Table of contents of currently written content:

  1. Introduction & Housekeeping notes
    Who this book is for, and what is in there.

  2. Book status
    For beta readers: what to expect at this stage

  3. A brief history of 4 billion years of life
    Covers a lot of history, but also lays out the very basics of how life works

  4. The size of life: 350 kilobytes
    Just how small can life get? Is more DNA better? How much information is really in there?

  5. Ribosome: The Bio Constructor
    In all life hides the ribosome, a 3D printer that easily prints copies of itself. Or of basically anything that lives.

  6. Central Dogma & RNA World
    Why do we need RNA? Or, why do we need DNA? Could you build life out of nothing but RNA?

  7. How life actually gets stuff done: the lac operon
    DNA is a lot about information. But how does life get anything done? This chapter presents a basic bacterial algorithm, implemented in DNA, RNA and proteins.

  8. The mysteriously universal codon table
    Three letters of DNA map to an amino acid. The mapping table is almost entirely identical among all of life, and has been so for billions of years.

  9. A bit of chemistry
    While this book may sometimes take a somewhat digital, information-centric, look at life, there is also a lot of chemistry and physics going on. Here we delve deeper into that world.

  10. Recapping: how bacterial life works, on one page
    A preposterously brief summary of how bacterial life works, bringing a lot of previous chapters together.

  11. Intermezzo: the discovery of the genetic code & synthesis of insulin
    So how did we work out the codon table? Or even that there was a table? And how did this lead to the unreasonably swift synthesis of insulin?

  12. DNA’s repair mechanisms
    The rate at which DNA mutates needs to be kept very low. Nature uses stupendous tricks to repair damage.

  13. How labs select and copy DNA: PCR
    Made famous by the COVID-19 pandemic, this key technique deserves a full explanation.

  14. Reading/sequencing DNA
    How do you read/sequence DNA in practice? What kind of files come out? What does it cost?

  15. Files and Resources: where to find them
    With the advent of open data, you can be quite the biologist from your home, without ever going to a lab. Here is where to find the data.

  16. Life as technology: the acorn
    Is life technology? How would you make building materials from scratch? Behold the technology of the.. acorn

  17. Storing the pan-genome
    Current DNA file storage technologies capture singular sequences. But life is nothing like this. Eventually software will have to change.

  18. Error correction: why sex exists
    Without sex, it turns out life would degrade quickly. It turns out the concept of sex, or things a bit like it, is absolutely vital for life. Even bacteria ‘do it’.

  19. Diving into DNA: Patterns & Entropy
    Although DNA is a complicated molecule, we can also study it as pure information. Turns out this can teach us a lot

  20. Okazaki Fragments & GC Skew: How an odd asymmetry could teach us a lot
    DNA replication proceeds in a rather bizarre way that no sane designer would ever have come up with. This asymmetrical replication has led to some interesting forensic traces in bacterial DNA, as yet unexplained. WARNING: Original research!

  21. Modularity, complexity, intelligence: what nature tells us
    We previously talked about the acorn as technology that vastly outclasses anything we can do. What else can we learn from nature’s technology?

  22. Life within us: Transposable elements
    There is life in the sea, in the air, on plants, underground, in rocks, between our toes. And it turns out: there is also life within our genomes.

  23. DNA Forensics, Crime and genealogy
    Supposedly our DNA is copied very faithfully, and we share almost all of it with the rest of our species. So just how do forensic investigators use DNA to do their investigations? And how can it be used to trace family links?

  24. Epigenetics, methylation and imprinting
    DNA is more than four nucleotides. It turns out genetic material can be annotated in many ways, some of which are heritable, while some only impact a single generation, depending on circumstances.

  25. Special chromosomes & Haplogroups
    Our X, Y and mitochondrial chromosomes are special in how they (don’t) recombine. This gives them a certain purity that makes them an attractive way to study family relations, but also migration and inter-species breeding patterns. Yes.

  26. Mutations and Changes
    Are DNA mutations random? Where do they come from? Do all genomes and genes evolve at the same rate?

  27. What’s in a gene? Introns & Exons
    Even genes consist of vast tracts of unused DNA. And we barely understand how that came to be, or why it is so?

  28. Bacterial Virus Warfare
    Bacteria and viruses have been waging war for billions of years, and we are privileged to watch what techniques attackers and defenders have developed over that time. Because microbial life puts an existential premium on simplicity, the solutions found are elegant and minimal, and also highly reusable by science and medicine.

  29. Genetic Manipulation, CRISPR & beyond
    So how does genetic manipulation actually work? Touches on historical techniques, upcoming ones like CRISPR, and what it might mean for the ability to ‘live patch’ the DNA of living human beings.

  30. Our amazing immune system
    DNA is the way our body stores data. Normally DNA is quite static, but our immune system very much is not: it learns from earlier diseases by evolving novel defenses. And of course, it uses DNA to store this knowledge.

  31. How the SARS-CoV-2 vaccines work: mRNA
    So just what IS in those vaccines? And how do they turn some of our cells into compelling lessons for our immune system?

  32. Intermezzo: DNA, RNA and Cancer treatments
    With all we have learned, great things are becoming possible in the treatment of cancer. Here we discuss what cancer is on a fundamental level, and what new techniques are being used to combat it.

  33. The forgotten RNA genes & RNA-seq
    We hear the human genome consists of 20,000 genes. But there are another 20,000 RNA genes we rarely hear about. These are simultaneously very important and also very badly understood. Here we learn about these RNA constructs and how they are studied.

  34. Is biology too complex to understand?
    Although we know many things already, will we ever truly understand life and biology? And if not, what should we do?

  35. Protein folding & quantum things We know the “source code” of proteins. Proteins act through their specific shape, and it would be great if we could predict this shape from the DNA source. But we can’t. Recently there have been some tremendous deep learning breakthroughs, and these are indeed breakthroughs, but perhaps not quite the ones they are presented to be.

  36. 23 and you: what your genome doesn’t mean
    When the human genome was first sequenced the world hoped that this would deliver immediate benefits on how disease worked, and which genetic variations were harmful. Now over 20 years later it has become clear that most DNA mutations don’t tell us anything meaningful

  37. But is it safe?
    With DNA and molecular biology, both life and we can do astounding things. But also terrible things. In this chapter I take a look if what we are doing is inherently scary or not, and what could possibly go wrong. Not a fun chapter.

  38. Intermezzo: Curing disease with gene therapy
    What is the state of gene therapy really like? Which diseases can be cured, and what are the technologies used?

  39. Recommended and fun literature
    References, but also recommended books that complement this book and are great fun to read

  40. Glossary
    A quixotically ordered list of terms used in this book

TODO .. perhaps .. :