Adventures of a Wetware Hacker

2009-03-14T18:07:00.000-07:00

A Happy Pi Day to all!

For your viewing pleasure:

2009-02-26T15:17:00.000-08:00

Here's what I got with for this random little game that's going around the internets. If you want to create your own album cover, here are the rules:

1. Go to http://en.wikipedia.org/wiki/Special:Random - The first article title on the page is the name of your band.

2. Click http://www.quotationspage.com/random.php3 - Click "New Random Quotations", The last four words of the very last quote is the title of your album.

3. Visit http://www.flickr.com/explore/interesting/7days/ - The third picture, no matter what it is, will be your album cover.

4. Use your graphics program of choice to throw them together, and post the result.

2009-02-21T13:48:00.000-08:00

Navy-funded report warns of war robots "going Terminator"

ONR Report [pdf]

The report urges programmers of war-robots to include ethics subroutines, resembling a warrior code of ethics.

Patrick Lin, the chief compiler of the report, says: "There is a common misconception that robots will do only what we have programmed them to do. Unfortunately, such a belief is sorely outdated, harking back to a time when programs could be written and understood by a single person."

He says the key to avoiding robotic rebellion is to include "learning" logic which teaches the robot the rights and wrongs of ethical warfare. This logic would be mixed with traditional rules based programming. "We are going to need a code. These things are military, and they can’t be pacifists, so we have to think in terms of battlefield ethics. We are going to need a warrior code."

So... The military will pay programmers to write ethics subroutines? As a programmer with a philosophy major... I might one day have a job! Terminator scenarios: Employing those with unmarketable skills since 2009.

I'm reminded of something a friend (Dan, who probably got it from a scifi fanfic) once wrote:
"What is the Universal Truth?"
"The geeks shall inherit the Earth!!"
"Why?"
"Because they’ll save our asses someday!!"

Hmm. The more I think about this, the more I wonder if it's something I'd actually like to do with my life. My views on artificial ethics and intelligence are certainly unconventional, but I do think about it a lot. I have built robots. I have programmed for the military. I have read a great deal on ethics and logic. And I thoroughly enjoyed it all. This might be one of the few jobs that could successfully compete with the Internet for my attention span...

I'll be back. To make sure that you're doing alright.
Would you like a cup of tea?

--
Sources:
DailyTech Article
Fox News Article (polemically hilarious)
ONR Report [pdf]

2009-02-18T09:52:00.000-08:00

How to Evade Your Civil Duties:

1. Move to Arkansas. Their newly-amended constitution should serve you right:

HJR 1009: AMENDING THE ARKANSAS CONSTITUTION TO REPEAL THE PROHIBITION AGAINST AN ATHEIST HOLDING ANY OFFICE IN THE CIVIL DEPARTMENTS OF THE STATE OF ARKANSAS OR TESTIFYING AS A WITNESS IN ANY COURT.

Seriously.

So, if you want to commit murder, do it in a room full of your friends! (Who are probably all godless heathens like you.) If you get called for jury duty, don't fret, silly atheist -- you're not the peer of a believer!

2. Alternatively, you could move to Texas. Their Bill of Rights has a section for you:

Article 1, Section 4: No religious test shall ever be required as a qualification to any office, or public trust, in this State; nor shall any one be excluded from holding office on account of his religious sentiments, provided he acknowledge the existence of a Supreme Being.

Whew. Almost thought we were going to be granted the public trust of Texas. That would have been embarrassing. When you're not given full rights in these states, you're doing something right.

We atheists, therefore, should enjoy being persecuted! As USN says, there's a special place in heaven for atheists who endure this nonsense.

2009-02-17T14:10:00.001-08:00

Four suns connected by a ring in the sky!

Beautiful! Incredible! One of nature's wonderful illusions!

...I won't say it, but you know I'm thinking it.

2009-02-12T16:50:00.000-08:00

Darwin Day Cake!

Happy 200th Birthday, Darwin!

2009-02-12T11:31:00.000-08:00

Happy Darwin Day to all!

Fun Darwin Facts:

1. Darwin saw no significance at first in the finches of the Galapagos. He dutifully collected and tagged his samples, and it was only when some of the labels were lost and he became frustrated about how similar they appeared that he thought they might all be related.

2. Darwin performed a substantial amount of his research by becoming a Victorian era pigeon fancier. These men doted over their birds and bred them for specific characteristics, and although some breeders claimed that they could develop any trait given enough time, none of his fellow fanciers thought this might possibly be an indication that all the known breeds were actually the result of breeding from one ancestor pigeon.

3. Some scholars feel that Darwin believed in recapitulation. What is that? Basically, it's the idea that a blastula is the equivalent of primordial soup, and as the fetus develops, it mirrors evolutionary development. We know Darwin thought this because he wrote about how similar all puppies look (round, chubby, tiny appendages), and yet they all develop into very different breeds. This is because the “essential puppy” morphology is actually the original dog morphology.

4. In Darwin's first edition of the Origin of Species, he asks his reader to contemplate the possibility of a bear becoming a whale-like animal if it spends all of its time in a river hunting. We know today from skeletal structures such as the pelvis and vestigial legs that whales are indeed actually land animals that returned to the aquatic environment.

5. Darwin married his cousin, but only after long debate. He drafted a pro and con list to decide whether or not he was the marrying type. Although he would have less freedom, he decided in favor of marriage because it would offer him good company. At least company better than a dog, he wrote.

6. Erasmus Darwin, Charles's grandfather, had many ideas that are very similar to what we know as (Charles) Darwinian Evolution and contributed a lot to Charles's own ideas. Erasmus is best known for 'Zoonomia' which is filled with precursors. However, Erasmus also writes that whatever the male is fancying during the time of copulation will be what the fetus develops into. In other words, a mating frog may see a chicken walk by and think that the chicken is rather sexy, thus producing a baby frog that very closely resembles a chicken.

