It allows you to do full, incremental or differential backups, run programs before & after, compress with any one of a number of methods, and works under windows & mac os x as well as linux.
I've got cron calling it weekly for a number of dirs in $HOME, and daily for my main working directory.
Bayesian approaches have really taken off in studies of molecular evolution (Phylogenetics).
For those of you who don't know, phylogenetics is a set of techniques for working out a 'family tree' of taxa (taxa = basically units of analysis, normally species or genetic sequences). The main reason for doing this is that it gives an objective way of testing evolutionary hypotheses. For example - If I predict a certain protein has evolved through stages A, B then C, but my tree shows a pattern of A - C - B, I can reject that hypothesis.
Phylogenetics is extremely powerful and has allowed us to investigate many many cool things (like the origin of modern humans in Africa, and the migrations out of). The problem is that there is a *huge* number of trees to search to find the optimal set of trees. The formula (IIRC) is 5N-2!!, where N is the number of taxa. So, 10 taxa (species or whatever) has 34 million trees, and when you get up to a real dataset it gets much worse: There are 10^132 ways of connecting my 77 taxa dataset.
Bayesian approaches can really really speed up this process. We used to have to do a large number (100-1000) of heuristic analyses and then bootstrap (a resampling procedure) these to get a confidence interval, of say, a date of a divergence time or a model fit. These Bayesian techniques allow us to do, say, 10 long runs whilst simultaneously estimating parameters.
Sooo much faster (ie - that 77 taxa dataset mentioned before - instead of ~250 hours x 1,000, I can do the same in about ~100 hours x 10.
There are some problems - it possibly over-estimates support (ie underestimated uncertainty in the data) for taxa groupings, compared to the bootstrap method. This isn't terribly surprising given the hill-climbing approach these algorithms use, but no-one's really sure whether this is a good or bad thing (since no-ones really sure how to interpret the alternative bootstrap support)
Why is it that everytime I hear that Hollywood is making a movie about a) a book or b) a remake of a movie I liked or c) a radio show (H2G2, and this), my immediate reaction is 'Oh dear god please don't f**k it up'. Don't get me wrong, I'm not expecting Shakespeare, but just don't screw it the hell up like Solaris or The Italian Job or Planet of the Apes or hell, even A Clockwork Orange.
Although, maybe since a certain Mr Jackson didn't screw up a recent three book trilogy, this signals a change in the approach? We can only hope.
Over the past five years there's been a major research effort looking at primate cultures mainly under the guidance of Cristophe Boesch (Chimps - Pan troglodytes spp) and Carole van Schaik (Orang-utans - Pongo pygmaeus), and even Monkeys (the village idiots of the primate family) have been shown to have culture traits.
See also - Whiten et al. Nature, 399:682-685 van Schaik et al. (2003). Orangutan cultures and the evolution of material culture. Science 299:102-105. Perry & Manson (2003). Traditions in Monkeys. Evolutionary Anthropology 12:71-81
Oh, and it's not only primates - Fish biologists have also jumped on board - Bshary et al (2002). Fish cognition: a primate's eye view. Animal Cognition 5:1-13
which shows that fish can do all sorts of massively complex social behaviors - e.g. predator avoidance and something which is very cool, inter-specific (ie: different species co-operating) co-operative hunting. For example: Moray eels (Gymnothorax javanicus) and Red sea coral groupers (Plectropomus pessuliferus). The Morays sneak through holes whilst groupers wait to catch escaping fish - they actually 'go hunting together' and signal each other by shaking their bodies.
Hunt & Gray (2003). Diversification and cumulative evolution in New Caledonian crow tool manufacture. Proceedings of the Royal Society of London, Series B, Biological Sciences.
Lefebvre et al (2002). Tools and Brains in Birds. Behaviour, 139, 939-973.
It's well known that mammalian brain size is clearly related to body size.
So - let's keep it simple, and look just within the primate family: Kevin Reader & Simon Laland did a study a few years ago of a comparative analysis of 533 instances of innovation, 445 observations of social learning & tool use, 607 episodes of tool use in primates.
This shows quite a clear relationship between primate brain size and social learning (& hence, complexity of social groups), in that, large brained primates innovate / learn from others / use tools more than small-brained primates.
