Biological noise and the burden of proof

Yes:

But this does not change the fact that we strongly disagree with the fundamental argument put forward by Clark et al., which is that the genomic area corresponding to transcripts is more important than their relative abundance. This viewpoint makes little sense to us. Given the various sources of extraneous sequence reads, both biological and laboratory-derived (see below), it is expected that with sufficient sequencing depth the entire genome would eventually be encompassed by reads. Our statement that “the genome is not as not as pervasively transcribed as previously reported” stems from the fact that our observations relate to the relative quantity of material detected.

Of course, some rare transcripts (and/or rare transcription) are functional, and low-level transcription may also provide a pool of material for evolutionary tinkering. But given that known mechanisms—in particular, imperfections in termination (see below)—can explain the presence of low-level random (and many non-random) transcripts, we believe the burden of proof is to show that such transcripts are indeed functional, rather than to disprove their putative functionality.

Dueling viewpoints on pervasive transcription

PLoS Biology does point-counterpoint on whether our entire genomes are transcribed (and, by implication, whether the majority of our DNA is functional):

The Reality of Pervasive Transcription  – Clark, et al.

Response – van Bakel, et al.

Interestingly, these two viewpoints tend to split somewhat cleanly between those who came into biology as computational people, and those who came in as experimentalists. (The split’s not perfect but the trend is there, and you can see it in the authorship of the two papers above.)  Computational people (or, at least those who came in as computational people – I’m not making judgments about anyone’s experimental skills) are more likely to believe in pervasive transcription, and while others are more likely see it as experimental and biological noise.

Following the trend, I fall into the latter camp.

Is it “Doctor Princess” or “Princess Doctor”?

Thanks to the enjoyable Bragg Lecture by Sir Paul Nurse (Nobel laureate and president of the Royal Society) at the Physics of Living Matter conference here in Cambridge, I now know a bit more about how to order British titles. The correct order is “Professor Sir Paul Nurse”, much like “Vice Admiral Lord Nelson“.

This got me to thinking about how we would sort it out if one the British royalty dedicated themselves to the pursuit of knowledge. Would it be “Doctor Her Royal Highness Princess Whatsherface”? Would it be acceptable to shorten it to “Her Royal Doctorness”?

With the dedication of Prince Charles to more mystical medical remedies, I’m not sure they’ll need to worry about this issue any time soon.

Eagles at Rugby World Cup

Having played with and/or traded knocks with many of the players on the Eagles World Cup side, I could not be more pleased with their play so far. These guys are playing up to their potential. The quality of the play (as well as the improved TV coverage in the US) should make everyone hopeful for the future of rugby in the US. Also, coach Eddie O’Sullivan deserves high marks for his selection of talented and complementary players.

Ask for Evidence

Sense about Science, a UK based group trying to equip the public to understand scientific and medical claims to which they are exposed, has launched a new campaign Ask for Evidence that seems well worth supporting.

The concept is simple and should make sense to most people. When someone makes a claim, you should (and have every right to) ask why you should believe that claim. Ask for evidence. Below, I have illustrated an example of this: Continue reading “Ask for Evidence”