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alanine is, in fact, an amino acid. the four building blocks of dna are cytidine, guanosine, thymidine, and adenosine. its also worth mentioning that doing in silico molecular dynamics simulations (which is what the original poster describes, i think) is not the same as doing genetic engineering. genetic engineering is the process of cutting, pasting, and changing dna sequences to produce novel functional characteristics. this does not require a computer at all. instead, a reasonably well-equipped laboratory is what is needed. Bio-scriptkiddies are _never_ going to become a threat. unlike computers, which are sufficiently useful for everyone to have (and thus for everyone's kids to use for hacking), the tools required to do basic genetic manipulations (centrifuge, storage systems, enzyme sets, bacterial incubators, electrophoresis setups) are both expensive and _not_ something the average person would ever buy.

bioterrorism is a real threat, but to carry it through it would (and likely will always) require a reasonably well-funded set of individuals with at least some background in experimental science.

Here's what I'd recommend. It'll cost you about $10 per mow, but it's worlds easier than building your robomower.

I'd be really surprised if the idea didn't come from Emacs in the first place. outline-mode has existed in Emacs since the '80s, and before it was made to play nicely with other programming modes by default (it used to take a lot of configuration for anything other than bullet-point text like the Emacs NEWS file), someone wrote a folding-mode (apparently in 1992) specifically for curly-brace languages (C/C++ etc).

By 1989, I had already started numbering Apollo objects using gaulish gods. One which I had not used was Toutatis since I thought it was an invention of Goscinny and Uderzo, authors of the well known comic book series "Les aventures d'Asterix". There are several dozens sites about this comic book series, you may want to look at few of them :

• Stephane Riviere Asterix's page
• Page on asterix in different languages
• The international Asterix homepage which contains many more links to Asterix pages elsewhere

One of their constant saying is "By Toutatis", another one is that their only fear is that the sky may fall onto their heads.
I discovered my ignorance of gaulish culture when I learned that Toutatis was ( or had been ) a real God. I also learned that the citation in Asterix was not a joke, but that it had been reported by some historians of Alexander the great who had met some gaulish warriors ( who had once invaded Italy and Great Britain ).
One of the first thing we learned about Toutatis was its record low inclination. This meant that it is indeed ( in a remote future ) a good candidate to fall onto our heads. The name stuck almost immediately at the telescope when I proposed it. Toutatis, also sometimes spelled "teutates" is a totemic deity, to which human sacrifices were made.
Don't be misled, very few french persons do know about the cruel god Toutatis, but most will talk to you about Asterix and his friends if you come to swear " By Toutatis ! ", provided you get the right (i.e. french) accent...

Well if you want to impress a Swede, pronounce it as Ångstöm. Here is a link with some info on the Ångstöms.

Apart from the obvious reference to the village I live in (Svista), is this some Firefly reference going on right under our noses?

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

The company distributes a SDK.

For the older version of these devices, before they were spun off by Logitech - seems they're supported navitely by OpenGL.

From this page.

Linux GLut-OpenGl-X. Glut v3 seems to support the Spaceball directly. Should try aeroplane demo.

First-Year Calculus Notes
Difference Equations to Differential Equations: An Introduction to Calculus
Lectures on Calculus
Elementary Calculus: An Approach Using Infinitesimals
The Calculus Bible

My bedroom, you insensitive clod!

On the bright side I get a 622 Mbps broadband hookup for free and my kitchen can make a bag of microwave popcorn in 0.97 seconds (it tends to scorch if you leave it for a full second).

-

My bedroom, you insensitive clod!

On the bright side I get a 622 Mbps broadband hookup for free and my kitchen can make a bag of microwave popcorn in 0.97 seconds (it tends to scorch if you leave it for a full second).

-

You can try some of these:

http://awstats.sourceforge.net/

http://www.multicians.org/thvv/webtrax-help.html

http://www.ftls.org/en/examples/cgi/ewla.shtml

http://www.watchwise.net/

http://www.weblogexpert.com/

For a detailed list of web log analyzers, go to this page. It has listing of various platform specific and platform independent analyzers:
http://www.uu.se/Software/Analyzers/Access-analyze rs.html

No big wars, only small ones, and everyone lives happily together. A real land of peace...

Good thing it's safe to live in Europe! Maybe if we don't speak up about terrorists, they'll leave us alone...

