Dave Lunt

"Here we show that BI, unlike ML, is biased in favor of topologies that group long branches together, even when the true model and prior distributions of evolutionary parameters over a group of phylogenies are known. Using experimental simulation studies and numerical and mathematical analyses, we show that this bias becomes more severe as more data are analyzed, causing BI to infer an incorrect tree as the maximum a posteriori phylogeny with asymptotically high support as sequence length approaches infinity. BI's long branch attraction bias is relatively weak when the true model is simple but becomes pronounced when sequence sites evolve heterogeneously, even when this complexity is incorporated in the model." - Dave Lunt from Bookmarklet

"One should not see, goes the old saw, laws or sausages being made. This is also true of science, for a reason. Before something is published, scientists argue, insult each other, discuss things in casual ways and use unclear jargon and terminology that looks like, to an outsider who is uninformed, as if the whole thing is just being made up on the spot for political and personal reasons. The recent fooraw about climate fraud is just such a case." - Dave Lunt from Bookmarklet

Inspired by Tarzan novels.... 'I like the idea of referring to humans, common chimpanzees, bonobos, Ardipithecus, "Lucy", Australopithecus, Floresian "hobbits", Homo erectus, Neandertals, etc. as "mangani". ' - Dave Lunt from Bookmarklet

....The selective force is the public. They listen to the songs, rate them, and so define their fitness. You can participate too! We started with a population of randomly generated loops and are currently at ~2000 generations. To find out more go to http://DarwinTunes.org log on, and be a selective force! best Armand Leroi" - Dave Lunt

"SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building" Looks great, MUSCLE alignment, trees by PhyML, multiplatform, and open source. Ugly, but I'll use it. - Dave Lunt from Bookmarklet

"The final HMMER3 beta test release is available... For the first time, we’re seeing some searches peek above NCBI BLAST search speed. Yes, you read that right, profile HMM speeds have started to exceed BLAST speed. And we’re far from done." - Dave Lunt from Bookmarklet

"However... as for the idea that those bird-like dinosaurs might have evolved into bolt upright, tailless humanoids... well, it's a thoroughly stupid idea" - Dave Lunt from Bookmarklet

Well said Tet Zoo! I also like the phrase "Magic human syndrome" for those that seem to go to extraordinary lengths to show we are special and different from all other animals. - Dave Lunt

"I've been posting about my experiments with Xgrid on a plain Mac OS X 10.6 installation with my one-year old MacBook. I was getting to the point of closing out these experiments, because although I did have BLAST working on Sunday, it was only accomplished by using a security-compromising hack. I've concluded there is no way to use this for anything serious without Server." - Dave Lunt from Bookmarklet

Disappointing. I was thinking about doing an Xgrid version of BLAST (and a few phylogenetic things) myself, but I may have to put aside some time. Xgrid looks absolutely great, but Google searching reveals very few people using it for bioinfo stuff. Anyone got any positive experiences? Last time I needed distributed BLAST I was in a rush and used Squid (doi:10.1186/1471-2105-6-197) on a bunch of Windows machines. Worked nicely. - Dave Lunt

"We describe the system architecture and template design of "Scratchpads", a data-publishing framework for groups of people to create their own social networks supporting natural history science." - Dave Lunt from Bookmarklet

Nice mention for Rod Page- "Rod is a one-man informatics initiative that is behind many of the most substantive ideas in the field." - Dave Lunt

"Not many taxpayers know what university faculty are doing. In fact, not many university administrators or even other faculty know what research their colleagues are performing." - Dave Lunt

"The origin of new genes and their contribution to functional novelty has been the subject of considerable interest. There has been much progress in understanding the mechanisms by which new genes originate. Here we examine a novel way that new gene structures could originate, namely through the evolution of new alternative splicing isoforms after gene duplication." - Dave Lunt from Bookmarklet

Background The availability of newly sequenced vertebrate genomes, along with more efficient and accurate alignment algorithms, have enabled the expansion of the field of comparative genomics. Large-scale genome rearrangement events modify the order of genes and non-coding conserved regions on chromosomes. While certain large genomic regions have remained intact over much of vertebrate evolution, others appear to be hotspots for genomic breakpoints. The cause of the non-uniformity of breakpoints that occurred during vertebrate evolution is poorly understood. Results We describe a machine learning method to distinguish genomic regions where breakpoints would be expected to have deleterious effects (called breakpoint-refractory regions) from those where they are expected to be neutral (called breakpoint-susceptible regions). Our predictor is trained using breakpoints that took place along the human lineage since amniote divergence. Based on our predictions, refractory and susceptible... more... - Dave Lunt from Bookmarklet

Joel Parker from the University of Southampton very confidently stated on the EvolDir mailing list that Lamarck, not Darwin, published the first (evolutionary) tree. He described "falsely attributing" to Darwin as an "embarrassing mistake". I don't agree. This post doesn't either. - Dave Lunt from Bookmarklet

SOME QUOTES; Back in the early 1970s, computers were still huge and typically overseen by men in white coats who jealously guarded access to the machines. The idea of users directly interacting with the machine was downright revolutionary. In May 1975 it got another boost by becoming the chosen operating system for the internet. The decision to back it is laid out in the then-nascent Internet Engineering Task Force's document RFC 681, which notes that Unix "presents several interesting capabilities" for those looking to use it on the net. "Unix is the best screwdriver ever built," said Dr Salus. - Dave Lunt from Bookmarklet

The successful development of open access publishing by organizations including the Public Library of Science (PLoS) in recent years is a dramatic illustration of how the Internet is revolutionizing scientific communication. Today, after several months of work, I’m delighted to announce that PLoS is launching PLoS Currents (Beta) — a new and experimental website for the rapid communication of research results and ideas. In response to the recent worldwide H1N1 influenza outbreak, the first PLoS Currents research theme is influenza. - Dave Lunt from Bookmarklet

Spent the day writing perl scripts to turn one minor variant of phylip format into another, then I found this. Nice. "nexml is an exchange standard for representing phylogenetic data — inspired by the commonly used NEXUS format, but more robust and easier to process." - Dave Lunt from Bookmarklet

"And, as with many broad-reaching sequence-based analyses, there is a house-of-cards structure to the argument here, so if these tables in the supplementary data cannot be trusted, nor can the final conclusions, which now have to be regarded as “unsafe”. Anyhow, the above counts as just a quick dirty look at this paper and I may have missed some important points or got my wires crossed somewhere along the line. But I hope that others will now take an even closer look at it." - Dave Lunt from Bookmarklet

They're a weapon! Nice post by Will Ratcliff - Dave Lunt from Bookmarklet

how is a direct physical effect distinguished from a signalling reaction? - Mike Chelen

yeah but the lag makes it really difficult to play quake :D - Mike Chelen

A nice discussion of the role of Wikipedia and Britannica as secondary sources of information. Starts slow, but worth reading to the end. - Dave Lunt from Bookmarklet