HeyJaredthe biology reboot.
My notes on synthetic biology and cellular computing. In your inbox, weekly.
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cellular function, the chinese room, and the wall (opens the original)
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A man finds himself locked in a room with a booklet that maps one set of symbols to another. He sees that a message on paper has been slipped under the door, and when he looks it over, sees that it contains the same symbols in the booklet. Following the instructions in the booklet, he maps the message to its outputs, writes it out on the piece of paper, and slides it back under the door.This goes on for a while. The people outside the room think they are having an intelligent conversation in Chi
dna watermarking (opens the original)
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JCVI-syn1.0 was revealed in 2010 by the J. Craig Venter Institute as the first self-replicating bacterial cell to contain a completely synthetic genome. But that wasn’t the only interesting thing about it: its creators also announced that they had inserted DNA sequences into its genome that encoded the names of 46 project contributors, several famous historical quotations, and finally, an email address to write to if anyone cracked the code containing these messages. The scientists behind JCVI-s
could a synthetic biologist understand a microprocessor? (opens the original)
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Molecular biology is centered on a belief that cells have some sort of decipherable structure that we can piece together through experimental and theoretical inquiry. However, it’s not really clear whether the way we go about learning about biological systems will actually help us understand1 how they work. In 2002, cancer biologist Yuri Lazebnik published a now well-known paper (also a fun read!) attempting to answer this question by thinking through how a biologist might fix a broken radio.
quantifying biological information (opens the original)
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[The second short post in an exploration of biological information that I started here last month.]Information is an important word in biology, and one that has many meanings. It can be used to refer to evidence from which we can infer a biological state (such as using tree rings to estimate the age of a tree), a statistical dependence between two variables (like a genotype associated with a particular phenotype), and features that regulate and specify cellular behavior (like gene regulatory net
revisiting “cellular computing” (opens the original)
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The words “computing,” “information processing” and “circuit” (and related engineering language) are thrown around loosely in molecular biology and synthetic biology (including in earlier posts in this newsletter, unfortunately). Molecular biologists claim that processes like computation occur in various biological modalities, including gene expression, gene regulatory networks and signaling pathways, but there is no clear definition for most of the engineering language that they use. The lack o
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