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Biology is Chemistry Plus Algorithms
Biology is Chemistry Plus Algorithms
Manoj Gopalkrishnan
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Biology is Chemistry Plus Algorithms
The quaint inhabitants of the planet Htrae worship Soup. Their religion preaches that all life is made up of sachets of soup. Every time they have a question (is my food safe? am i going to get better from this sickness?) or a wish (make me a potion that will build my strength, give me seeds that can withstand drought and pestilence), they give priests their requests to drop into bowls of soup. The bowls of soup answer their questions and grant their wishes. If you noticed that Htrae is Earth written backwards, you may have guessed that we are talking about our own planet, not some alien civilization. Soup is molecular testing which has become familiar to us in Covid times. All life is indeed made up of small sachets of sentient soup which we call cells. Every day on our planet, our priests whom we call pathologists and microbiologists, get hundreds of millions of requests for testing samples for viruses or genetic modifications or food safety and myriad other use cases.
Since at least tens of thousands of years, humanity has known that trees arise from seeds. Ancient and modern philosophers have wondered how mighty trees can emerge from tiny seeds. Where is the tree inside the seed? Today we know that all life is made up of small sachets of sentient soup which we call cells. These cells contain DNA which has been called the blueprint of life. In other words, there is no miniature tree inside a seed, but there are instructions for making a tree. When these instructions are executed, the miracle of life unfolds.
The Philosophical Foundation
There is something surprising about this insight that seeds contain the blueprint for making trees which I want to attempt to bring out. Consider a cell from another point of view: that of Chemistry. Let me set down three assertions which I am going to use as axioms for my argument:
A cell is made up of nothing more than molecules.
Each individual molecule in a cell is an ordinary molecule obeying the laws of Chemistry and Physics as we know them.
You can pick any single molecule from a cell for study, and you can study it for as long as you like, and you will not find any deviation from these laws.
These axioms were not self-evident to even great scientists of the 19th century. One of the great unremarked philosophical shifts in our thinking has been the universal acceptance of some form of these axioms among all scientific workers engaged in the study of Biology in the 20th century. I believe this acceptance has played a key role in enabling the advances of Molecular Biology and Biotechnology.
The Nature of Potential
Archimedes was famously asked by King Hieron II whether a bar of gold had silver in it. Imagine if the king had asked Archimedes whether a seed had a tree in it. Perhaps a modern-day Archimedean chemist might make a list of all molecules that a tree produces, and find at least one kind of molecule that a tree produces that the seed does not contain. This would conclusively prove that a seed does not have a tree in it. This would be right, in a way. But as we have seen, it is also wrong, in a way.
This is the surprising insight. The tree is not there inside the seed in fact, but it is there in potential. We are used to thinking of matter as inert, something that "is." The idea that it can have potential and can "become" is something so surprising that for millennia we have rejected it except in our fantasies of magicians and sorcerers. We have been unwilling to accept that the same laws of nature apply to both living and non-living systems. We have invented dualities in our philosophies to set aside room for this ability of living systems to become.
From Computer Programs to Biological Systems
Just like DNA is "just another molecule", a computer program is "just another string." A program to play the game of Pacman does not contain within it the game of Pacman in fact. I can read the program as a string and I will not experience the joy of playing Pacman, at least not unless I run the program in my head. But it does contain the game in potential. When the program is run, the game unfolds.
I hope I have convinced you that a living cell is a bag of molecules obeying chemistry plus the potential to become other bags of molecules encoded in a blueprint. In other words, Biology can be understood as Chemistry plus Algorithms. Chemistry helps understand "what is" and the Algorithmic viewpoint helps us understand "what can become."
The Birth of Molecular Computing
There is a practical side to this equation that holds the potential to building technology that the world desperately needs today. We started with a biological cell and understood it as a sum-of-parts consisting of Chemistry and Algorithms. Going the other way, we can ask what can we build by introducing Algorithms into a Chemical milieu.
Len Adleman asked precisely this question in 1994. He encoded an instance of a computational problem known as the Traveling Salesman Problem into molecules of DNA so that the solution to the problem would be revealed by Chemistry. This was a demonstration that there was a path the other way: we can add Algorithms to Chemistry and create systems of molecules that can exhibit behaviour of a sophistication we do not typically associate with Chemistry. This field has come to be known as Molecular Computing.
The Future of Molecular Computing
Molecular Computing is building molecular systems that can respond to their environment in sophisticated ways. We are rediscovering the abilities of biological systems, but this time from an engineer's lens. We are still early in this journey, and what we are building is to the marvels of biology as a flea is to an elephant. But the field is growing fast. We are seeing another Moore's law, this time in our ability to program molecules to do our bidding. As we progress on this journey, we will create technology that will help humanity eat better, live healthier, build in a net-zero manner, and get the power to protect our communities, our ecosystems and our planet. This time, it is the turn of soup to save the planet.
