The Wellcome Library

Via BoingBoing: the Wellcome Trust releases its image library under Creative Commons license 2.0. Here’s their news release, the Wellcome Library website and the new Wellcome Images site. It’s a little slow for me just now.

How old is old?

Last week, my imagination was captured by the story of the whale and the 19th century harpoon. If you want to explore beyond the headline, look no further than Carl Zimmer’s post over at The Loom. He’s written a short NYT piece on the evolution of ageing and points us to the AnAge database, a curated database containing age and longevity records for many species.

“Junk” DNA story for today

‘Junk’ DNA makes compulsive reading

Whatever the truth, the results pose fresh puzzles about how genes work. “It would now take a very brave person to call non-coding DNA junk,” says Greally.

It would. So stop it, New Scientist. Putting the “junk” in quotation marks doesn’t distract us from the usage of the word.

The article is a summary of recent findings from the ENCODE project (ENCyclopedia Of DNA Elements). More details in:

• Nature abstract
• Nature news and views
• Nature news (without views)
• Genome Research ENCODE special issue (everything open access)

Random summary of interesting things

Way too busy for a proper blog post, here’s some links to resources that caught my eye in the past week:

• Very big science: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls (Nature). Everyone is discussing this tour-de-force study.
• More big science: Genome-Wide Mapping of in Vivo Protein-DNA Interactions (Science)
• Thanks to Euan for my invite to Scintilla, a new NPG aggregator that seems to build on his previous work with Postgenomic
• A great series of how-tos from Pierre: Mapping NCBI/PUBMED, testing Nature Network batch invites and Translating DNA to protein with the Google Web Toolkit
• Nature Precedings, another NPG initiative to share early research findings, via Pedro

Feed reader irony

This just appeared in my Google Reader.

Well I thought it was funny.

School physics education in the UK

Via BoingBoing comes a sorry tale of physics education in the UK. Wellington Grey, physics teacher and cartoonist has written an open letter to the Department of Education to complain about changes to the high school physics syllabus:

One question asks “why would radio stations broadcast digital signals rather than analogue signals?” An acceptable answer is:

* Can be processed by computer / ipod [sic]

Authorship now meaningless?

How’s this for a couple of multi-author papers?

Genome-Wide Association Analysis Identifies Loci for Type 2 Diabetes and Triglyceride Levels

A Genome-Wide Association Study of Type 2 Diabetes in Finns Detects Multiple Susceptibility Variants

I count 69 commas in the first author list, 269 in the second. People = #commas + 1 + 1 (for the “and last author”) = 71 and 271, respectively. And some of the names are consortia.

If you’re in there and I didn’t spot you, congratulations! Don’t tell me that author order means anything in this case though.

Nature snippets

• Academics strike back at spurious rankings
  “Thomson Scientific’s ISI citation data are notoriously poor for use in rankings; names of institutions are spelled differently from one article to the next, and university affiliations are sometimes omitted altogether. After cleaning up ISI data on all UK papers for such effects, the Leeds-based consultancy Evidence Ltd, found the true number of papers from the University of Oxford, for example, to be 40% higher than listed by ISI, says director Jonathan Adams.”

  Someone explain to me: why do scientists willingly submit to assessment using the rubbish from ISI?

• Complex set of RNAs found in simple green algae
  “A class of RNA molecule, called a microRNA, has been found in a unicellular green alga. The discovery, made independently by two labs, dismantles the popular theory that the regulatory role of microRNAs in gene expression is tied to the evolution of multicellularity.”

  Like I keep saying – it’s the biological process that’s important, not the organism. Why this constant surprise based on ill-founded notions of complexity?

• Algae bloom again
  “A handful of pioneers are trying to bring algae-based biofuels back from a near-death experience.”

Science snippets from last week

There are weeks when you skim through the TOCs of your favourite journals and nothing really grabs your attention. And then there are weeks like last week, when there’s almost too much to read. This is where a system to grab a web page comes into its own – you just mark the page using e.g. Zotero, Google Notebook or del.icio.us and come back to it later.

Stuff that I grabbed for later from last week includes:

• An Open Mouse

In which Carl Zimmer ponders fair use policy, as exemplified by PLoS

And from PLoS Computational Biology:

• HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation – interesting use of a method often applied in protein-protein interaction studies
• A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes – overlapping reading frames not confined to prokaryotes

As an aside – does anyone else find that PLoS journal websites take ages to load in Firefox and use a lot of CPU?

From Science:

• A New Window on How Genomes Work discusses tag sequencing. Key quote: “if you are not thinking about your experiments on a whole-genome level, you are going to be a dinosaur”.
• ATM and ATR Substrate Analysis Reveals Extensive Protein Networks Responsive to DNA Damage is a large-scale proteomic analysis of a phosphorylation network.

From Nature:

• Celebrity genomes alarm researchers – should they?
• Help flies in for human genome – highlights the need for comparative genomics in understanding the human genome
• Molecular biology: RNA in control – discusses the discovery of riboswitches (mRNAs that control gene expression) in eukaryotes (full paper). For some reason, people always seem amazed when prokaryotes teach us about eukaryotes. It’s evolution, people – what matters is the biological process, not the organism.

Quiet passing of pioneer

I almost missed the news that Stanley Miller, of the famous Miller-Urey experiment, recently passed away.

The experiment has been criticised in recent years for making incorrect assumptions and encouraging an over-simplified view of how life originated. However, I think it’s important to place this work in the context of its time. It showed that the basic “building block” molecules of life could be synthesised via known, understood and relatively simple chemical processes. This means that given the right environment and ingredients, biochemistry goes from being unlikely to almost inevitable, with profound implications for the likelihood of life emerging both on the earth and elsewhere.