From what I've seen (and IAAEP - I am a evolutionary psychologist), most modern definitions of 'culture' for scientific research seem to have settled something like: culture is non-genetic information transmitted between organisms.
Oh: and there's a quote from one of the books authors (Frans de Waal) in a Nature paper from 1999:
"The question of whether animals have culture is a bit like asking whether chickens can fly. Compared with an albatross or a falcon, perhaps not, but chickens do have wings, they do flap them, and they can get up in the trees."
Yeah, sure *they* don't have Beethoven's Ninth or the Magna Carta, but they do have some ability / capability for 'culture' which we've managed to go crazy with.
Slashdot Mirror
I've been using Miguel Angelo Martins Leite Simplebackup for things like this - it's fantastic:
simplebackup
It allows you to do full, incremental or differential backups, run programs before & after, compress with any one of a number of methods, and works under windows & mac os x as well as linux.
I've got cron calling it weekly for a number of dirs in $HOME, and daily for my main working directory.
Yeah - Safari is fantastic. I only use Firefox on the mac to view pages that don't render in Safari. IE's probably sitting around here somewhere..
Looks exactly the same in Safari v1.2.3 as it does in Firefox 1.0PR (Mac OS X).
:)
Nice 'n' clean
Anyone got any other (non-cranky geocities-type website) sources? the BAAS website (www.brit-assoc.org.uk) seems to be down.
This looks very cool (and isn't a goatse link!), I'm just setting it up now. Trying to get html2text to kill things like font tags.
Also - your default pdftotext setting seems to barf on files with spaces in their names. I changed the line to '%s' and this seems to work.
Cheers,
Simon
No, the penis enlargement quotes are in the FA. As to what this says about Mr Stephenson...
Simon
"I disapprove of what you say, but I will defend to the death your right to say it" - Voltaire
Another vote for this - whoever thought this movie up was just sick.
Simon
A link to Nature's copy: Watson & Crick 1953 (HTML)
and a PDF
Both contain the original drawing of the structure, as done by Crick's wife Odile Speed.
Simon
"Dungeon Siege"
What an awesome movie!
Walk - walk - chop - chop - walk - chop - walk - chop - walk - chop - go back find damn lost donkey - walk - chop - walk - chop.
No Santa or the Easter Bunny did
Not only that but there are at least 65 (yes, 65) phylogenetically distinct eye-forms. Wow - independant evolution 65 times.
see: Weiss, K. (2002). "How the eye got its brain." Evolutionary Anthropology 11: 215-219.
Cheers,
Simon
Not really a space battle but has to be said:
Cat: "Is that what I think it is?"
Lister: "What do you think it is?"
Cat: "An orange whirly thing in space?"
and later on:
Cat: "I hate to get all technical on you guys, but - all hands on deck! Swirly thing alert!"
Where the orange swirly thing was obviously just orange colored water being stirred, with added glitter.
accomodating (not communist) apartment complexes
Er.. Sorry to have to ask, but just what the hell is a communist appartment block?
Does it have a swimming pool shaped like Stalin's moustache?
For those of you who don't know, phylogenetics is a set of techniques for working out a 'family tree' of taxa (taxa = basically units of analysis, normally species or genetic sequences). The main reason for doing this is that it gives an objective way of testing evolutionary hypotheses. For example - If I predict a certain protein has evolved through stages A, B then C, but my tree shows a pattern of A - C - B, I can reject that hypothesis.
Phylogenetics is extremely powerful and has allowed us to investigate many many cool things (like the origin of modern humans in Africa, and the migrations out of). The problem is that there is a *huge* number of trees to search to find the optimal set of trees. The formula (IIRC) is 5N-2!!, where N is the number of taxa. So, 10 taxa (species or whatever) has 34 million trees, and when you get up to a real dataset it gets much worse: There are 10^132 ways of connecting my 77 taxa dataset.
Bayesian approaches can really really speed up this process. We used to have to do a large number (100-1000) of heuristic analyses and then bootstrap (a resampling procedure) these to get a confidence interval, of say, a date of a divergence time or a model fit. These Bayesian techniques allow us to do, say, 10 long runs whilst simultaneously estimating parameters.
Sooo much faster (ie - that 77 taxa dataset mentioned before - instead of ~250 hours x 1,000, I can do the same in about ~100 hours x 10.
