Science is enforced humility

What is the core, immutable quality of science?

It's not formal publication, it's not peer review, it's not properly citing sources. It's not "the scientific method" (whatever that means). It's notreplicability. It's not even Popperian falsificationism – the approach that admits we never exactly prove things, but only establish them as very likely by repeated failed attempts to disprove them.

Underlying all those things is something more fundamental. Humility...@ Science is enforced humility | Mike Taylor | Science | guardian.co.uk:

Further quote:

But the same self-corrective mechanisms apply to more important science in other fields. The most visible recent example is probably the "arsenic life" story. An article written by a team headed by a Nasa scientist made it through peer review to publication in Science, a well-respected journal. It claimed that the bacterium GFAJ-1 could grow using arsenic in place of phosphorus – a finding with possible implications for extraterrestrial life. That study was badly flawed. But rather than being blindly accepted because it was in a prestigious journal, it was strenuously critiqued: immediately on blogs, then after peer review in print – not once, but several times.

Update

Humility is just another day at the officc lab.


Systematic investigation of insertional and deletional RNA-DNA differences in the human transcriptome
Cai Chen and Ralf Bundschuh

Abstract (provisional)
Background
The genomic information which is transcribed into the primary RNA can be altered by RNA editing at the transcriptional or post-transcriptional level, which provides an effective way to create transcript diversity in an organism. Altering can occur through substitutional RNA editing or via the insertion or deletion of nucleotides relative to the original template. Taking advantage of recent high throughput sequencing technology combined with bioinformatics tools, several groups have recently studied the genome-wide substitutional RNA editing profiles in human. However, while insertional/deletional (indel) RNA editing is well known in several lower species, only very scarce evidence supports the existence of insertional editing events in higher organisms such as human, and no previous work has specifically focused on indel differences between RNA and their matching DNA in human. Here, we provide the first study to examine the possibility of genome-wide indel RNA-DNA differences in one human individual, NA12878, whose RNA and matching genome have been deeply sequenced.

Results
We apply different computational tools that are capable of identifying indel differences between RNA reads and the matching reference genome and we initially find hundreds of such indel candidates. However, with careful further analysis and filtering, we conclude that all candidates are false-positives created by splice junctions, paralog sequences, diploid alleles, and known genomic indel variations.

Conclusions
Overall, our study suggests that indel RNA editing events are unlikely to exist broadly in the human transcriptome and emphasizes the necessity of a robust computational filter pipeline to obtain high confidence RNA-DNA difference results when analyzing high throughput sequencing data as suggested in the recent genome-wide RNA editing studies


BMC Genomics 2012, 13:616 doi:10.1186/1471-2164-13-616
Published: 13 November 2012