Bayesian Inference

Bayesian inference is way of reasoning which integrates uncertainty. It is a statistical approach to reasoning.

Strong syllogisms are statements like:
1. A implies B
2. B implies C
3. A is true, therefore C is true

However most experimental, and almost all daily reasoning works within a much weaker framework

1. D implies E
2. E is true, therefore the existent of D becomes more probable.

Example 1:
(E) It is cloudy, therefore (D) it is more likely to rain later --> Decision: Take an umbrella.

Most practical and scientific reasoning relies on this.

However consider the case of Ireland:

Example 2, Ireland:
(E1) It is sunny now (E2) we are in Ireland (E) it is still likely to rain later --> Decision: Taka an umbrella

Obviously, the fact that you are located in rainy Ireland modifies the reasoning process (in Bayesian language it represents a high prior probability of rain) . Many facts may modify the reasoning process, Bayesian inference provides a simple mathematical framework to perform

I was introduced to these ideas in E.T. Jaynes book, a very readable chatty introduction to probability, http://bayes.wustl.edu/for more infor

10 Facts about R-Loops

10 facts about R-loops (please add facts in the comments)

1. Cellular structures that are a DNA-RNA Hybrid
2. R-loops are 3 stranded Structures: Made when an RNA hybridizes to a complementary DNA and a single-stranded DNA
3. First described in 1976
3.1 First evidence for R-loop formation in Bacteria 1994, then rapidly in other organisms as well
4. First observed by electron microscopy under conditions of 70% formamide, more thermodynamically stable then double-stranded DNA under these conditions
5. Essential positive function in human mitochondrial DNA replication
6. Can be probed with antibodies
7. Two views:
  7.1 Co-Transcriptional -- RNA forms in cis during transcription behind the RNA polymerase
  7.2 Movable -- can hybridize to homologous DNA at another location besides the location of transcription.
8. R-loops are associated with epigenetic mechanisms governing transcription.
9. Many proteins regulate R-loop concentration either directly or indirectly, most prevent RNA from hybridizing to DNA
10. Repetitive non-template DNA strand can form structures which stabilize R-loops.

The article below discusses R-loop mechanisms implicated in human disease, and R-loops as drug targets:

Out of Balance: R-loops in Human Disease

Groh M, Gromak N (2014) Out of Balance: R-loops in Human Disease. PLoS Genet 10(9): e1004630. doi: 10.1371/journal.pgen.1004630