7. While in the Galapagos, Darwin gave special attention to the lizard population. He referred to a species of black lizard as “imps of darkness” that were extremely ugly, and performed experiments in which he would hurl a lizard as far as possible into the ocean to puzzle over how it well it could swim, yet how it hated being in the ocean.

8. Darwin remarks repeatedly on the naiveté of the birds of the Galapagos, and how easy it is to kill them. He observed a local boy catching the birds for food by simply sitting next to a source of water, grabbing a visiting bird, and SNAP.

9. Another scientist, Alfred Russell Wallace, also came up with evolution. He wrote to Darwin asking for his opinion, Darwin panicked, and at the advice of colleagues, finished the Origin of Species as soon as possible, leaving out much of what was intended to be included. Wallace and Darwin published together, but as the idea stuck, Wallace began referring to evolution as “Darwin's idea” and considered himself lucky to even be friends with Darwin.

10. Darwin was a tad neurotic, and wrote down almost every idea. From all his letter, notebooks, diaries, etc., it is easy to see the evolution of the idea of evolution. The biggest obstacle to Darwin scholars today is not finding material, but reading Darwin's handwriting.

2009-02-06T16:55:00.001-08:00

The Media.

I rarely watch TV. The news is much easier to get online; it's much easier to access a wide variety of sources, to learn background information about current events, and to speak to people directly involved in the news at hand. However, I'm wondering if my neglect of television has been a mistake.

I spend a lot of time in a particular coffee shop; I take my laptop here during the day, and sit under a huge flatscreen TV that is forever tuned to CNN. Now, CNN is one of the more reputable news sources out there, especially when compared to Fox News or MSNBC. However, the last few days of exposure to this mainstream news channel have startled me -- CNN is an incredibly polemic channel.

The rhetoric they use is absolutely sensational, although this was easily guessed. But the news they provide is utterly unhelpful -- all about soundbites, entirely one-sided -- I guess, it's everything I've read about mainstream media. The media is constantly denigrated by reasonable people, for a variety of reasons. But the shocking part is: these reasons, they're all true.

I'm watching coverage of the Salmonella outbreak now. They're interviewing a little kid that got Salmonella from peanut butter -- he's spouting words and concepts he clearly doesn't understand: "I think... (pause, looks questioningly off camera) I think we should re... recall all peanut butter products, and... (looks off camera again) ..test them all, and create another federal institution in charge of testing all the food. The FDA isn't keeping me safe. The FDA made me want to die." [Reporter smirks satisfactorily at camera.] The camera pans to some seriously disgusting-looking peanut butter, as the off-screen voice tells us, "The FDA is incapable of keeping us safe. This has been the largest food recall in history."

How is this helpful at all? How does this do anything except incite panic? If CNN were reasonable, they'd put together a nice report on the pros and cons of the FDA, how it's helped, where it's failed, and compare/contrast the possibility of a new food regulatory agency. The situation would have been handled calmly, intelligently, and informed the American people, who will instead undoubtedly be calling their representatives in a panic, screaming blindly for reform. No wonder Americans are ignorant about politics -- this is the news we stand.

Journalism is dying, not because people aren't consuming, but because we all want to be in a reality TV show. The problem is, real life doesn't have an editor to step in and save the day at the end. The more polemic entertainment we demand, the more Americans walk around feeling as though the world will end. It's a self-fulfilling prophecy.

There will, mark my words, be talk of a new regulatory agency in the wake of these outbreaks. And maybe that's a good thing. God knows the FDA is terrible. But will the process be nuanced? Will our choices be educated? I doubt it. This television is sickening. That's what we call the news...

2009-02-03T14:31:00.001-08:00

Robot Love

I read an interesting passage today in Ger Gigerenzer's Gut Feelings: The Intelligence of the Unconscious. The focus of his book is the idea that effective intuitive processes are the product of discarding information -- not retaining it. He illustrates his point with a short story, The Fable of Robot Love. The point is interesting, so bear with it:

In the year 2525, engineers finally managed to build robots that looked like humans, acted like humans, and were ready to reproduce. Ten thousand robots of various types had been built, all of them female. A research team set out to design a male robot who would be able to find a good mate, found a family, and take care of the little robots until they were able to take care of themselves. They called their first model Maximizer-1, M-1 for short.

Programmed to find the best mate, M-1 proceeded to identify a thousand female robots that fit his goal of not marrying a model older than himself. He detected five hundred features on which individual female robots varied, such as energy consumption, computing speed, and frame elasticity. Regrettably, the females did not have their individual feature values printed on their foreheads; some even hid them, trying to fool M-1. He had to infer these values from samples of behavior.

After three months had passed, he had succeeded in getting reliable measures on the first feature he tested, memory size, from each female robot. The research team made a quick calculation of when M-1 would be ready to pick the best and discovered that no one in the team would still be alive at that point -- nor would the best female robot.

The thousand females were upset that M-1 could not make up his mind, and as he began recording the second feature, the serial number, they pulled out his batteries and dumped him in a scrap yard. The team went back to the drawing board.

M-2 was designed to focus on the most important features and to stop looking for more when the costs of collecting further information exceeded its benefits. After three months, M-2 was exactly where M-1 was, and in addition was busy measuring the benefits and costs of each feature so that he could know what to ignore. The impatient females ripped out his wires and got rid of him, too.

The team now adopted the proverb that the best is the enemy of the good, and designed G-1, a robot who looked for a mate that was good enough. G-1 had an aspiration level build in. When he encountered the first female who met his aspiration level, he would propose to her -- and ignore the rest. To make sure that he found a mate if his aspirations were too high, he was equipped with a feedback loop that lowered the aspiration level if none of the females were good enough for him over too long a period. G-1 showed no interest in the first six females he met, but then proposed to number seven. Short of alternatives, she accepted.

Three months later, to everyone's pleasure, G-1 was married and had two small kids. While writing the final report, however the team learned that G-1 had left his wife for another robot. Nothing in his brain had prevented him from running off to what looked to him like a better deal. One team member pointed out that M-1 would never have left his wife, because he would only have accepted the best in the first place. That's true, responded the others, but at least G-1 found one.