Biology is Chemistry Plus Algorithms
The quaint inhabitants of the planet Htrae worship Soup. Their religion preaches that all life is made up of sachets of soup. Every time they have a question (is my food safe? am i going to get better from this sickness?) or a wish (make me a potion that will build my strength, give me seeds that can withstand drought and pestilence), they give priests their requests to drop into bowls of soup. The bowls of soup answer their questions and grant their wishes. If you noticed that Htrae is Earth written backwards, you may have guessed that we are talking about our own planet, not some alien civilization. Soup is molecular testing which has become familiar to us in Covid times. All life is indeed made up of small sachets of sentient soup which we call cells. Every day on our planet, our priests whom we call pathologists and microbiologists, get hundreds of millions of requests for testing samples for viruses or genetic modifications or food safety and myriad other use cases.
Since at least tens of thousands of years, humanity has known that trees arise from seeds. Ancient and modern philosophers have wondered how mighty trees can emerge from tiny seeds. Where is the tree inside the seed? Today we know that all life is made up of small sachets of sentient soup which we call cells. These cells contain DNA which has been called the blueprint of life. In other words, there is no miniature tree inside a seed, but there are instructions for making a tree. When these instructions are executed, the miracle of life unfolds.
The Philosophical Foundation
There is something surprising about this insight that seeds contain the blueprint for making trees which I want to attempt to bring out. Consider a cell from another point of view: that of Chemistry. Let me set down three assertions which I am going to use as axioms for my argument:
A cell is made up of nothing more than molecules.
Each individual molecule in a cell is an ordinary molecule obeying the laws of Chemistry and Physics as we know them.
You can pick any single molecule from a cell for study, and you can study it for as long as you like, and you will not find any deviation from these laws.
These axioms were not self-evident to even great scientists of the 19th century. One of the great unremarked philosophical shifts in our thinking has been the universal acceptance of some form of these axioms among all scientific workers engaged in the study of Biology in the 20th century. I believe this acceptance has played a key role in enabling the advances of Molecular Biology and Biotechnology.
The Nature of Potential
Archimedes was famously asked by King Hieron II whether a bar of gold had silver in it. Imagine if the king had asked Archimedes whether a seed had a tree in it. Perhaps a modern-day Archimedean chemist might make a list of all molecules that a tree produces, and find at least one kind of molecule that a tree produces that the seed does not contain. This would conclusively prove that a seed does not have a tree in it. This would be right, in a way. But as we have seen, it is also wrong, in a way.
This is the surprising insight. The tree is not there inside the seed in fact, but it is there in potential. We are used to thinking of matter as inert, something that "is." The idea that it can have potential and can "become" is something so surprising that for millennia we have rejected it except in our fantasies of magicians and sorcerers. We have been unwilling to accept that the same laws of nature apply to both living and non-living systems. We have invented dualities in our philosophies to set aside room for this ability of living systems to become.
From Computer Programs to Biological Systems
Just like DNA is "just another molecule", a computer program is "just another string." A program to play the game of Pacman does not contain within it the game of Pacman in fact. I can read the program as a string and I will not experience the joy of playing Pacman, at least not unless I run the program in my head. But it does contain the game in potential. When the program is run, the game unfolds.
I hope I have convinced you that a living cell is a bag of molecules obeying chemistry plus the potential to become other bags of molecules encoded in a blueprint. In other words, Biology can be understood as Chemistry plus Algorithms. Chemistry helps understand "what is" and the Algorithmic viewpoint helps us understand "what can become."
The Birth of Molecular Computing
There is a practical side to this equation that holds the potential to building technology that the world desperately needs today. We started with a biological cell and understood it as a sum-of-parts consisting of Chemistry and Algorithms. Going the other way, we can ask what can we build by introducing Algorithms into a Chemical milieu.
Len Adleman asked precisely this question in 1994. He encoded an instance of a computational problem known as the Traveling Salesman Problem into molecules of DNA so that the solution to the problem would be revealed by Chemistry. This was a demonstration that there was a path the other way: we can add Algorithms to Chemistry and create systems of molecules that can exhibit behaviour of a sophistication we do not typically associate with Chemistry. This field has come to be known as Molecular Computing.
The Future of Molecular Computing
Molecular Computing is building molecular systems that can respond to their environment in sophisticated ways. We are rediscovering the abilities of biological systems, but this time from an engineer's lens. We are still early in this journey, and what we are building is to the marvels of biology as a flea is to an elephant. But the field is growing fast. We are seeing another Moore's law, this time in our ability to program molecules to do our bidding. As we progress on this journey, we will create technology that will help humanity eat better, live healthier, build in a net-zero manner, and get the power to protect our communities, our ecosystems and our planet. This time, it is the turn of soup to save the planet.