Wed, 06 Oct 2004
Mark and Sweep
It's official. The human body uses a Mark and Sweep algorithm for garbage collection. From the Nobel Prize for Chemistry Press Release:
Aaron Ciechanover, Avram Hershko and Irwin Rose have brought us to realise that the cell functions as a highly-efficient checking station where proteins are built up and broken down at a furious rate. The degradation is not indiscriminate but takes place through a process that is controlled in detail so that the proteins to be broken down at any given moment are given a molecular label, a 'kiss of death', to be dramatic. The labelled proteins are then fed into the cells' "waste disposers", the so called proteasomes, where they are chopped into small pieces and destroyed. The label consists of a molecule called ubiquitin. This fastens to the protein to be destroyed, accompanies it to the proteasome where it is recognised as the key in a lock, and signals that a protein is on the way for disassembly. Shortly before the protein is squeezed into the proteasome, its ubiquitin label is disconnected for re-use.
Isn't this the opposite of mark-and-sweep?
Mark-and-sweep says: go through marking all the good stuff, then throw away anything that hasn't been marked.
Ciechanover, Hershko and Rose say: go through marking all the bad stuff, then throw away anything that has been marked.
If good stuff is easy to identify and relatively scarce, you want to do mark-and-sweep GC. If bad stuff is easy to identify and relatively scarce, you want to do ubiquitin marking.
Posted by g at Fri Nov 12 01:22:26 2004
Mark-and-sweep says: go through marking all the good stuff, then throw away anything that hasn't been marked.
Ciechanover, Hershko and Rose say: go through marking all the bad stuff, then throw away anything that has been marked.
If good stuff is easy to identify and relatively scarce, you want to do mark-and-sweep GC. If bad stuff is easy to identify and relatively scarce, you want to do ubiquitin marking.
Posted by g at Fri Nov 12 01:22:26 2004
I came this close to updating the entry after I submitted it, but forgot about it almost immediately after posting it. You're right of course, but the similarity was striking.
Posted by Zachery Bir at Fri Nov 12 02:44:47 2004
Posted by Zachery Bir at Fri Nov 12 02:44:47 2004