The team discussed this for a while and then came up with GE-1. He was happy with a good enough female, just like G-1, but was additionally equipped with an emotional glue that was released when he met a good enough robot and adhered more strongly with physical contact. Just to be sure, they inserted a second form of emotional glue into his brain that discharged when a baby was born and tightened after each physical contact with the baby.

GE-1 proposed to a female as quickly as G-1 did, married, and fathered three babies. He was still with them when the team finished their report. He was somewhat clingy, but dependable. Ever since, GE-1 robots have conquered the earth.

In the fable, M-1 failed because he tried to find the best, as did M-2. Both ran out of time. G-1 was fast by going for a good enough choice, but was also fast in dropping it. However, the capacity for love, the glue, provided a powerful stopping rule that ended GE-1's search for a partner and strengthened his commitment to his loved ones.

Similarly, feelings of parental love, triggered by an infant's presence or smile, free parents from having to decide every morning whether they should invest their resources in their children or in some other business. The questionof whether it is worthwhile to endure all the sleepless nights and other frustrations of having a child simply does not arise, and our memory ensures that we forget these tribulations soon.

The evolved brain keeps us from looking too long and thinking too much. That is what love is. ;-) The culture it is embedded in influence what the objects of love or trust can be, or what makes us upset or feel hurt.

Gigerenzer goes on to discuss this problem in humans -- the deliberate search for the best can conflict with emotions (pride, honor) in humans. Johannes Kepler, for instance, was short, sickly, and born into a poor family. However, his fame and intellect ranked him a good catch. In 1611, he left his unhappy and arranged marriage, and embarked on a systematic search for a second wife. Unlike Barbara Bush, who "married the first man she kissed," Kepler investigated eleven (!) possible replacement wives in under two years. His friends urged him to pick bachelorette number four, a refined lady of high status and dowry, but he insisted on being thorough. This insulted the fine lady, and she rejected him in the end.

2009-01-27T18:41:00.000-08:00

An interesting resource on martial law in the US.

2009-01-23T00:53:00.001-08:00

The Wisdom of Jean Rostand:

Falsity cannot keep an idea from being beautiful; there are certain errors of such ingenuity that one could regret their not ranking among the achievements of the human mind.

In order to remain true to oneself one ought to renounce one's party three times a day.

In politics, yesterday's lie is attacked only to flatter today's.

Stupidity, outrage, vanity, cruelty, iniquity, bad faith, falsehood - we fail to see the whole array when it is facing in the same direction as we.

Science has made us gods even before we are worthy of being men.

It is sometimes important for science to know how to forget the things she is surest of.

There are certain moments when we might wish the future were built by men of the past.

Think? Why think! We have computers to do that for us.

Truth is always served by great minds, even if they fight it.

It takes a very deep-rooted opinion to survive unexpressed.

Never feel remorse for what you have thought about your wife; she has thought much worse things about you.

A few great minds are enough to endow humanity with monstrous power, but a few great hearts are not enough to make us worthy of using it.

The divine is perhaps that quality in man which permits him to endure the lack of God.

A man is not old as long as he is seeking something

2009-01-22T13:06:00.000-08:00

How to debug a C program.
--------------------------

1] If at all possible, don't. Let someone else do it.
2] Change majors. (Win.)
3] Insert/remove blank lines at random spots, re-compile, and excecute.
4] Throw holy water on the terminal.
5] Dial 911 and scream.
6] There is rumour that "printf" is useful, but this is probably
unfounded.
7] Port everything to CP/M.
8] If it still doesn't work, re-write it in assembler. This won't fix the
bug, but it will make sure no one else finds it and makes you look bad.

PASCAL is not a language. It was an experiment combining the flexibility of C with that of a drug-crazed penguin. It is also the 'language' of choice of many CS professors who aren't up to handling REAL programming. Hence, it is not a language.

C is almost a real language. (see assembler) Even the name sounds like it's gone through an optimizing compiler. Get rid of all of those stupid brackets and we'll talk. (see LISP)

ASSEMBLER is a language. Any language that can take a half-dozen keystrokes and compile it down to one byte of code is all right in my books. Though for the REAL programmer, assembler is a waste of time. Why use a compiler when you can code directly into memory through a front panel?

How to program in C
---------------------
1] Use lots of global variables.
2] Give them cryptic names such as: X27, a_gcl, or Horace.
3] Put everything in one large .h file.
4] Implement the entire project at once.
5] Use macros and #defines to emulate Pascal.
6] Assume the compiler takes care of all the little details you didn't quite
understand.

If you put garbage in a computer nothing comes out but garbage. But this garbage, having passed through a very expensive machine, is somehow enobled and none dare criticize it.

Any sufficiently advanced bug is indistinguishable from a feature.

2009-01-21T10:06:00.000-08:00

Dethroning Python? Brief Words On Haskell.

Python had long been my favorite programming language -- its power and ease of use made for short, elegant, and readable code. But then, a year or so ago, I started messing around with Haskell. And even though I've yet to use it for a practical purpose, I loved it. So subtle! So sophisticated! And it gets better with age. If programming languages were men, I may have met James Bond.

2009-01-20T13:08:00.000-08:00

American Atheists, Agnostics, and Nonbelievers celebrate: Obama just made us citizens.

"We are no longer just a Christian nation; we are also a Jewish nation, a Muslim nation, a Buddhist nation, a Hindu nation, and a nation of nonbelievers."

This sentence from Obama's inaugural address is buzzing all over atheist blogs, twitters, and status messages. I got three text messages quoting it within 30 seconds after it was spoken. Already, "nonbelievers" feel justified -- this is, after all, the first time we've been recognized in an inaugural speech. In fact, it's one of the first times "nonbelievers" were mentioned in politics without being followed by, "...aren't citizens," or "...are ruining Christmas," etc. And we think this is progress.