Yeah, Chalmers is heavily into functional programming, specifically using Haskell

Most of the other unis tend to focus on algorithms and numerical analysis, notably The Royal Institute of Technology and Uppsala University. In general all the unis are more into computer engineering type research rather than comp sci.

Here is some info what happened:

A few people have asked me "what's happening with Erlang.org?". I called Kent today. Seems they've moved some servers from one building to another and it's taking longer than expected to get the external network connection up again (i.e. several days). Until they do that, erlang.org, erlang.se and the mailing list all don't work.

The UU mirror seems ok:

http://www.csd.uu.se/ftp/mirror/erlang/

Matthias

Regards,
Marc

Seriously though - Fink allows me to do this.

Here is a 700+ page book similar in content to a freshman college text MotionMountain

This is a Classical Electrodynamic book at a graduate level Classical Electrodynamics-Bo Thide

A site for Statistical and Thermal Physics with some good notes by Harvey Gould Statistical and Thermal Physics (STP) Curriculum Development Project

Quantum Mechanics--Niels Walet-- see the "Big .ps file

Lecture Notes on General Relativity-- Sean M. Carroll

A list of books to look into Cease's Book List

A few authors I like are A.P. French, Halliday Resnick for intro, Griffiths

A very respectable Oxford Physics booklist can be found in their handbook here

It'd be great now if he offered an implementation which we coudl all use.

I think a progressive, ever-going implementation is best. I also think its best to filter based on headers first, and not download any spam (to save bandwidth) and then filter based on message content (for the messages downloaded) and move any spam to a spam folder.

Then the user simply looks at the spam folder and looks for false-positives, and marks them as "legit". Then the Bayesian filter recalculates.

Same thing for false negatives, and for the messages not downloaded. The user can look at the headers of the messages not downloaded and say if they're spam. Then the Bayesian filter recalculates.

Another good thing to do is to give a "password" to your friends for them to put in headers sent to you. I.e., 13y4890dshfpljk2134y9073254y32p9ur. Any message with that in the header would be given a 0% probability of being spam, as only those you gave that to would know to put it in the header. Should it become compromised, you can change it (or just don't give it to people who might compromise it).

Back to the Bayesian filter, another good thing might be to have varying levels of "spam". I.e., if something is almost certailny spam (i.e., 99.99999999% likely to be spam, as would a message with the header "Get fucked for free and make lots of $$$$$"), it would be placed in a DEFINATELY SPAM FOLDER. Other things would be placed in a "PROBABLY SPAM FOLDER". Etc.

Anyways, Bayesian Analysis is a really great method.

If your interested in Bayesian Analysis, there's a great phylogeny program which gives you (basically) a bootstrapped maximum likelihood tree (calculated from millions of trees) via Bayesian Analysis: MrBayes.

There's more at Linné Online. He really was a fascinating scientist!

Heads are Gonna Roll: The Lexical Connection Between Capitalism and Death

While doing research for a longer expose on the correlation between Western Economics and the worst forms of human violence, such as war, slavery, and murder, I have discovered a most fascinating bit of history. There apparently is a connection between the economic system known as Capitalism and a killing device known as a Guillotine. The connection may leave your head spinning ;^)

We begin by examining our language, for our language has evolved along with our human cultures. Studying word origins (etymology) may give us insightful clues into our history, the unpleasant parts of which the historians may have sanitized in order to make their product (history books) more marketable. We humans, it seems, don't like to be reminded of our savage origins, or the logical inconsistency of our savage nature.

In this essay, I will begin to explore some ideas I have which may explain our violent culture, which Rutgers University Law Professor Gary Francione says exhibits a "moral schizophrenia", a society which Frank Zappa called "socially retarded" and "dumb all over", a community defined by for-profit media corporations spewing confused doublespeak to unquestioning alcohol anesthetic brains, a culture which, rather than condemning all violence, attempts to justify that violence which suits our own savage lust for blood, fills our bellies, is good for our investments, or guarantees us a cheap tank of gas for our sport utility vehicles.

Contrarily, I assert the premise that a civil and democratic society with a stable population (i.e. not growing) based on the principles of non-violence is the only logically consistent, sustainable, and morally defensible kind, a society where the civil order is spontaneous, arising from social contracts amongst morally responsible beings. This utopian ideal is opposed to our current world, where a kind of fascist order is imposed by gangs of violent thugs with high-tech weapons, operating only under color of an ersatz law imposed by a savage and non-representative elite ruling class.

