Thursday, January 20, 2011

Entropy - on large and small scales

As stated by the Second Law of thermodynamics, entropy in the entire universe continually increases as time progresses into the future, entropy being a measure of 'disorder' or 'randomness'.
While this holds true at the scale of the entire universe, local decreases in entropy seem to be a fundamental requirement for life. All living things are remarkably ordered (and thus improbable) arrangements of matter. Enormous amounts of energy are dedicated to producing this localised order. Eventually, however, all life is doomed as the global increase in entropy progresses. Of course this will take a very long time, so for now life is still safe.
Where does this energy come from that maintains life? The Sun, our nearest star. It is also the main provider of low entropy. Apparently, the dense organisation of matter in the Sun reduces the number of degrees of freedom, compared to this matter or energy being radiated into the vacuum of space. This matter and energy can take on many more configurations outside the Sun than inside the sun.
So on a larger scale, even with all the unlikely arrangements of molecules inside living organisms, the entropy of the sun is still much lower than that of Earth. Eventually, most of this energy will evaporate into space, approaching a uniform distribution. According to the Second Law, this is the fate of our universe: an inert uniform distribution of matter and energy at a global thermal equilibrium, the state of maximum entropy.

Sunday, March 11, 2007

Hooray, genetic code!


Ever wondered why the genetic code is the way it is and exactly the same for most organisms? The explanation might come from this article, which arrives at the conclusion that the genetic code is best at encoding higher information apart from translating nucleotide triplets into amino acids.

It has already been known that the genetic code probably evolved to minimise the probability of misreads during translation by giving similar codons to the same or similar amino acids.

So what other sequence information is relevant within the coding region? Splicing sites, for instance, or sequences influencing the secondary structure of mRNA and the regular binding of histones. Also, some regulatory proteins bind to the coding region.

Of course, this calls for conflicts between the encoding of proteins on the one hand and this additional information on the other hand. The genetic code seems to minimize these conflicts.

The main reason, however, for the code to arise is thought to lie in the properties of stop codons:
first, when a frame-shift occurs during translation the probability for creating a stop codon is maximised. This is important, because otherwise the ribosome might create a useless or even harmful protein;
second, when you frame-shift a stop codon you get common codons instead of rare ones or even other stop codons. This seems to increase the higher-level information content of the genetic code.

Original paper:
Itzkovitz, S. & Alon, U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 9 February 2007

Saturday, March 10, 2007

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This is to collect and discuss ideas related to science.