remain high so that
E. coli
will produce more heat-shock proteins. And once
E. coli
cools down to a comfortable temperature, its thermostat shuts down the heat-shock proteins almost completely.
E. coli’
s robust self-control comes from the feedback loops built into its network. To engineers this principle is second nature. The autopilot in a Boeing 777 uses the same kinds of feedback to keep the plane level as it is buffeted by wind shears and downdrafts. In neither case does robustness come from some all-knowing consciousness. It emerges from the network itself.
THE BIG PICTURE
Put genes together into circuits and they can do much more than they could on their own. Put circuits together and you create a living thing.
In the 1940s, Edward Tatum and other scientists got the first hints of what certain genes in
E. coli
were for. As of 2007, researchers had a pretty good idea of what about 85 percent of its genes do, making
E. coli
the gold standard of genetic familiarity. Scientists have created online databases for
E. coli’
s genes, its operons, its metabolic pathways. Mysteries remain—there are forty-one enzymes drifting around inside
E. coli
for which scientists have yet to find genes, for example—but a rough portrait of
E. coli’
s entire system is emerging, the closest thing biologists have to a complete solution to any living organism.
Bernhard Palsson, a biologist at the University of California, San Diego, has overseen the construction of a model of
E. coli’
s metabolism. As of 2007, he and his colleagues had programmed a computer with information on 1,260 genes and 2,077 reactions. The computer can use this information to calculate how much carbon flows through
E. coli’
s pathways, depending on the sort of food it eats. Palsson’s model does a good job of predicting how quickly
E. coli
will grow on a diet of glucose and how much carbon dioxide it will release. If Palsson switches off the oxygen, the model shunts carbon into an oxygen-free metabolic pathway, just as
E. coli
does. If Palsson leaves out a particular protein, the model metabolism rearranges itself just as the metabolism of a real mutant
E. coli
would. It predicts
E. coli’
s behavior in thousands of conditions. The model and
E. coli
alike make the best of whatever situation they face, adjusting their metabolism in order to grow as fast as they can.
How does
E. coli’
s metabolism manage to stay so supple when it is made up of hundreds of chemical reactions? With thousands of possible pathways it could choose from, why does it choose among the best few? Why doesn’t the whole system simply crash? Part of the solution lies in the shape of the network itself, the very layout of its labyrinth.
When scientists map the pathways that a carbon atom can take through
E. coli’
s metabolism, the picture they see looks like a bow tie. On one side of the bow tie are the chemical reactions that draw in food and break it down. These reactions follow each other along simple pathways, a fan of incoming arrows. Eventually the arrows all converge on the bow tie’s knot. There the pathways get much more complicated. The product of a reaction may get pulled into many different reactions, depending on the conditions at that moment. It is there, in the knot, that
E. coli
creates the building blocks for all its molecules. The building blocks enter the other side of the bow tie—an outgoing fan of pathways. Each pathway produces a very different sort of molecule—this one a membrane molecule, that one a piece of RNA, another one a protein. The pathways on the far side of the bow tie fan out without crossing over. A molecule on its way to becoming a protein does not become a piece of DNA.
The bow tie architecture in
E. coli
makes good engineering sense. Man-made networks, such as a telephone network or a power grid, are often laid out in a bow tie as well. A bow tie architecture lets networks run efficiently and robustly. The Internet, for example, has
E. coli
will produce more heat-shock proteins. And once
E. coli
cools down to a comfortable temperature, its thermostat shuts down the heat-shock proteins almost completely.
E. coli’
s robust self-control comes from the feedback loops built into its network. To engineers this principle is second nature. The autopilot in a Boeing 777 uses the same kinds of feedback to keep the plane level as it is buffeted by wind shears and downdrafts. In neither case does robustness come from some all-knowing consciousness. It emerges from the network itself.
THE BIG PICTURE
Put genes together into circuits and they can do much more than they could on their own. Put circuits together and you create a living thing.
In the 1940s, Edward Tatum and other scientists got the first hints of what certain genes in
E. coli
were for. As of 2007, researchers had a pretty good idea of what about 85 percent of its genes do, making
E. coli
the gold standard of genetic familiarity. Scientists have created online databases for
E. coli’
s genes, its operons, its metabolic pathways. Mysteries remain—there are forty-one enzymes drifting around inside
E. coli
for which scientists have yet to find genes, for example—but a rough portrait of
E. coli’
s entire system is emerging, the closest thing biologists have to a complete solution to any living organism.
Bernhard Palsson, a biologist at the University of California, San Diego, has overseen the construction of a model of
E. coli’
s metabolism. As of 2007, he and his colleagues had programmed a computer with information on 1,260 genes and 2,077 reactions. The computer can use this information to calculate how much carbon flows through
E. coli’
s pathways, depending on the sort of food it eats. Palsson’s model does a good job of predicting how quickly
E. coli
will grow on a diet of glucose and how much carbon dioxide it will release. If Palsson switches off the oxygen, the model shunts carbon into an oxygen-free metabolic pathway, just as
E. coli
does. If Palsson leaves out a particular protein, the model metabolism rearranges itself just as the metabolism of a real mutant
E. coli
would. It predicts
E. coli’
s behavior in thousands of conditions. The model and
E. coli
alike make the best of whatever situation they face, adjusting their metabolism in order to grow as fast as they can.
How does
E. coli’
s metabolism manage to stay so supple when it is made up of hundreds of chemical reactions? With thousands of possible pathways it could choose from, why does it choose among the best few? Why doesn’t the whole system simply crash? Part of the solution lies in the shape of the network itself, the very layout of its labyrinth.
When scientists map the pathways that a carbon atom can take through
E. coli’
s metabolism, the picture they see looks like a bow tie. On one side of the bow tie are the chemical reactions that draw in food and break it down. These reactions follow each other along simple pathways, a fan of incoming arrows. Eventually the arrows all converge on the bow tie’s knot. There the pathways get much more complicated. The product of a reaction may get pulled into many different reactions, depending on the conditions at that moment. It is there, in the knot, that
E. coli
creates the building blocks for all its molecules. The building blocks enter the other side of the bow tie—an outgoing fan of pathways. Each pathway produces a very different sort of molecule—this one a membrane molecule, that one a piece of RNA, another one a protein. The pathways on the far side of the bow tie fan out without crossing over. A molecule on its way to becoming a protein does not become a piece of DNA.
The bow tie architecture in
E. coli
makes good engineering sense. Man-made networks, such as a telephone network or a power grid, are often laid out in a bow tie as well. A bow tie architecture lets networks run efficiently and robustly. The Internet, for example, has
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