However, Rick Warren's "prayer" (which felt more like an empty, obligatory political manifesto) was a tragedy to be laughed at. Half-hearted, insincere, and startlingly lame. He didnt even register in my brain as an adversary -- as most atheists would expect him to. He came of as pitiful, stupid, confused -- so distanced from reality it was almost sad. This article might be relevant.

It does seem, at least on paper, that Obama is also paying lip service to the Constitution. Have a look at the (shiny new!) whitehouse.gov's technology page. Is there still hope for civil liberties in America? Let's hope so. Good luck, President Obama!

2009-01-18T16:50:00.000-08:00

2009-01-17T11:17:00.000-08:00

Israel.

Upon learning that it's a federal offense to boycott Israel, I immediately wondered what products would be boycotted. After a quick search, there seems to be a myth floating out there that says Israeli products can be recognized by a barcode that starts with 729. This doesn't seem to be true, according to this Bar Code FAQ:

Does the barcode number indicate the country of origin of a product?

No it doesn't. The 3-digit prefix code indicates which GS1 numbering organization has allocated the block of numbers to the company. Once the company has been assigned the block of numbers, they self assign each individual number in the block to a given product. For example, a company may have it's headquarters in South Africa. The GS1 organization in South Africa has the code "600", but all the products of the company may be manufactured in England. The English-made products would still have the "600" prefix code. The prefix code is a way to have 70-plus GS1 member organizations issuing numbers without having to worry about duplicate numbers. The 3-digit prefix indicates the country of the GS1 organization that issued the block of numbers, not the country of origin of the product. GS1 (the international organization that administers UPC and EAN) has a clear statement that the prefix DOES NOT indicate the country of origin of the product. A list of country codes can be found on the UPC & EAN Page.

If you're outside of the US, and/or don't mind breaking this federal law, you might wonder how one might spot a product exported from Israel.

The answer is to download a database that matches all UPC product codes (barcodes) on the market as of yet to their respective manufacturers. You can actually download such a database as it is free and distributed under the Creative Commons license (here). Then, simply do a search for "Israel" to find which companies market products which are made in Israel.

Good news: A user named Toshibu has already done the work for us!

Here is a comprehensive spreadsheet of all companies exporting products from Israel.
Here is a comprehensive chart of all Israeli products registered by UPC to date.

To recreate the above results, the following commands may be used:

$ wget >
$ tar zxf upcdatabase-2009.01.01.tar.gz
$ cd upcdatabase-2009.01.01
$ grep -i "israel\"" glns.csv | awk -F, '{ print $1 }' | cut -c 8- --complement | awk '{print "^"$0}' | grep -f - items.csv > items-israel.csv
$ cat items-israel.csv | awk -F, '{ printf( "%s %*s %s\n", $1, 36, $2, $3 ) }'

That said, maybe Israel doesn't deserve a boycott. After all, the point here isn't the mass slaughtering of innocent civilians in a brutal, racist manner -- oh, wait. After the Holocaust, didn't we all swear it, "Never Again"? Glad to see we haven't forgotten.

Maybe it's genuinely self-defense. Maybe Israel has no choice here. Maybe it's because the Palestinian rockets are so powerful compared to Israeli airstrikes? Oh, wait. Can you guess which is which?

Or maybe it's because Israel can do no wrong. Maybe they are teaching their children to learn from the past, preaching tolerance and love instead of violence and hate? "With love, from Israel." Yeah. I can see that. Good job, guys, you killed the terrorist.

The worst part is, when the UN made a plea for the violence to cease, nobody listened. Because we all expected them to listen, right? Right?

2009-01-15T11:50:00.001-08:00

Happy Birthday, Wikipedia!

It's funny because that's how it's pronounced... [citation needed]

2009-01-14T11:28:00.000-08:00

Lasantha Wickrematunge, a Sri Lankan journalist for The Sunday Leader, wrote an editorial to be published in the event he were assassinated. He was assassinated. Here is the editorial: And Then They Came For Me.

Even if the middle paragraphs are obscure, the last few paragraphs are very worth reading.

Since access to this site has been sketchy, here is the text:

Editorial

And Then They Came For Me

No other profession calls on its practitioners to lay down their lives for their art save the armed forces and, in Sri Lanka, journalism. In the course of the past few years, the independent media have increasingly come under attack. Electronic and print-media institutions have been burnt, bombed, sealed and coerced. Countless journalists have been harassed, threatened and killed. It has been my honour to belong to all those categories and now especially the last.

I have been in the business of journalism a good long time. Indeed, 2009 will be The Sunday Leader's 15th year. Many things have changed in Sri Lanka during that time, and it does not need me to tell you that the greater part of that change has been for the worse. We find ourselves in the midst of a civil war ruthlessly prosecuted by protagonists whose bloodlust knows no bounds. Terror, whether perpetrated by terrorists or the state, has become the order of the day. Indeed, murder has become the primary tool whereby the state seeks to control the organs of liberty. Today it is the journalists, tomorrow it will be the judges. For neither group have the risks ever been higher or the stakes lower.

Why then do we do it? I often wonder that. After all, I too am a husband, and the father of three wonderful children. I too have responsibilities and obligations that transcend my profession, be it the law or journalism. Is it worth the risk? Many people tell me it is not. Friends tell me to revert to the bar, and goodness knows it offers a better and safer livelihood. Others, including political leaders on both sides, have at various times sought to induce me to take to politics, going so far as to offer me ministries of my choice. Diplomats, recognising the risk journalists face in Sri Lanka, have offered me safe passage and the right of residence in their countries. Whatever else I may have been stuck for, I have not been stuck for choice.

But there is a calling that is yet above high office, fame, lucre and security. It is the call of conscience.

The Sunday Leader has been a controversial newspaper because we say it like we see it: whether it be a spade, a thief or a murderer, we call it by that name. We do not hide behind euphemism. The investigative articles we print are supported by documentary evidence thanks to the public-spiritedness of citizens who at great risk to themselves pass on this material to us. We have exposed scandal after scandal, and never once in these 15 years has anyone proved us wrong or successfully prosecuted us.

