Stupid Science Terminology Award #2: “Shaq-teria”
Congratulations to ScienceDaily for this, um, baffling introduction:
"Cornell researchers are studying bacterium big enough to see -- the Shaquille O'Neal of bacteria. Well, perhaps not quite Shaquille O'Neal. But it is Shaq-teria."
Uh. ok. Anyway, they're reporting on this paper: "Extreme polyploidy in a large bacterium", which does sound interesting, and really didn't deserve that pun. The authors have discovered a gigantic bacteria Epulopiscium, which is around the size of a grain of salt. Bacteria visible to the naked eye? So why is Epulopiscium so big? all the better to hold tens of thousands of copies of its genome, of course.
The press release is worth reading if you ignore the shaq-ing introduction, and the paper is here.
Edit: and hey, I know one of the authors. Hi Kendall!
Stamping his mark – on the bacterial genome
Andrew Pollack in the NYTimes reveals the secret message implanted in the recently announced synthetic bacterial genome.
You were expecting poetry perhaps? The secret messages hidden in scientist J. Craig Venter’s synthetic bacterial genome have now been revealed. They are — his name, and that of his research institute and co-workers.
I can't decide whether this is kinda cute, kinda arrogant, or totally cool in a yay-for-hubris sort of way. Answers on the back of a postcard, please.
Nature Archives Online
The journal Nature has digitised their entire publication archive - dating all the way back to November 4th, 1869. Nature has been one of the most influential journals in science (the wikipedia has a good history), so this is a good chance to poke around their archives. Unfortunately, all the good stuff is still behind a pay-to-view firewall, but the history page has some interesting information.
It's fascinating to see the differences in science writing that 140 years can bring. This paper, in the second issue, discusses the "Dulness of Science" (sic), and sounds like a mix between a Dickens novel and an allegory:
But, alas ! the blind in this sense are numbered by myriads ; and as they, for a time, almost threaten to carry their point, a few remarks upon the dulness of science, or rather, perhaps, the dulness of men, may not be out of place.
We have in out mind's eye at the present moment several notable specimens of blind men. One of these lives not very far from where we write - a most hopeless individual; we had better not inquire too narrowly concerning his occupation; he will be found somewhere in the purlieus of this great city. His one sense is the sense of gain. We remember once seeing through a microscope the animalcules of a drop of water, and we noticed that one of the largest of these had one end fixed to the side of the vessel, while its arms and mouth were busy gathering up and swallowing its smaller neighbours. Now, the man of whom we speak is only this animalcule magnified without the microscope. Ignorant of all laws, civil, religious, physical, moral, social, sanatory, he rots in his place until Dame Nature, in one of her clearing-out days, fetches at him with her besom the plague; and he is swept aside and seen no more.
"F.R.S.", Page 43, Nature, vol 1, iss.2, 1869
Ruth Barton also cherry-picks a few gems (doi):
The most bitter exchange was between the physicists P. G. Tait, a regular controversialist from Edinburgh, and John Tyndall of London, whom Tait accused of scientific error in his Lectures on Light. Tyndall had won distinction as a popularizer but, according to Tait, at the cost of "martyring" his scientific authority. Tyndall retaliated, accusing Tait of lacking "manhood" (11 and 18 September 1873). The following year, Tait accused the renowned evolutionary philosopher Herbert Spencer of being confused about newtonian mechanics (26 March 1874). The ensuing debate ran in Nature for five months, with contributors from three continents.
Coevolution with viruses drives the evolution of bacterial mutation rates
Bacteria with greatly elevated mutation rates (mutators) are frequently found in natural and laborator populations, and are often associated with clinical infections. Although mutators may increase adaptability to novel environmental conditions, they are also prone to the accumulation of deleterious mutations. The long-term maintenance of high bacterial mutation rates is therefore likely to be driven by rapidly changing selection pressures, in addition to the possible slow transition rate by point mutation from mutators to non-mutators.
One of the most likely causes of rapidly changing selection pressures is antagonistic coevolution with parasites. Here we show whether coevolution with viral parasites could drive the evolution of bacterial mutation rates in laboratory populations of the bacterium Pseudomonas fluorescens. After fewer than 200 bacterial generations, 25% of the populations coevolving with phages had evolved 10- to 100-fold increases in mutation rates owing to mutations in mismatch-repair genes; no populations evolving in the absence of phages showed any significant change in mutation rate.
Furthermore, mutator populations had a higher probability of driving their phage populations extinct, strongly suggesting that mutators have an advantage against phages in the coevolutionary arms race. Given their ubiquity, bacteriophages may play an important role in the evolution of bacterial mutation rates. (doi:10.1038/nature06350)
Horizontal gene transfer regulation as a spandrel of DNA Repair mechanisms
This sounds most interesting -
Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination.
(...)
The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.
The full article is available at PLoS one: Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms