Archive for the ‘Travel’ Category

Book Battle 4: The Hare with Amber Eyes vs The World of Yesterday

When I’m off on my travels, I like to read books that are set in my destination. And ordinarily I read fiction, as real pastos (pron: past-ohs) aren’t really my cup of tea. However, in an effort to combat my long-standing antipathy towards History (in the sense of the school subject, rather than the past itself), I recently read two exceptional memoirs that were partially set in Vienna. The Hare with Amber Eyes and The World of Yesterday, by Edmund de Waal and Stefan Zweig, respectively, have been extensively lauded elsewhere (de Waal: The Spectator, The Guardian; Zweig: The Guardian, Quarterly Conversation, but also see London Review of Books), and with good reason. My understanding of Europe in the first half of the 20th century has improved immeasurably, and the narratives of the people in the book were genuinely gripping. (I did sneak in a bit of fiction too, again partially set in war-torn Austria, in the shape of Shadow Without A Name, by Ignacio Padilla. It’s somewhat challenging, due to the multiple narrators and lots of identity-swapping, but it’s superbly written and plotted, which made it a rewarding and enjoyable read.)

So, given two excellent memoirs, how does a historically-ill-informed monkey assess which is best? Why, a book battle of course! The books themselves, rather than the books’ characters, duke it out, and the rounds are decided using the ‘Condition’ list of adjectives from my random word generator.

Round 1: Modern
The Hare with Amber Eyes saunters up to the table, and smooths its cornflower-blue jacket before sitting down. The World of Yesterday, heavy-set yet elegant, strides purposefully to meet its opponent, and sits on the opposite side of table. Beautifully sculpted chess pieces have been set out on a walnut board with inlaid nacre squares. Both books start their game confidently, but a reckless move by The World of Yesterday leads to the loss of a knight, as the innovative approach of The Hare with Amber Eyes comes into play. Verdict: The Hare with Amber Eyes.

Round 2: Tender
The World of Yesterday is clearly rattled, and its lack of personal details about Zweig enables The Hare with Amber Eyes, with its lovingly rendered family portraits, to threaten its opponent’s king. The danger is averted, but the damage has been done. Verdict: The Hare with Amber Eyes.

Round 3: Concerned
Furrowing its metaphorical brow, The World of Yesterday moves on the offensive, cutting through a swathe of its adversary’s pawns with a concern for humanity and pan-European culture. The Hare with Amber Eyes counters with evocative descriptions of 20th century turmoil, but the round has already been won. Verdict: The World of Yesterday.

Round 4: Powerful
The autobiographical nature of The World of Yesterday gives it a striking immediacy, and the stoicism and, ultimately, optimism of Zweig lends it a power that sends rooks and bishops into imposing positions. But the historical perspective that is necessarily lacking in the The World of Yesterday is the strength of The Hare with Amber Eyes, and it responds with aggressive sacrifices that set up a finely balanced endgame. Verdict: Draw.

Round 5: Wandering
Both books are fundamentally peripatetic, dealing as they do with Jews in the twentieth century, but while the author of The Hare with Amber Eyes travels as widely as Zweig, the latter’s first-person sketches of the Europe of last century carry this round. The World of Yesterday advances its pieces with nimble fingers, and The Hare with Amber Eyes is backed into a corner, but isn’t quite beaten yet… Verdict: The World of Yesterday.

The winner: Draw. An entertaining stalemate; neither book has enough pieces left to force a checkmate, so they nobly acknowledge the draw, don smoking jackets, and retire for port and cigars in the drawing room.

MASAMB XXI, in Vienna

I was pleased to be invited to present some of my work at the MASAMB conference in Vienna recently (11-12th April 2011). My talk was titled “Quantifying the effect of evolution and genomic alignment on de novo RNA gene prediction”. I have a similarly themed manuscript in preparation, so won’t go into detail here. But if you have any questions about the presentation, then please get in touch by . The abstract is included below the nice pics.

I enjoyed both the conference and the time I spent in Vienna, where I appreciated the architecture and culture, as well as the beer and the wildlife:

Quantifying the effect of evolution and genomic alignment on de novo RNA gene prediction

James Allen and Simon Whelan
University of Manchester, Faculty of Life Sciences, UK

Non-coding RNA is biologically important and linked to a range of diseases, yet there are potentially many RNA genes of unknown function that do not belong to characterized RNA families. The de novo prediction of RNA genes is difficult because they are heterogeneous, and tend to have fewer restrictions than protein-coding genes. These problems are compounded by the lack of independent datasets for benchmarking predictions. We identify alignments of genes from 9 well-defined RNA families in UCSC genomic data for 32 vertebrate species, totaling 296 gene regions, and use randomization to create appropriate negative-control datasets. We evaluate three popular prediction programs (CMfinder, EvoFold, and RNAz), testing their ability to detect RNA genes and accurately determine gene boundaries. Our results show that RNA genes in genomic alignments have different evolutionary characteristics to structurally-aware RNA alignments, affecting gene prediction, and provide practical suggestions for the development and application of prediction programs.