The free media serve as a mirror in which the public can see itself sans mascara and styling gel. From us you learn the state of your nation, and especially its management by the people you elected to give your children a better future. Sometimes the image you see in that mirror is not a pleasant one. But while you may grumble in the privacy of your armchair, the journalists who hold the mirror up to you do so publicly and at great risk to themselves. That is our calling, and we do not shirk it.

Every newspaper has its angle, and we do not hide the fact that we have ours. Our commitment is to see Sri Lanka as a transparent, secular, liberal democracy. Think about those words, for they each has profound meaning. Transparent because government must be openly accountable to the people and never abuse their trust. Secular because in a multi-ethnic and multi-cultural society such as ours, secularism offers the only common ground by which we might all be united. Liberal because we recognise that all human beings are created different, and we need to accept others for what they are and not what we would like them to be. And democratic... well, if you need me to explain why that is important, you'd best stop buying this paper.

The Sunday Leader has never sought safety by unquestioningly articulating the majority view. Let's face it, that is the way to sell newspapers. On the contrary, as our opinion pieces over the years amply demonstrate, we often voice ideas that many people find distasteful. For example, we have consistently espoused the view that while separatist terrorism must be eradicated, it is more important to address the root causes of terrorism, and urged government to view Sri Lanka's ethnic strife in the context of history and not through the telescope of terrorism. We have also agitated against state terrorism in the so-called war against terror, and made no secret of our horror that Sri Lanka is the only country in the world routinely to bomb its own citizens. For these views we have been labelled traitors, and if this be treachery, we wear that label proudly.

Many people suspect that The Sunday Leader has a political agenda: it does not. If we appear more critical of the government than of the opposition it is only because we believe that - pray excuse cricketing argot - there is no point in bowling to the fielding side. Remember that for the few years of our existence in which the UNP was in office, we proved to be the biggest thorn in its flesh, exposing excess and corruption wherever it occurred. Indeed, the steady stream of embarrassing expos‚s we published may well have served to precipitate the downfall of that government.

Neither should our distaste for the war be interpreted to mean that we support the Tigers. The LTTE are among the most ruthless and bloodthirsty organisations ever to have infested the planet. There is no gainsaying that it must be eradicated. But to do so by violating the rights of Tamil citizens, bombing and shooting them mercilessly, is not only wrong but shames the Sinhalese, whose claim to be custodians of the dhamma is forever called into question by this savagery, much of which is unknown to the public because of censorship.

What is more, a military occupation of the country's north and east will require the Tamil people of those regions to live eternally as second-class citizens, deprived of all self respect. Do not imagine that you can placate them by showering "development" and "reconstruction" on them in the post-war era. The wounds of war will scar them forever, and you will also have an even more bitter and hateful Diaspora to contend with. A problem amenable to a political solution will thus become a festering wound that will yield strife for all eternity. If I seem angry and frustrated, it is only because most of my countrymen - and all of the government - cannot see this writing so plainly on the wall.

It is well known that I was on two occasions brutally assaulted, while on another my house was sprayed with machine-gun fire. Despite the government's sanctimonious assurances, there was never a serious police inquiry into the perpetrators of these attacks, and the attackers were never apprehended. In all these cases, I have reason to believe the attacks were inspired by the government. When finally I am killed, it will be the government that kills me.

The irony in this is that, unknown to most of the public, Mahinda and I have been friends for more than a quarter century. Indeed, I suspect that I am one of the few people remaining who routinely addresses him by his first name and uses the familiar Sinhala address oya when talking to him. Although I do not attend the meetings he periodically holds for newspaper editors, hardly a month passes when we do not meet, privately or with a few close friends present, late at night at President's House. There we swap yarns, discuss politics and joke about the good old days. A few remarks to him would therefore be in order here.

Mahinda, when you finally fought your way to the SLFP presidential nomination in 2005, nowhere were you welcomed more warmly than in this column. Indeed, we broke with a decade of tradition by referring to you throughout by your first name. So well known were your commitments to human rights and liberal values that we ushered you in like a breath of fresh air. Then, through an act of folly, you got yourself involved in the Helping Hambantota scandal. It was after a lot of soul-searching that we broke the story, at the same time urging you to return the money. By the time you did so several weeks later, a great blow had been struck to your reputation. It is one you are still trying to live down.

You have told me yourself that you were not greedy for the presidency. You did not have to hanker after it: it fell into your lap. You have told me that your sons are your greatest joy, and that you love spending time with them, leaving your brothers to operate the machinery of state. Now, it is clear to all who will see that that machinery has operated so well that my sons and daughter do not themselves have a father.

In the wake of my death I know you will make all the usual sanctimonious noises and call upon the police to hold a swift and thorough inquiry. But like all the inquiries you have ordered in the past, nothing will come of this one, too. For truth be told, we both know who will be behind my death, but dare not call his name. Not just my life, but yours too, depends on it.

Sadly, for all the dreams you had for our country in your younger days, in just three years you have reduced it to rubble. In the name of patriotism you have trampled on human rights, nurtured unbridled corruption and squandered public money like no other President before you. Indeed, your conduct has been like a small child suddenly let loose in a toyshop. That analogy is perhaps inapt because no child could have caused so much blood to be spilled on this land as you have, or trampled on the rights of its citizens as you do. Although you are now so drunk with power that you cannot see it, you will come to regret your sons having so rich an inheritance of blood. It can only bring tragedy. As for me, it is with a clear conscience that I go to meet my Maker. I wish, when your time finally comes, you could do the same. I wish.

As for me, I have the satisfaction of knowing that I walked tall and bowed to no man. And I have not travelled this journey alone. Fellow journalists in other branches of the media walked with me: most of them are now dead, imprisoned without trial or exiled in far-off lands. Others walk in the shadow of death that your Presidency has cast on the freedoms for which you once fought so hard. You will never be allowed to forget that my death took place under your watch. As anguished as I know you will be, I also know that you will have no choice but to protect my killers: you will see to it that the guilty one is never convicted. You have no choice. I feel sorry for you, and Shiranthi will have a long time to spend on her knees when next she goes for Confession for it is not just her owns sins which she must confess, but those of her extended family that keeps you in office.

