Rewriting the invention of DNA barcoding

Today I got an email from David E. Schindel, who is the Executive Secretary of the Consortium for the Barcode of Life, announcing Google funding for DNA barcoding. The project aims to create a reference library of endangered species COI sequences so that DNA barcoding can be used as a tool against wildlife trafficking. Good for…

Printing out GenBank- Nucleotide Sequences 1984

 I have in front of me a copy of the book “Nucleotide sequences 1984 Part 1 A compilation from the GenBankTM and EMBL data libraries” published by IRL Press. Wow, what a surreal book for anyone used to dealing with sequence databases today. The idea that DNA sequences would be printed out, in an actual book…

How many species are there really?

Rod Page at iPhylo draws attention to a new paper in Systematic Biology (Costello et al 2011) estimating the total number of species. They come to a much lower figure than a previous paper (Camilo Mora et al 2011). Rod said something interesting that linked in to my thoughts on species numbers. “The fuss over…

Genomics and ethics

There is a really interesting take on the ethics of human genomics from Dienekes’ Anthropology Blog prompted by the aboriginal genome recently released. I can’t say I disagree with anything. Potential bad ethical outcomes of genetic sampling are very rarely clearly explained and just left hanging in the air as something that must be true….

Bio-Linux in a VirtualBox

For those of you who haven’t come across it before Bio-Linux is an operating system set up for bioinformatics with a huge number of programs pre-installed. It can be obtained (for free) from the NERC Environmental Bioinformatics Centre. I’ve spent quite a while recently messing with installations of software packages and wanted to see how…

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…

From White to Meselson

One of the most talked about ideas in genetic studies of asexual reproduction has been that of extreme Allelic Sequence Divergence (ASD), often called the “Meselson effect” after Matthew Meselson who is usually credited with this idea. In obligatory asexuals (apomicts), which never have the opportunity to recombine during meiosis, the once homologous chromosome pairs…

Wolfram Alpha and Taxonomy

I’ve been exploring Wolfram alpha the new “computational knowledge engine”. If you want to see what it can do have a look at the introductory screencast. It looks really interesting. Taxonomy and information about species is not what it does, its designed I guess to summarize and display primarily numerical data “GDP France / UK”…

The Origins of Phylogeny

I just saw a very interesting piece by Ben Zimmer, whose post details 144 words for which Darwin has the earliest recorded use in English (and he compares to Lincoln, who has one). One of these words is “phylogeny”. I was a little surprised because surely Haeckel invented the term phylogeny. Indeed he did, but…

Big Trees in the NY Times

The New York Times has an article talking about constructing and especially visualizing the tree of life called “Crunching the Data for the Tree of Life“. Its interesting, especially since I think it touches on many issues concerning tree size that even phylogenetic biologists haven’t really considered. There are lots of talk of “big” trees,…