularly liked. You can also find a list of popular science books on Michael Jennions’ website, and some ‘topicology’ books on Hanna Kokko’s website.
Ecology and Evolution
- Improbable Destinies by Jonathan Losos - Predictability of evolution, long-term evolution
- Beak of the finch by Jonathan Weiner - long term evolution in wild populations
- Darwin comes to town by Menno Schilthuizen - urban evolution
- The Loom of life by Menno Schilthuizen - Community ecology. Discusses niche models, neutral models, etc.
- A taste for the beautiful by Michael Ryan - Mate Choice
- Modeling Nature by Sharon Kingsland - history of modern ecology
- An Immense World by Ed Yong - Sensory ecology
Philosophy of science/biology/ecology/evolution
- This is Biology by Ernst Mayr - Overarching view of biology. Rather dated, but somewhat of a classic.
- Metazoa by Peter Godfrey-Smith - Speculative book on the evolution of consciousness that I thought was quite nice.
- What is this thing called science? by Alan Chalmers - Introduction to philosophy of science.
- The Dialectical Biologist by Richard Levins and Richard Lewontin - Argues that the act of doing science is political and is influenced by sociopolitical biases, and advocates for a dialectical approach to biology.
- Letters to a Young Scientist by E.O. Wilson - Inspiring series of essays directed towards young scientists.
- Evolution and the levels of selection by Samir Okasha - Discusses multi-level selection. Rather philosophically heavy, but worth the read.
- Idealization and the aims of science by Angela Potochnik - Discusses the role of idealization and simplification in science.
Other science
- I Contain Multitudes by Ed Yong - How microbes affect our daily lives
- The Gene: An Intimate History by Siddhartha Mukherjee - History of genetics
- The Epigenetics Revolution by Nessa Carey - Fantastic introduction to epigenetics
- Lost in Math by Sabine Hossenfelder - Critical overview of the current state of the use of mathematics in particle physics. Argues that particle physicists are too enamoured by beautiful mathematics, to the point where it is detrimental to discovery in the physical sciences.
- The Life of the Cosmos by Lee Smolin - Proposes the ‘cosmological natural selection’ hypothesis, which states that the values of the fundamental constants that we see today is the product of a natural selection-like process occurring on universes.
- The Oxford Book of Modern Science Writing , edited by Richard Dawkins - Collection of essays that are meant to showcase good popular science writing.
- The Idea of the Brain by Matthew Cobb - Fantastic book discussing the history of ideas and metaphors used to describe the brain (and sometimes neurons more generally). Very interesting book, makes you think about how bound humans are to the technology around them when it comes to thinking of metaphors (Ex: Today we think of the brain as a ‘computer’, but people used to draw analogies with telegraphs and hydraulics).
- Fermat’s last theorem by Simon Singh (Speaks about various mathematicians who worked on Fermat’s last theorem and/or developed tools that contributed to Andrew Wiles’ proof of the theorem)
- It must be beautiful by various authors, edited by Graham Fermelo. Collection of essays about the use of mathematics in the science from a list of authors that includes Roger Penrose, John Maynard Smith, and Robert May.
Biographies and Autobiographies of scientists
I often like reading about scientists just as much as I like reading about science. Here is a list of biographies and autobiographies that I particularly enjoyed.
- Naturalist by E.O. Wilson
- Surely you’re joking, Mr. Feynman by Richard Feynman
- A Mind at Play by Jimmy Soni (Biography of Claude Shannon)
- The Code Breaker by Walter Isaacson (Biography of Jennifer Doudna)
- Genius by James Gleick (Biography of Richard Feynman)
- A feeling for the Organism by Evelyn Fox Keller (Very inspiring biography of Barbara McClintock)
- The Price of Altruism by Oren Harman (Biography of George Price)
Articles on the interplay of theory and experiment in biology
I firmly believe that integrative approaches which combine theory with empirical knowledge are sorely needed in ecology and evolution. Below are some articles that discuss this idea very well (in my opinion).
- Zuk and Travisano 2017 - Models on the runway: How do we make replicas of the world?, a paper that discusses the utility of models in understanding the world, and an argument that the distinctions between ‘models’ and ‘reality’ are often blurred.
- Grainger et al. 2022 - An Empiricist’s guide to using ecological theory, a paper that discusses ways to use theory in empirical work.
- Tribalism in the sciences, a blog post on Small Pond Science discussing the theorist vs empiricist debate
- The two cultures of mathematics and biology, a fantastic blog post on Lior Pachter’s blog which talks about how biology and mathematics suffers from a ‘two cultures problem’ (Named after the essay by Tim Gowers, which is in turn named after a famous lecture by C.P. Snow)
Data visualization
- ggplot2 cheatsheet
- Fundamentals of Data Visualization
- A collection of graphs made in R
- A collection of graphs made in Python
Coding
- The good research coding handbook
- Pro git, an introduction to using git and GitHub for version control
- The tidyverse, a set of packages for data wrangling and data visualization in R
- Using the tidyverse for data wrangling in R
- Hands-on tutorial on using dplyr for data wrangling in R
- A mapping of MATLAB functions to numpy functions in Python
- python-ternary, a library for making ternary plots in Python using matplotlib
- High-performance computing using SLURM: - Introduction to SLURM and job scripting
Reading, writing, and presentation
- Playlist on academic writing by the Leadership Lab at UChicago
- How to speak by Patrick Winston at MIT
- List of commonly used phrases in academic writing
- Ten simple rules for making good oral presentations
Miscellaneous
- Lecture notes that I took during my education at IISER Pune. Currently has notes on NLD (from Strogatz), genetics (chromosome mapping, transposons, genetic screens, forward & backward genetics, CRISPR), neurobiology (mostly cellular stuff. Hodgkin-Huxley and its precursor models), statistical inference (sufficient statistics, hypothesis testing, confidence intervals, etc. from a math view. No prerequisites), statistical mechanics (Covers all of Reif’s intro textbook, culminating in statistically deriving the laws of thermodynamics. No prerequisites), measure theory (The whole thing: intro to measures, lebesgue integration, product measure and Fubini’s theorem, L^p spaces, Radon-Nikodym theorem, differentiation of measures; No prerequisites. Important results are presented in a separate document in case you don’t care for proofs), probability (Markov chains, intro to measure theoretic probability, martingale theory; Knowing measure theory is helpful for the second half, but all necessary results are introduced), stochastic processes (Markov chains ‘properly’, Brownian motion, stochastic calculus; This needs some measure theory and probability, important results are presented in the first few pages) and PDEs (transport eqn, method of characteristics, Poisson eqn and associated results for harmonic function, heat eqn, wave eqn, intro to Fourier transforms and their properties; Some proofs here and there need some results from measure theory).
- Applied Analysis, a textbook by John Hunter and Bruno Nachtergaele that covers various topics from Analysis that are relevant for (mathematically oriented) modellers (Ex: Function spaces, Linear operators, Fourier transform, Measure spaces, calculus of variations)
- Dynamic Ecology, a blog by Jeremy Fox. Discusses various aspects of ecology, evolution, modeling, etc.
- Major Revisions, an ecology podcast by working ecologists
- A guide to metaphors in ecology and evolution
- Various notions of stability in ecology
- Fantastic interview of John Maynard Smith