DNA: The Code of Life

At the most magical SHA2017 gathering I gave two presentations, “DNA: The Code of Life” and the followup, “DNA: More greatest hits” (slides). The first presentation was recorded by the wonderful CCC C3VOC streaming crew, the second one by my friend Bart Smit (who is also wonderful). Without making this post too long, I want to thank everyone who helped me do this presentation — a lot of people contributed time, advice, recording abilities, great questions and enthusiasm. Also, without the magic environment of SHA2017 it would never have happened!

After introducing how DNA works (more or less), the argument of the presentations is this: DNA in the living cell is a computing environment that can usefully be described, understood and studied using computer terminology. I of course do not say there is a CPU in there faithfully executing for-loops! I do say it has all the elements we use in programming to do things, however.

This brief blog post is meant for those of you that need some convincing before watching two hours of video. Please be aware that without narration, the slides do not make a lot of sense. Both videos are linked below.

With the exception of one clearly marked slide, nothing in these presentations is in any way controversial, and in fact, all of the actual biologists present (>7) were invited to interrupt the moment they thought something was wrong. And luckily for me, they didn’t feel the need!

Video of part 1 is here (original), YouTube copy:

Some key things covered:

  • DNA really is digital, 2 bits per nucleotide, 100 megabytes of DNA for the pufferfish, 750MB for a human being, 5 kilobytes for a virus
  • Fully compatible, atom for atom, across all life
  • Where to download the human genome & what it looks like on disk, plus what is in there.
  • What a gene is (a .o file) and isn’t and that a potato has more genes than you do
  • The DNA helix is internally redundant, like a RAID1 array, and on top of that there is a spare helix too. Except sometimes, and then some examples what the effects of that are
  • How DNA relates to RNA relates to proteins
  • The stupendous 3D printer inside our cells (Ribosome) that builds proteins from DNA and the 21 amino acid building blocks, and how 3 DNA nucleotides map to these building blocks (‘the codon table’)
  • Function calls: how the insulin DNA converts to preproinsulin (yes), and sends a signal to the insulin receptor, and why this is a stupendous computing challenge
  • How bacteria use DNA and proteins to implement an if/else if/else statement to regulate glucose levels using Boolean logic (‘Lac operon’)
  • How one bacterium implements a simple algorithm with DNA to find food
  • The three domains of life & their suspected origin, and how the original two domains merged to create us, plants, fungi etc, and how we know
  • How DNA does (stupid) code reuse and movies about that (Okazaki fragments)
  • A little bit on CRISPR, genetic fingerprinting, how the first genome sequenced was one guy who founded the consortium
  • How biological viruses are really doing exactly the same thing as when we exploit computers and launch ‘worms’.
  • RNA-SEQ: running top(1) on a living cell
  • A ton of Q&A
Second presentation

Enjoy!

Some further reading