Tardigrade comparative genomics

There is now a second Tardigrade genome described in a manuscript (Koutsovoulos et al 2015), only days after the first (Boothby et al 2015– not OA). Koutsovoulos et al however strongly suggests that the widely publicised rampant horizontal gene transfer (HGT) is problematic. This alternate genome comes from Mark Blaxter’s group in Edinburgh, and has in fact…

Steve Jones should publish more

In today’s Guardian newspaper geneticist Steve Jones has a short column replying to a 7 year old child who had asked “Will humans evolve into a new species?“. Jones is known in the UK as the media’s favourite geneticist and evolutionary biologist; he is a frequent guest on media shows and contributor in print media….

How can we ensure the persistence of analysis software?

I’ve been thinking about sustainable and accessible archiving of bioinformatics software, I’m pretty scandalized at the current state of affairs, and had a bit of a complain about it before. I thought I’d post some links to other people’s ideas and talk a bit about the situation and action that is needed right now. Casey Bergman…

Why can’t Nature just copy and paste?

I just noticed that an old publication of mine has a typo in the title on the Nature website “Animal mitochondrial DMA recombination”, anyone want to guess what the error is? Web of Science has the correct title, Pubmed has the correct title, and it used to be correct on the Nature website, but somehow…

The Eighth Day of Creation and the weight of knowledge

There have been several obituaries for Horace Judson recently [1][2], and today Larry Moran in an excellent Sandwalk blog post talked about the lack of knowledge of the history of their field by molecular biologists modern researchers are completely unaware of the history of their field. That’s partly because the work on bacteria and bacteriophage—where…

Manuscript writing with Google Docs

I hope I’m going to submit my PhD student’s first comparative genomics paper very soon. Three of us have written the manuscript collaboratively using Google Docs. GDocs is an online word processor and although I’ve used it quite a bit before, this is the first time I’ve used it to write a manuscript with colleagues….

Anonymous peer review

I’ve heard a number of people saying anonymous peer review is broken and we need a different publishing model. One where reviewers cannot hide behind their anonymity. I don’t think it is broken. Actually I think anonymity is essential, one of the few things that protects science from politics and human nature. Sure there can…

Beer and Publications

OK, so I was going to write about bioinformatics and phylogenetics in this blog, and here is my second post already that ignores both!I just read a paper testing the relationship between beer consumption and publication output of ecologists in the Czech Republic. Apparently the higher your consumption the lower your total number of publications,…

Are books now obsolete?

Well no, I guess they’re not. But I’ve been thinking about whether some types of book publishing are even worthwhile. So, what’s my complaint? Well, in many cases I don’t see why either publishers or paper books are of any use. I think researchers can easily self-publish PDFs that are open access, free and may…