In 2011, Marc Andreessen proclaimed that software is eating the world.
He argued that software would be a key driver of innovation and value creation. The time had finally come to build on the shoulders of giants:
Six decades into the computer revolution, four decades since the invention of the microprocessor, and two decades into the rise of the modern Internet, all of the technology required to transform industries through software finally works and can be widely delivered at global scale.
And he wasn’t wrong. Over the past decade, software businesses have redefined our lives from innocent things like cat gifs to less innocent things like governmental tracking of individuals. Information was the input, algorithms were the engine, and software was the end product.
Developers were kings and they ruled over our bits.
And while software will continue to drive economic value and technological innovation we must open our blinds. The biggest challenge of this decade is climate change. Bits alone will not solve our problems in this physical world. It’s time to roll up the sleeves and get dirty with atoms.
The key to shaping our world is right under our feet 🍄
Lil’ Yeasty and I: A Symbiotic Love Story 🧫
Last weekend I started brewing a beer.
Not only was I doing research for this essay but I was also finally using the brewing kit that my girlfriend gifted me almost two years ago 🤦♂️
An entire Sunday was spent cooking up a “barley tea”, flavoring it with hops, and sanitizing the living Christ out of each and every utensil in my kitchen. The end result was a sugary liquid that would go on to meet my friend Lil’Yeasty (my girlfriend retains the naming rights).
Lil’Yeasty is a magical fungus that is addicted to sugar. Our deal is simple: I prepare a sugar bath and in return, Lil’Yeasty leaves behind the aftermath of his epic sugar binge: alcohol, carbon dioxide, and aroma. A symbiotic love story.
Lil’Yeasty starts off as a single yeast cell. He’s hungry and he likes company. After consuming sugars he doesn’t even have to invite other yeast cells, he just creates other copies of himself.
1 - 2 - 4 - 8 - 16 - 32 …. after fifteen replication cycles we have 32,768 Lil’ Yeasties. This is how small gatherings get out of hand. We call them the Yeasty Boys.
“But I always say, one's company, two's a crowd, and three's a party” - Andy Warhol
Since I didn’t know all of this just a couple of months ago, I don’t want to pretend like I know it all. What helped me was to think of fermentation in three simple steps: Feedstock → Culture → Product
🍭 Feedstock(e.g. Sugar): A feedstock is a nutrient, which is consumed and converted by a culture. In the case of beer, it is grains like barley that contain various types of sugars.
🧫 Culture(e.g. Yeast): A culture is a group of hungry little microorganisms. They go nuts when they find sugar. They consume the feedstock and convert it into a product.
💨 Product(e.g. Alcohol): A product is the end result of a crazy binge. Microorganisms consume the feedstock and transform its sugars into other chemical substances like alcohol, carbon dioxide, or aromatic esters - all the good stuff in beer 🍻
The science of brewing beer can be as easy as 1-2-3.
The “Interesting Facts About Beer Yeast” Excursion 🍻
Now that you know the basics, I’d like to push you a little deeper into the beer yeast rabbit hole 🕳
I think you’ll find it interesting and it will teach you an important lesson: Cultures have a huge impact on the end product.
We can divide beer yeasts roughly into 4 categories. Think of each category as a distinct lineage on a large family tree.
A type of yeast that replicates by creating an exact carbon copy of itself. When the copy is done it splits away. The mother cell and daughter cell have the same size and float around separately in a liquid.
The carbon dioxide molecules that the yeast produces are larger than the cell itself, that’s why single yeast cells are not carried to the top by the carbon dioxide molecules microbubbles. They just roll off and remain at the bottom of the liquid. That’s why we call them bottom-fermenting yeasts.
Another fun fact is that bottom-fermenting yeasts don’t produce a large number of aromatic compounds. That’s why bottom-fermented beers taste very clean. Think of a Lager beer or a Pils.
2) Top-fermenting Yeast (Saccharomyces cerevisiae) Meet Lil’ Yeasty’s lineage. This type of yeast replicates by budding - a process whereby the mother cell creates a new bud on its own surface. That bud is also the daughter cell. They are stuck together like a ball and chain.
Over time this collection of budding cells increases the surface area and hence acts like a sail for the carbon dioxide which is moving upward in the liquid. The yeast is carried to the top. That’s why we call them top-fermenting yeasts.
Top-fermenting yeast produces all sorts of aromatic compounds and is hence the basis for a variety of flavorful beers. Think of English Ales, Belgian strong beers, and American IPAs. All thanks to the products of top-fermenting yeasts.
3) Wild Yeast (Brettanomyces)
Bottom-fermenting and top-fermenting yeasts are different but at least they are pure-bred. It’s the stuff that is packaged and sold. Wild yeast on the other hand is feral. It lives in nature and is a completely different breed of yeast.
Wild yeast is the reason why you can’t leave food or sugary drinks out in the open for extended periods of time. Wild yeast will go ham and start converting those sugars into all sorts of funky flavors and colors.
Some beer styles depend on this funk. Think of Belgian sour beers or Aged Beef. This is the power of rotting.
In my beer sommelier training, we would describe the distinct flavor as “sweaty horse saddle”. And that’s a desired flavor … go figure 🤷♂️
Technically, a wild yeast, the interesting thing about this guy is that it has indigestion. It cannot convert maltose and maltotriose. This means that you get the carbonation minus the alcohol.
Also, since maltose and maltotriose are not consumed and converted they still remain in the non-alcoholic beer. This is why most non-alcoholic beers taste slightly sweet.
The point I want to drive home with this: Using exactly the same feedstock with four different cultures will get you four vastly different results. The starting point is the same but the end result is different.
All of those cultures carry different instructions.
Fermentation Is a Primal Technology
Think of all the culinary products like beer, wine, kombucha, kimchi, sauerkraut, pickles, kefir, tempeh, miso, yogurt, cheese, bread, vinegar, hot sauce, and so much more. Other applications include pharmaceuticals, antibiotics, bioplastics, and energy from bioreactors. All of those are products of fermentation.
We got here by domesticating microorganisms.
First, we identified, isolated, and understood them, then, we kickstarted a symbiotic relationship. We give them feedstock, they give us product. Cultures all around the world have utilized fermentation for millennia.
Barley tea → Yeast → Beer
Grapes → Yeast → Wine
Milk → Lactobacillus → Kefir
Cabbage → Lactobacillus → Kimchi
The process is always the same: Feedstock → Culture → Product
In my case, I gave Lil’ Yeasty a sugary barley tea and he is giving me an IPA. Sounds fair to me.
In a way, fermentation has been one of our oldest technologies.
In computer science - a newer technology - algorithms are a set of instructions to solve a specific problem. This means manipulating input data into output data. In fermentation, a culture acts in a similar way to a computer algorithm: It converts an input into an output. Each microorganism carries a different set of instructions.
Computer science and fermentation are not too different after all. Both help us to solve problems. One in the digital world, the other in the real world.
Cracking the Code of the Real World 🌎
Alright, alright… so why does all of this matter?
To solve climate change we have to reduce, replace, and remove carbon.
It is not enough to hack into the matrix and change a couple of lines of code. Instead, we have to work with the laws of physics and chemistry. For centuries, scientists have tried to decode the laws of nature and we are finally at a point where we start to comprehend the symphony that makes our world tick.
Building on the Shoulders of Giants
Breakthroughs in machine learning and AI have expanded the scope of the possible.
Today in partnership with @emblebi, we’re releasing predicted structures for nearly all catalogued proteins known to science, which will expand the #AlphaFold database by over 200x - from nearly 1 million to 200+ million structures: dpmd.ai/AF-22-TW 1/
I’ll explain the Protein Folding breakthrough in simple terms:
Previously: For a long time, scientists have known about ~200 million different proteins. They knew which elements these proteins consisted of. Think of it as a one-dimensional (1D) chain of letters that spells out each and every element of a protein.
Problem: Despite knowing the various elements of the proteins, scientists didn’t know how the protein’s three-dimensional (3D) structure would look like. As DeepMind says “knowing a protein’s structure unlocks a greater understanding of what it does and how it works”. It was like seeing a library of books but not knowing the alphabet.
Solution: DeepMind used an AI system called AlphaFold “to predict the 3D structure of a protein just from its 1D amino acid sequence”. They predicted ~200,000,000 protein structures and put them up in a freely searchable database 🤯
This is what they have done 👇
We hoped this groundbreaking resource would help accelerate scientific research and discovery globally, and that other teams could learn from and build on the advances we made with AlphaFold to create further breakthroughs. That hope has become a reality far quicker than we had dared to dream. Just twelve months later, AlphaFold has been accessed by more than half a million researchers and used to accelerate progress on important real-world problems ranging from plastic pollution to antibiotic resistance.
Where it gets interesting is that this protein database includes newly predicted protein structures from plants (feedstock), bacteria, and fungi (cultures).
My bet is that this breakthrough unlocks the READ function to our biological library and as a result, we will learn much much faster.
WRITE: Faster Experimentation Cycles
CRISPR/Cas9 is another mega trend which will accelerate scientific progress.
Think of CRISPR as a text editor for genomes. This part of the genome is causing a malfunction. It allows you to isolate and edit parts of a genome that might cause a malfunction. Just like I did up here 👆
Since 2013, this technology has been used to edit wine yeast to improve flavor and quality of the final product. Science gives us WRITE access to the code base of our world 🤯 How cool is that?!
Faster learning and faster experimentation are like a cheat code for accelerated progress. It’s the scientific method on steroids.
I wish I’d had this combo back in school.
Fermentation Is Eating the World 🍄
Let’s bring it full circle.
Over the past decade, software has dined well and we are reaping the benefits. Advances in AI and gene-editing are allowing us to finally advance at a much faster rate. These trends also accelerate one key technology: Fermentation.
Not only does all of this sound like science fiction but it is also great for the planet. Smaller footprint, fewer emissions, better products. What’s not to like?
Technology pioneer Steven Brand once said: “We are as gods and might as well get good at it.” It seems we’re finally getting there. All of the technology required to transform industries through fermentation finally works and can be widely delivered at a global scale.
Whatever it is that you can relate to, whether it is brewing beer, baking a loaf of bread, or just enjoying some pickled cucumbers, I would ask you one favor: Use your passion for this product to learn a little bit more about fermentation.
Who knows… maybe you’ll follow your curiosity and learn how to re-shape the atoms around you.
The world is our feedstock and fermentation is our alchemy.
Dear reader, I’d love to hear from you. If you enjoyed this essay, please help a brother out and share it with people who might find this interesting. Thank you!
