## Posts Tagged ‘infotheory’

### Alignment-free sequence comparison: benefits, applications, and tools

Monday, November 13th, 2017

Might be useful for noncoding comparisons

Alignment-free seq. comparison: benefits, apps & tools
https://GenomeBiology.biomedcentral.com/articles/10.1186/s13059-017-1319-7 Great tidbits, viz: Shannon asked von Neumann what to call his info measure – “Why don’t you call it entropy…no one understands entropy…so in any discussion, you’ll be in a position of advantage.”

QT:{{”
“Reportedly, Claude Shannon, who was a mathematician working at Bell Labs, asked John von Neumann what he should call his newly developed measure of information content; “Why don’t you call it entropy,” said von Neumann, “[…] no one understands entropy very well so in any discussion you will be in a position of advantage […]” []. The concept of Shannon entropy came from the observation that some English words, such as “the” or “a”, are very frequent and thus unsurprising” ….
“The calculation of a distance between sequences using complexity (compression) is relatively straightforward (Fig. ). This procedure takes the sequences being compared (x = ATGTGTG and y = CATGTG) and concatenates them to create one longer sequence (xy = ATGTGTGCATGTG). If x and y are exactly the same, then the complexity (compressed length) of xy will be very close to the complexity of the individual x or y. However, if x and y are dissimilar, then the complexity of xy (length of compressed xy) will tend to the cumulative complexities of x and y.”

“Intriguingly, BLOSUM matrices, which are the most commonly used substitution matrix series for protein sequence alignments, were found to have been miscalculated years ago and yet produced significantly better alignments than their corrected modern version (RBLOSUM) []; this paradox remains a mystery.”
“}}

### Professor Sir David MacKay, physicist – obituary

Monday, July 4th, 2016

QT:{{”
“It was here that the consumer could make a difference: “ ’Turn your thermostat down’ is, by my reckoning, the single best piece of advice you can give someone,” he told an interviewer. “So is ‘fly less’ and ‘drive less’. But hybrid cars and home windmills are just greenwash.”

David MacKay (with energy-efficient bicycle): ‘I love renewables, but I’m also pro-arithmetic’ Credit: Graham Turner

In July 2015 MacKay was diagnosed with terminal stomach cancer, for which he underwent chemotherapy, a process he documented on a blog, “Everything is Connected”.

On April 10, just four days before his death, he posted an “open letter” to the directors of Addenbrooke’s Hospital in Cambridge in which he wrote: “The hospital is a great one, the staff are wonderful, and I’m grateful for everything the NHS does for me here. But I do have just one impassioned question and plea… Why oh why oh why does [the hospital] not have any semblance of intelligent thermal environmental control?””
“}}

http://www.telegraph.co.uk/obituaries/2016/04/15/professor-sir-david-mackay-physicist–obituary/

Obit quotes him days before his death: “Why oh why…does [the hospital] not have any…intelligent thermal…control?”

### How Information Theory Handles Cell Signaling and Uncertainty

Tuesday, February 4th, 2014

Matthew D. Brennan, Raymond Cheong, and Andre Levchenko

Science. 2012 October 19; 338(6105): 10.1126/science.1227946. doi: 10.1126/science.1227946
PMCID: PMC3820285
NIHMSID: NIHMS512743

How Information Theory Handles #Cell Signaling & Uncertainty… really well since it’s ideal for noisy communication
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820285/?report=classic

### Quantum physics: A grip on misbehaviour : Nature : Nature Publishing Group

Thursday, September 12th, 2013

Interesting discussion of how to tell apart classical and quantum systems using Bells inequality. The basic idea is finding more correlated events between two separate
systems than one might expect classically were they are decoupled. This implies that there is a quantum characteristic to the system. This fact can be exploited to measure the degree to which two systems are behaving as a “quantum unit” in relation to cryptographic applications and large-scale quantum
computation.

http://www.nature.com/nature/podcast/v496/n7446/nature-2013-04-25.html

#Quantum physics: A grip on misbehaviour – explains how Bell’s inequality quantifies #entanglement
http://www.nature.com/nature/journal/v496/n7446/full/496436a.html #QM