Book Notes: Microbes, Gene Editing and a Terrible Disease

It is something I don’t talk about very often but I love science, biology , biotech and in I try to stay up to date on these topics so from time to time I try to read scientific divulgation books.

I had some pending books on my “to-read list” so in November I bought three of those books (birthday present to myself) and spent the Christmas holidays reading them. I’ll share some notes in this post.

1. The emperor of all Maladies: This has become a classic book on the subject of cancer and has received extensive media coverage (it even became a PBS documentary). The books tells the story of cancer, how the first treatments were developed and why it is so complex and hard to cure. Some Insights and facts that caught my attention reading this book:

  • Until “very recently” , we were in the dark ages of medicine: From the perspective of scientific and technological progress, the 1800’s don’t feel so far away. I don’t know why but in my head I had imagined these period somehow as being part of our “modernity”, yet it was only in 1846 that we started using anesthesia to do surgeries, and in 1867 we started using carbolic acid to perform surgeries. No doubt surgeries were perceived as a last resource remedy. Imagine the agony and the risk involved in a simple surgery.
  • As a disease Cancer has been documented since very ancient times. In 1862 Edwin Smith an American Egyptologist, purchased a Papyrus in Luxor, Egypt from an Egyptian dealer. It happened to be an ancient medical text, describing 48 cases of injuries, fractures, wounds, dislocations and yes, a case (number 45) that seems to describe a breast tumor.
  • How aggressive , disruptive and experimental the evolution of treatments have been. In our attempt to eradicate malignant cancer cells the treatment itself almost kills us.
  • A lot of progress has been made both in treating and preventing cancer and there are genetic treatment that have demonstrated excellent results but the book explains that part of the complexity in our fight to defeat cancer is that it exploits the fundamental logic of evolution unlike any other illness. Even though we are closer than ever to target very specific mutations (as described in the other books covered in this article) we are not even close to understand the million ways that the approximately 20,000 proteins in our cell interact with dozens if not hundreds of other proteins so that altering one specific mutation to prevent cancer does not lead to an unexpected additional mutation worst that the original.

2 . I Contain Multitudes: We have always perceived microbes and parasites as something to avoid at all costs, they are to blame for terrible diseases. Ed Yong’s book take us on a tour to the latest research about microbes and gives a more nuanced and balanced view about these very special creatures that live inside and among us.

With the use of Metagenomics we are now able to detect at a very precise degree, what combination of microbes exist in a biological sample. The latests research shows that microbes are very relevant to our general well-being, so we shouldn’t try to avoid them,and instead we should strive to get a balanced mix of microbes. They not only influence how we digest food. They play a major role in our complete immune system, our mental well being and are related to diseases as Autism, IBD, Depression and Obesity to name a few. The immune system isn’t just a means of controlling microbes. It is at least partly controlled by microbes.

It has been shown that the use of Probiotics doesn’t really make a big difference in our gut microbiome balance, but when we eat certain foods, we feed our microbes and indirectly promote the growth of some microbes over the other, this is called Prebiotics.

Just as genetic sequencing gave birth to companies like 23andMe offering sequencing as a commercial product to end users. There are a few companies now that can give you personalized health recommendations based on your gut biome and also early success stories in therapeutic use.

It is worth noting that, as a Science Journalist, Ed Yong made a terrific job covering Covid-19 during 2020 in the Atlantic. I also recommend taking a look at his TED talk.

3. Editing Humanity: This is the most recent of the three books. It covers the story of how the new CRISPR gene editing techniques developed. The scientists and labs behind them (also the patent disputes). The breakthroughs and innovation in disease treatment currently being developed and the inevitable arrival of the possibility of human genomic editing and the implications to us as a society.

CRISPR is part of the bacteria inmune system, it is a mechanism that allow bacteria to defend against viruses by cutting their DNA ( viruses are some of the bacterias fiercest enemies).

This book, tells the story of how the mechanism was first discovered by a Spanish scientist and confirmed by some researchers from a Danish dairy company, then it describes how this mechanism was engineered (taking advantage of the latest mRNA research) , so that we could tell the enzymes the exact piece of DNA to cut and replace it with a new sequence.

The book also explains how error prone the first experiments where with the basic CRISPR Cas9 mechanism and how the technology is evolving to become a precise “molecular editor” capable of replacing single bases without cutting DNA.

One major difference in the approach to gene editing is whether it used to edit someone cell to repair an unwanted mutation that causes a disease (somatic gene editing) versus editing a single reproductive cell or gamete, just before the fertilization takes places.

The first approach involves fixing DNA in millions of cells and is error prone, the second approach involves just editing one single cell but it makes the change heritable, so it basically implies the potential ability to alter human evolution. This has triggered a lot of debate in the scientific community, specially because most of the tools and supplies to perform have a very low barrier to entry.

Final Thoughts

Since I read Ray Kurzweil’s book The Singularity Is Near: When Humans Transcend Biology (back in 2005) I have tried to follow up on the promise of Genetics, Nanotechnology and Robotics. Of the three , I guess Nanotechnology really has not delivered on Kurzweil expectations (who by the way , works at Google since 2012), but Robotics has continued to evolve to a very impressive degree, you can check the Boston Dynamics Christmas christmas robot dance.
But of the three, I think nothing has evolved as fast, as genetics and biotech in general.

We have been hearing that software is eating the world, but now we also now that bio is eating the world. Advances in Biotechnology are evolving at neck breaking speed. Just a few years ago this all sounded like science fiction but just as I was finished reading these books DeepMind announced the Protein Folding problem has practically been solved.

Like the Silicon Valley Startup ecosystem, there is a whole ecosystem of biotech startups. This is also leading to a whole new wave of investment opportunities.

Having the ability to edit genes in a precise way while also solving the folding problem are two major achievements, I wonder why they receive so little attention.

I am sure in the following years (months?) we will be hearing a lot of new discoveries and breakthroughs.

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