In my studies and experiences, the correlation between savagery and our dominant religious beliefs were always clear (the topic of a different essay!), but at some point I began to formulate a hypothesis that there may be more to blame than just religion as the source of Western violence.

During my research, I discovered that our happy, G-rated, warm and snuggly word "capital" shares it's roots with the not-so-splendid word "decapitate". "How curious!", I thought. What could be the common thread connecting these things? Any ideas? Well, it turns out the key is right inside your head.

Well, not inside exactly. It's in all heads. It *is* all heads, in the abstract sense: a roundish bone covered with flesh and hair containing eyes and a brain, the center of consciousness of an autonomous creature possessing the animating force, which roams the earth of its own free will, self-aware, and aware of its surroundings.

So where the hell can I be going with this, you ask!

Well, open up any dictionary, and you will learn that the Latin root of the word "capital" is "capitalis", from the Indo European "kaput", which means head. Remember the guillotine we spoke of before? This is a device used for decapitation, where the unlucky victim loses his head. Are you beginning to see how this all fits together?

Now our Economic System has become a "sacred cow", so to speak, as the people who criticize it are labeled the most horrible names. All of us who grew up in America were taught from the earliest age the evils of "Communism", a rival economic system, but never told exactly why it was evil. During the 1950s and 1960s, Senator Joseph McCarthy lead one of the largest witch-hunts in modern history, and many professional actors and musicians were blacklisted as being suspected members of Communist organizations.

But because we enjoy challenging the herd-think, let's see if we can find other lexical connections between our economic "sacred cow", and death. Perhaps it will lead us to some other sacred things which are often overlooked, even trampled upon by the stampeding mob, so obsessed by greed, so absorbed with getting stroked by Adam Smith's Invisible Hand of self-interest, they can't even hear the cries of those they hurt, or don't think those others matter. Perhaps they simply don't care.

But maybe, just maybe, Adam Smith and all his followers (like Ayn Rand) are wrong. Perhaps selfishness, since all life is connected, is a kind of self-hatred. And since self-hatred seems to often lead to self-destruction, those of us who actually enjoy life and feel it is worth living, and worth sustaining, want to see self-hatred transformed by love into something better.

Every man, woman, and child, every smelly leper, every prisoner, every bird, every bee, and every cockroach and spider are all perfect reflections of the Divine Spirit, so perhaps the greed embodied by Capitalism is a kind of blasphemy, perhaps a capital offense.

Which provides a nice segue back to our topic! A "capital offense" is a crime deserving the death penalty, a possible sentence for which is when the accused heads off to the guillotine. Notice however, that a capital letter is at the head of different sort of sentence. A Capitol is where the head of the government lives, which is (hopefully) a man with a good head on his shoulders. Finally, in Russian, a thing which is "kaput" is as dead as Marie Antoinette. If you begin to see how this all fits, go the the head of the class!

But all of these capital-death denotations come from etymological connection between the word "capital" and the word "head". But from where does this connection derive?

The Cult of the Cow: Capitalism and The Idea that Things with Eyes and a Brain are Ownable Property

The connection between capitalism and the Indo European word for "head" comes from another nexus, that between economics and cows. From antiquity to the present, cattle have been referred to "heads of cattle"; even the word Cattle derives from "chattel" also from the Indo European word for head. Note the word "chattel" has been used to refer to "animal property" (horses, pigs, sheep, cows, and yes, even human slaves), for hundreds of years. Heads are Money, or so our language seems to be telling us.

The capitalism-cow connections are endless: A successful business venture is a "Cash Cow". When investments are growing, it's a Bull Market. When you are exhausting some resource, you are "milking it for what it's worth". While not explicitly a cow connection, the phrase "making a killing" (meaning making a profit) may indirectly refer to the slaughter of innocents for profit, to sell to those that crave the taste of blood.

There are connections to other animals, and slavery: one United States Federal Reserve Note (a/k/a, a dollar) is also called a "buck", a unit of money. But a buck also means a male deer (a unit of food to a carnivore), and is also slang for a male slave.

Now I'm losing some of you right now, because you say the Bible allows killing animals. We need meat in order to be healthy. Animals aren't moral agents, and don't have souls. We've always exploited animals for our gain. Look at nature! Big fish eating little fish...

But I argue that the same idea that allows ownership of a cow, allows for the ownership of a man. And if you think that slavery is gone from the modern world, you are not seeing the forest for the trees. The same notion that allows for the killing of a cow for selfish reasons, can be used to justify killing *any* creature, or *any human society*, for those same selfish reasons.