As for the readers of The Sunday Leader, what can I say but Thank You for supporting our mission. We have espoused unpopular causes, stood up for those too feeble to stand up for themselves, locked horns with the high and mighty so swollen with power that they have forgotten their roots, exposed corruption and the waste of your hard-earned tax rupees, and made sure that whatever the propaganda of the day, you were allowed to hear a contrary view. For this I - and my family - have now paid the price that I have long known I will one day have to pay. I am - and have always been - ready for that. I have done nothing to prevent this outcome: no security, no precautions. I want my murderer to know that I am not a coward like he is, hiding behind human shields while condemning thousands of innocents to death. What am I among so many? It has long been written that my life would be taken, and by whom. All that remains to be written is when.

That The Sunday Leader will continue fighting the good fight, too, is written. For I did not fight this fight alone. Many more of us have to be - and will be - killed before The Leader is laid to rest. I hope my assassination will be seen not as a defeat of freedom but an inspiration for those who survive to step up their efforts. Indeed, I hope that it will help galvanise forces that will usher in a new era of human liberty in our beloved motherland. I also hope it will open the eyes of your President to the fact that however many are slaughtered in the name of patriotism, the human spirit will endure and flourish. Not all the Rajapakses combined can kill that.

People often ask me why I take such risks and tell me it is a matter of time before I am bumped off. Of course I know that: it is inevitable. But if we do not speak out now, there will be no one left to speak for those who cannot, whether they be ethnic minorities, the disadvantaged or the persecuted. An example that has inspired me throughout my career in journalism has been that of the German theologian, Martin Niem”ller. In his youth he was an anti-Semite and an admirer of Hitler. As Nazism took hold in Germany, however, he saw Nazism for what it was: it was not just the Jews Hitler sought to extirpate, it was just about anyone with an alternate point of view. Niem”ller spoke out, and for his trouble was incarcerated in the Sachsenhausen and Dachau concentration camps from 1937 to 1945, and very nearly executed. While incarcerated, Niem”ller wrote a poem that, from the first time I read it in my teenage years, stuck hauntingly in my mind:

First they came for the Jews

and I did not speak out because I was not a Jew.

Then they came for the Communists

and I did not speak out because I was not a Communist.

Then they came for the trade unionists

and I did not speak out because I was not a trade unionist.

Then they came for me

and there was no one left to speak out for me.

If you remember nothing else, remember this: The Leader is there for you, be you Sinhalese, Tamil, Muslim, low-caste, homosexual, dissident or disabled. Its staff will fight on, unbowed and unafraid, with the courage to which you have become accustomed. Do not take that commitment for granted. Let there be no doubt that whatever sacrifices we journalists make, they are not made for our own glory or enrichment: they are made for you. Whether you deserve their sacrifice is another matter. As for me, God knows I tried.

2008-12-31T21:20:00.000-08:00

FBI "Cryptanalysis"

The FBI encourages us all to try our hand at cryptanalysis. Their cipher is as follows:

VFWTDLCSWV. YD NSLMIJFWEJFD GSW SL NIJNQBLM FOBV EJFDVF DLNIGTFBSL. KBVBF YYY.AHB.MSK/NSCDC.OFZ FS EDF WV QLSY SA GSWI VWNNDVV.

--

Spoiler alert:

The first thing that stands out is the website, YYY.AHB.MSK/etc. Because of the formatting, we can assume it's a simple substitution cipher, and see what happens (we're not wrong). What website might this be? WWW.FBI.GOV, perchance? I think yes. The sentence with the URL begins with KBVBF, which is probably a verb in reference to the URL. What can we do to URLs? Go to them? Not five letters. Visit them? I think yes, given: visit, kbvbf. Keep doing this for a few more minutes (or, be smart/lazy and write a quick decoder), and you'll get the finished product:

"Stupendous. We congratulate you on cracking this latest encryption. visit www.fbi.gov/coded.htm to let us know of your success." Where, presumably, they log your IP. Thanks, FBI. You make us feel important.

Cheers.

2008-12-28T22:04:00.001-08:00

Something we can agree on...

2008-12-15T20:28:00.000-08:00

What would John McCarthy say if he saw you programming?

2008-11-26T03:07:00.000-08:00

Very interesting. A group of ~25k individual (unconnected) rat neurons are hooked up to a bed of electrodes, learning how to fly via a virtual flight simulator. An excellent video.

2008-11-23T23:18:00.001-08:00

Once you love something, you lose all ability to understand it.

2008-11-17T01:07:00.000-08:00

The Wisdom of Gchat

Jata: there is a pile of papers about as tall as i am

Nora: nice

Jata: it frightens me

Nora: wait seriously? you have to take a picture

Nora: like a dogbert cartoon

Jata: yeah, it's... bad

Nora: no no

its epic

Jata: no, because it is all work i have not done yet

Nora: just think of the epic-ness

its all that matters

in the end

Jata: yeah, epic in the way hector facing achilleus was epic. awesome story, didn't work out so well for hector.

Nora: well achilleus didnt turn out so hot either

all you have to do is find your homework's acchille's heel

Jata: that'll do it.

logically, i have to die first. then it will be dragged in its death from the back of a horse... oh wait, that's ME.

(however, zeus did protect the body from defacement... hmmm)

(zeus? a little help here?)

Nora: he will rape you in animal form * whinnies from on high *

Jata: oh god

i prefer jesus

not that way zomg gah eww im sorry jesus im sorry forgive me?

Nora: * squeals *

imagine if jesus took on animal forms

Jata: and raped people?

