Table of contents of currently written content:
- Introduction & Housekeeping notes
Who this book is for, and what is in there.
- Book status
For beta readers: what to expect at this stage
- 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
- The size of life: 350 kilobytes
Just how small can life get? Is more DNA better? How much information is really in there?
- 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.
- Central Dogma & RNA World
Why do we need RNA? Or, why do we need DNA? Could you build life out of nothing but RNA?
- 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.
- 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.
- 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.
- Recapping: how bacterial life works, on one page
A preposterously brief summary of how bacterial life works, bringing a lot of previous chapters together.
- DNA’s repair mechanisms
The rate at which DNA mutates needs to be kept very low. Nature uses stupendous tricks to repair damage.
- How labs select and copy DNA: PCR
Made famous by the COVID-19 pandemic, this key technique deserves a full explanation.
- Reading/sequencing DNA
How do you read/sequence DNA in practice? What kind of files come out? What does it cost?
- 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.
- Life as technology: the acorn
Is life technology? How would you make building materials from scratch? Behold the technology of the.. acorn
- Storing the pan-genome
Current DNA file storage technologies capture singular sequences. But life is nothing like this. Eventually software will have to change.
- 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’.
- 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
- 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!
- 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?
- 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.
- 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?
- 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.
- 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.
- Mutations and Changes
Are DNA mutations random? Where do they come from? Do all genomes and genes evolve at the same rate?
- 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?
- 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.
- 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.
- 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.
- 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?
- 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?
- 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
- 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.
- Recommended and fun literature
References, but also recommended books that complement this book and are great fun to read
A quixotically ordered list of terms used in this book
TODO .. perhaps .. :
- Work in non-coding RNA more!!
- Immortal cell lines, vero cells etc, how adenovirus vaccines are produced