Isn't it time for the cycle of violence to stop?

Even the word "stock market" derives from the slave trade, where "livestock" was sold at auction. Now this word only connotes non-human animals, but historically it was applied to human slaves as well. There are still remnants in our language of this. Today, human prisoners are kept in holding devices or cells called stockades or a bull pens.

Thus, cows, prisoners, slaves, and those murdered by the state for their crimes, are all connected in this way, not just to the roots of word Capitalism, but also to the Capitalist idea which treats each of these creatures as beings not of their own right, but ownable property, having no self interest nor the power of self determination, but existing only to serve the interests of their owner, the Master or the State.

We humans claim to be smarter than the animals, "higher" than those savage brutes. So why can't we use our heads for something more than a place to park our John Deere ball cap, and figure out a way to formulate peace? Can't we create a new economy which does not rely upon dominination of the weak, and explotation of those creatures which don't speak our language?

End.

Actually, that is often not true at all. Speaking as a grad student with experience in structural biology, the majority of programs actually used for NMR structures, X-ray structures, , molecular graphics, etc etc (the list it very long!) are all developed by university labs and given away free, generally open-sourced as well. Universities don't generally hold such things hostage, as there is the understanding that science is based on sharing, nor hoarding.

-Ted

Access Analyzers (Uppsala University)

Log Analyzers (reallybig.com)

Web Log Analyzers (2K Communications)

Only that he's not really a MBA. He got at least a honoris causa title from Holland, in a move by a business school-mistakenly-turned-University that is regretted by Edsger Wybe Dijkstra at his convocation speech for the graduates of the College of Natural Sciences of the University of Texas at Austin in December 1.996.

What kind of dope are YOU SMOKING? The Magellanic clouds are 160,000 light-years from the earth.

I guessed 500000 light years would get you at least as far as the Magellanic clouds. If they're 160000 light years away then I pegged it within one order of magnitude, which is a hell of a lot better than being off by three. And the Milky Way has about a dozen dwarf satellite galaxies that are up to 830,000 light years away.

And by the way, in re Marty's rant about cheerleaders: maybe we will never know if there is a higher power, but it certainly IS relevant, or does he disagree with Pascal's logic in the matter?

Pascal's Wager is a bad argument for belief. There are a ton of resources out there debunking it, but my favorite is that, considering the possible consequences of belief in the wrong God, atheism may actually be a better bet than theism.

The Secular Web has an index that provides a pretty thorough analysis.

-brennan

You don't even have to rely on Mozilla or Opera to do the transformation for you, both of which can give slightly icky results for paper versions.

html2ps is excellent for nicely formatting HTML as a paged document. It uses CSS, with a few of its own extensions (paper size, table of contents generation, hyphenation, page headers and footers, page numbers, and the like). It can even automatically swap in PostScript diagrams for gifs in the HTML source.

It has the advantage over a browser in being scriptable you can have one makefile that runs HTML Tidy on your source, then converts it to PostScript (and possibly PDF too).

You get all the benefits of a plain text format (CVS, etc), and paper/PDF output that many readers couldn't distinguish from having been word processed.

Smylers

• You can edit it with a plain editor, or with a pretty one like amaya, or of course emacs HTML mode...
• You can print it nicely with html2ps or in some cases with whatever browser you think doesn't do too horrible of a job.
• converting to HTML is a no-op
• if you keep it in CVS you can use easy hacks to cvsweb to make the revision history and current and past versions browsable on the web.

You're aware that Pascal's Wager is used as a classic example of flawed reasoning in freshman logic classes?

Most people cannot be trusted with such responsibility because in the process they'll fuck up other people's "bodies and lives".

So then, why should we obey a government voted into power by an electorate who can't even be trusted to run their own lives?

If most people can't be trusted to manage their own affairs, then certainly a government "by the people, for the people, and of the people" can't do it for them. Indeed, if that's the case then giving that government more power would just be letting the majority of people who can't handle personal responsibility, run the lives of the minority who can handle it!

To summarize the summary of the summary: people are a problem.

Tom Swiss | the infamous tms | http://www.infamous.net/

And if there isn't any life on Jupiter's moons, we can go out and start a party of our own... Recently, bacterial ecosystems have been discovered in Earth's clouds. This opens the possibility of using balloons on Venus to inject heat and acid loving bacteria into Venus' cloud droplets at 40-50 Km. Let's start colonizing space today!