There are some problems - it possibly over-estimates support (ie underestimated uncertainty in the data) for taxa groupings, compared to the bootstrap method. This isn't terribly surprising given the hill-climbing approach these algorithms use, but no-one's really sure whether this is a good or bad thing (since no-ones really sure how to interpret the alternative bootstrap support)
Fantastic software: Mr Bayes: Bayesian Inference of Phylogeny
and BAMBE: Bayesian Analysis in Molecular Biology and Evolution
Yes, those of us using IE have to type in the http://slashdot.org/article.pl?sid=04/01/30/042824 2&mode=thread&tid=113&tid=126&tid=133&tid=172&tid= 186&tid=95 Damn URL's so it does take us a bit of time to get around...
Why is it that everytime I hear that Hollywood is making a movie about a) a book or b) a remake of a movie I liked or c) a radio show (H2G2, and this), my immediate reaction is 'Oh dear god please don't f**k it up'. Don't get me wrong, I'm not expecting Shakespeare, but just don't screw it the hell up like Solaris or The Italian Job or Planet of the Apes or hell, even A Clockwork Orange.
Although, maybe since a certain Mr Jackson didn't screw up a recent three book trilogy, this signals a change in the approach? We can only hope.
Who cares about Trillian? I want to know who's going to play Eccentrica Gallumbits the triple-breasted whore of Eroticon IV.
Eccentrica Gallumbits
ps: A google image search gives some interesting results...
Over the past five years there's been a major research effort looking at primate cultures mainly under the guidance of Cristophe Boesch (Chimps - Pan troglodytes spp) and Carole van Schaik (Orang-utans - Pongo pygmaeus), and even Monkeys (the village idiots of the primate family) have been shown to have culture traits.
Anyway, a great webpage on this from Boesch's team Chimpanzee Culture
See also -
Whiten et al. Nature, 399:682-685
van Schaik et al. (2003). Orangutan cultures and the evolution of material culture. Science 299:102-105.
Perry & Manson (2003). Traditions in Monkeys. Evolutionary Anthropology 12:71-81
Oh, and it's not only primates - Fish biologists have also jumped on board -
Bshary et al (2002). Fish cognition: a primate's eye view. Animal Cognition 5:1-13
which shows that fish can do all sorts of massively complex social behaviors - e.g. predator avoidance and something which is very cool, inter-specific (ie: different species co-operating) co-operative hunting. For example: Moray eels (Gymnothorax javanicus) and Red sea coral groupers (Plectropomus pessuliferus). The Morays sneak through holes whilst groupers wait to catch escaping fish - they actually 'go hunting together' and signal each other by shaking their bodies.
Oh, and let's not forget the bird-people:
Corvus Moneduloides
Hunt & Gray (2003). Diversification and cumulative evolution in New Caledonian crow tool manufacture. Proceedings of the Royal Society of London, Series B, Biological Sciences.
Lefebvre et al (2002). Tools and Brains in Birds. Behaviour, 139, 939-973.
It's well known that mammalian brain size is clearly related to body size.
So - let's keep it simple, and look just within the primate family: Kevin Reader & Simon Laland did a study a few years ago of a comparative analysis of 533 instances of innovation, 445 observations of social learning & tool use, 607 episodes of tool use in primates.
This shows quite a clear relationship between primate brain size and social learning (& hence, complexity of social groups), in that, large brained primates innovate / learn from others / use tools more than small-brained primates.
The paper is available here: Social intelligence, innovation, and enhanced brain size in primates
From what I've seen (and IAAEP - I am a evolutionary psychologist), most modern definitions of 'culture' for scientific research seem to have settled something like: culture is non-genetic information transmitted between organisms.
Oh: and there's a quote from one of the books authors (Frans de Waal) in a Nature paper from 1999:
"The question of whether animals have culture is a bit like asking whether chickens can fly. Compared with an albatross or a falcon, perhaps not, but chickens do have wings, they do flap them, and they can get up in the trees."
Yeah, sure *they* don't have Beethoven's Ninth or the Magna Carta, but they do have some ability / capability for 'culture' which we've managed to go crazy with.
Hmm... I heard that bovine livestock was sacred in India... maybe this is why India respect him:
The Artwork of Jin Wicked || A portrait of Richard Stallman
Brilliant! if your jobs are being outsourced to cheap overseas countries, why not outsource yourself?
Stallman truly is the messiah.
pffft.