Nora: no. but only humble, desert animals

like kangaroo rats

or armadillos

Jata: wow... that is so... i dont even know what to say

Nora: jesus snuffling in the sand

curling up in a little ball

whimpering slightly in the shadow of a cactus

teehehe

Jata: aww

::pets jesus::

Nora: jesus's hard, armadillo shell

a grub clinging to his tiny armadillo teeth

fear gods wrath...

Jata: armadillos = cute. armadillos that produce wine = profit.
Nora: omg that's our next project!
Jata: field trip! imagine if we find jesus the wine-making armadillo. we'd have a profitable prophet on our hands

2008-10-25T22:42:00.000-07:00

I believe that there are some things people do entirely for their own sake, without possibility of ulterior motive or obfuscated goal. For instance, I make small yet hilarious edits on Wikipedia -- an altered verb, a few letters here or there -- with the requirements that 1) the edit is in the article's introduction and 2) it drastically changes the entry's meaning (in the patently false direction).

I get too much satisfaction from every such sabotage surviving more than a year -- what does it say about the thousands of careful readers, and their thousands of edits since? What does it mean for their ontological and epistemic reality -- is there a certain lifespan, a minimum readership, that allows an untested conjecture to graduate to truth? Of course not. But someone, somewhere out there, believes.

These edits bring me a solitary sort of joy, which keeps me smiling long after most have gone to sleep. This joy is my own: I'm friends with several of the Wiki admins, so if I ever share the edits I made, they'll be fixed. If I ever explain the rules of my game, I won't be able to play. It is a joyful abstraction I can never share, except in the name of the anonymous. I do it for the lulz -- And the lulz are enough...

2008-10-24T16:23:00.001-07:00

The Top 10 Philosophy Questions of All Time, Answered!

10. How do I know anything really exists?
Kick it *really* hard.
9. What is the essence of being human?
Not understanding the opposite sex.
8. If a tree falls in the forest, and there's no one there to hear it, does it make a sound?
Not if it lands on a bunch of pillows.
7. How do I know I'm not just a brain in a vat, hooked up to a computer simulation of life?
Look in the mirror. If you see a gray, spongy thing in a glass container, you are.
6. Can our minds exist seperately from our bodies?
If they could, we'd send our minds to class and sleep in every morning.
5. Is there a God?
A billion Hindus can't be wrong.
4. What is the nature of Knowledge?
I'm still trying to figure out the nature of *college*.
3. What is the meaning of life?
All evidence to date suggests it's probably chocolate.
2. Why get a Philosophy degree?
It's more respectable than a theater degree, but you still get to drink lots of espresso.
1. So, was Kant on drugs or what?
Probably.

2008-10-11T00:52:00.001-07:00

For Sale: One soul. Price negotiable. Assembly required.

2008-09-15T07:35:00.000-07:00

Through me the way to the woeful city;
Through me the way to eternal pain;
Through me the way to the lost people.

Justice moved my Maker above;
Caused by Divine power,
Supreme wisdom, and primal Love.

Before me was only Eternity,
And eternally I endure.
Abandon all hope, ye who enter here!

---

This is now taped to my microwave.

---

2008-08-19T14:09:00.000-07:00

Excerpts from Thomas Carlyle's On Great Men (1840)

We have undertaken to discourse here for a little on Great Men, their manner of appearance in our world's business, how they have shaped themselves in our world's history, what ideas men formed of them, what work they did; -- on Heroes, namely, and on their reception and performance; what I call Hero-worship and the Heroic in human affairs. To evidently this is a large topic; deserving quite other treatment than we can expect to give it at present. A large topic; indeed an illimitable one; wide as Universal History itself. For, as I take it, Universal History, the history of what man has accomplished in this world, is at bottom the History of the Great Men who have worked here.

The Hero as Divinity, the Hero as Prophet, are productions of old ages; not to be repeated in the new. They presuppose a certain rudeness of conception, which progress of mere scientific knowledge puts an end to. There needs to be, as it were, a world vacant, or almost vacant of scientific forms, if men in their loving wonder are to fancy their fellow-man either a god or one speaking with the voice of a god. Divinity and Prophet are past. We are now to see our Hero in the less ambitious, but also less questionable, character of Poet; a character which does not pass. The Poet is a heroic figure belonging to all ages; whom all ages possess, when once he is produced, whom the newest age as the oldest may produce; -- and will produce always when Nature pleases. Let Nature send a hero-soul; in no age is it other than possible that he may be shaped into a Poet.

2008-08-13T14:21:00.001-07:00

Open Source Penguin [PDF] )(From free-penguin.org)

The free-penguin project page: This project provides 'executables' that enable you to make your own soft-toy Linux® penguin. To put it straight: You can find sewing patterns and a community to sew your own soft toy or stuffed Linux® Tux penguin here. To help Google finding this, once again: You can find sewing patterns and community to sew your own soft toy or stuffed Linux® Tux penguin here. All downloads come under GPL (GNU General Public License).

Objective:

The starting point of this project was the question: "Why is it that on the one hand in the Linux® world all code of software is freely available and on the other hand the code to compile a soft toy penguin is still not open source?" This project will try to publish code that will enable people to sew soft toy penguins themselves provided they meet certain hardware requirements. [PDF]

2008-08-12T23:07:00.000-07:00

Accidental Suicide

Today, at approximately 4:31am, I "accidentally" killed Vista and was "forced" to reinstall Ubuntu. Windows failed to include a boot disk in their lovely package of coasters, so I'm "stuck" without it for now. While it seems strange, now that it's happening, for anyone to complain about not having Vista, my malaise stems from the fact that I didn't mean to wipe my hard drive; I didn't mean to free myself from the debacle that is Vista -- it was an accident. It was actually an accident. Somehow, despite knowing that nuking a drive takes at least two hours when you're trying to do it, despite the fact that I know how to use computers, I managed to destroy my primary operating system. This is due, I am ashamed to confess, to the fact that I have far more balls and far fewer brains when I am severely sleep-deprived. It was a tragic... accident. Note to self: when skating on the edge of creation and destruction thrills you more than usual, turn the machine off.