Recently, bacterial ecosystems have been discovered in Earth's clouds. This opens the possibility of using balloons on Venus to inject heat and acid loving bacteria into Venus' cloud droplets at 40-50 Km. Let's start colonizing space today!

So your hair follicle will be frozen solid and blasted into oblivion by cosmic rays over the millenia. Big deal. What everybody really wants is to get to space alive. I've had an idea for quite some time that could be expanded to cover this option ... and adding YOUR VERY OWN DNA (YVOD, registered trademark) might just provide the funding required....Basically, there are some bacteria that love heat and acid, and Venus just happens to have that environment in cloud droplets at 40-50 Km. So let's get space colonization underway and send these little guys on the ride of their life. Before they go, we could add plasmids spliced with YVOD (tm) and instead of inert frozen DNA, it would actually be active in the bacteria, contributing to its evolution and creation of the Venesian ecosphere by expression of your non-bacterial proteins. This isn't a nutty idea, already there is bacterial ecosystems being discovered in Earth's clouds. Any remaining dot-com millionaires out there who want to provide seed (pun) funding, I actually AM a rocket scientist and would love to get a project based on this idea (minus the plasmids, even) off the ground....or even just start a discussion about it.

use a package called html2ps. it can be found here. have a page generate the report, you can wget it if you have to. then convert and send to a printer.
if you wanna print to client machines, then use samba to send the print jobs to windows or linux clients.

gol

To have big fundings from the private sector is not necessarily a good idea. For one, CS courses are too "practical", that is, oriented to products, not to the fundamentals of the field. There are many courses in Universities that simply do not belong there, but are in the U. because of corporate funding.

I suggest reading Skyscrapers with Shack Foundations, by Fabian Pascal, and Edsger Dijkstra's Convocation Speech at Univ of Texas at Austin.

Am I the only one that thinks that this guy may be a little biased? His email address is an untypable lambda-expression, which has questionable logical meaning ;-)

Ok, actually, I agree with you, Tom. Turing machines are clumsy ways to view computation. The lambda calculus is nice, but it is awkward, whenever you are thinking about heterarchical computational problems (like graph algorithms). However, for heirarchical computational problems, the lambda-calculus works like a charm.

May I suggest an even better formalization of computation: The Fusion Calculus, which is related to Robin Milner's pi-calculus.

The pi-calculus is the result of Robin Milner's work, which he started after initially completing ML back in the late 70s and early 80s. Back then, Milner could see how the lambda-calculus was inadequate, as the foudation of a general purpose programming language.

The most interesting aspect of the lambda-calculus is the Curry-Howard isomorphism, which equated a program with a proof in intuitionistic logic (Brouwer Logic). To make a long story short, the lambda-calculus is sequential in computational nature, and in a way, the Brouwer Logic is a sequential form of proof. Here is the best part!!! Variations of the pi-calculus are showing a similar isomorphism with a newer kind of logic: Girard's Classical Linear Logic. Classical Linear Logic is a parrallel, constructive logic, which can encode Brouwer logic proofs. So we are begining to see that the pi-calculus and Linear Logic are generalizations of the lambda-calculus and Brouwer Logic.

Tom, and anyone else, if you want to learn more about the pi-calculus, then I suggest Robin Milner's new book

Another example is when Danish inventor Karl Krøyer in 1964 was denied a patent on an idea to raise sunken ships because of an earlier Donald Duck comic book story by Carl Barks. (This happened in 1964, and the story was first published in 1949.)

But even Darwin believed in a Creator God - and he said so himself.

This is what Darwin actually said about religion: http://www.update.uu.se/~fbend z/library/cd_relig.htm

A short excerpt:
Everyone who believes, as I do, that all the corporeal and mental organs (excepting those which are neither advantegous or disadvantegous to the posessor) of all beings have been developed through natural selection, or the survival of the fittest, together with use or habit[4], will admit that these organs have formed so that their possessors may compete succesfully with other beings, and thus increase in number.

Sure Darwin was religious, and sure he did believe in a "Creator God", but only before he set out with the Beagle.

Since that's what my univ runs, It's what i mess around with at home. (That and the fact that it's made in Uppsala, where I live ;)

Anyway, check it out at http://www.mimer.com.

Don't hate the media, become the media.

There are R4/x86 binaries and a source patch for the GeekGadgets source here. Note that I'm not the author of this, I've just made a distribution. Hopefully it'll be merged with the tree as soon as someone gets time to do it.

Johan Jansson