On the brighter side, I'm now forced, against all better judgment, to delve into the depths of Ubuntu, something I'm sorry to say I haven't done in almost half a month. There was something almost too satisfying, something too good to be true about Vista, it just... couldn't last. Too bad it's GONE! GONE HAHAHA YES GONE GONE HAHAHAHA. I'm here, again, my darling penguins. I've returned home.

2008-08-09T01:48:00.000-07:00

Hardtack: A Hardcore Food

Hardtack, also known as pilot bread, ship's biscuit, seafaring wafers, dog biscuits, tooth dullers, sheet iron, or molar breakers, is a delicious food. It is a simple type of cracker, made out of only flour, water, and occasionally salt. It's dirt-cheap, lasts forever, and has an excellent history feeding soldiers and sailors during some of the worst voyages and military campaigns in history.

Because it is so hard and dry, properly stored and transported hardtack will survive rough handling and endure extremes of temperature. During the Civil War, 3"x3" hardtack was shipped out from Union and Confederate storehouses. Some of this hardtack had been stored from the Mexican-American War (1846-1848!). The insect infestation was so bad during storage of these provisions, soldiers had to drop the tack into their morning coffee, wait for the insects to float to the to top, and skim off the bugs to resume consumption. Yummy!

It was a staple of the diet of soldiers in World War I, as well as of gold-diggers heading West to try their luck in California (during the 1840's Gold Rush, as opposed to modern gold-diggers, who probably do not enjoy hardtack). Since hardtack has such a glowing history, I decided to make some to try it myself. Also, I am a poor student working in academia, and I'd like the comfort of some delicious sheet iron during the long nights at the lab.How is this stuff made? Voila! A recipe!

Ingredients:

3 cups flour
1 cups water
~6 pinches of salt

Preparation:

1. Preheat oven to 350 degrees. That is, if you're not hardcore enough to use fire and a metal box.
2. Mix the flour, salt, and water until you have a dough.
3. Cut into biscuits; I used a cup to cut them into circles, but you can cut them into squares or anything you'd like. Place on a lightly floured/salted oven sheet.
3. Decorate! I poked cross-like designs into the dough with a fork to increase surface area and ease cooking, but you can do whatever you'd like.
4. Bake at 350 for an hour. Flip the crackers (optional, but recommended), and bake for another 2-4 hours at 250.
5. Some people recommend baking them up to four times at low temperatures (200-250 degrees), depending on the length of your conquest or journey.

I can personally assure you, they are delicious. And they last forever! Maybe not literally, but they were stored for decades and distributed to troops. Sailors would prepare them six months to a year ahead of a journey, and pack them away ready for use. Several museums display them; no preservatives were necessary. They resemble ceramic disks in texture and hardness. My cats do not recognize them as food. You can dunk them in coffee or soup, or eat them straight. They're super-tasty, plus they make you hardcore, and very, very awesome.

2008-08-08T12:17:00.000-07:00

Airing of Grievances:

-Comprehensive National Cybersecurity Initiative: What you don't know can hurt you.
-NIST's CNCI Challenge.
-This whole situation is upsetting. Ivins didn't have clearance at Fort Detrick to create the quality of weapons-grade anthrax he is accused of making. The claims of mental instability are a recent thing. Conveniently, he's dead now.
-The new border policy declares that agents don't need any reason to search, seize or copy travellers' laptop, PDA, or phones. No suspicion, no explanation. They can download all your data (everything on your hard drive, phone calls, contact numbers, schedule, etc) without letting you know or telling you why. The government spoke, and the Ninth U.S. Appeals Court has agreed.
-Chertoff gives the impression, in this interview, of being reasonable (or at least aware of his audience).

On a brighter note, here is a little poem written during the Dover trial by a very famous evolutionary biologist who has asked to keep it anonymous:

I think that I shall never see
A theory dumber than ID:
It says that God can make a tree,
A beaver or a honeybee-
That God can simply get a whim
To make the small E. coli swim.
He waves His hand through Heaven's air
And lo! Flagella everywhere!
But sometimes even God falls down
And makes a poor, pathetic clown:
Yes, poems are made by fools like me,
But only God can make Behe.

And now I move to Canada.

2008-08-06T01:55:00.000-07:00

I am living... with four cats... four... one, two, three, four... four cats. Spock, Quentin, Raptor, and Calypso. They are not all mine. Calypso might be pregnant. They all sleep in my bed. I love them, but.... there are four of them. They meow incessantly. They scratch at my arms and face. They pounce on me in my sleep. One of them is sitting on my back. One of them is tearing through my closet. One of them is in a box. One of them is on my dresser. There are four cats... four cats... I am a dog person, living in a state of cataclysm. My sanity is wearing thin. Survival is a distant notion. May God have mercy on my soul...

Om nom nom.

2008-07-29T23:42:00.000-07:00

This is a review I wrote a while back; due to popular demand (a friend's request), I'm posting it here, for all to read, love, and enjoy. It's a review of Sahotra Sarkar's book, Doubting Darwin?, a critique of Intelligent Design "theory," as well as an all-out attack on Michael "Irreducible Complexity" Behe's strange notions of biology. There is thinly masked disdain, dry humor, and gratuitous flighty/outright insulting rhetoric. It's kind of long. But anyone who gets a kick out of the depravity of creationists just might like it...

Doubting Darwin? by Sahotra Sarkar: Commentary & Review

“That the creationists have resorted to this subversion should surprise none of us, for the ethical poverty of their actions matches the intellectual poverty of their beliefs.” -- Peter Atkins

American author and social reformer Upton Sinclair once said, “It is difficult to make a man understand something when his salary depends on his not understanding it.” Likewise, it is difficult for a man to follow evidence to its logical conclusion when the conclusion demands he abandon his primary source of earthly comfort: his faith. Throwing up a web of fancy words and pseudoscience, man will do whatever he can, for as long as he can, to protect himself and his way of life. Intelligent Design (ID) supporters will exalt any succor they can muster, even if logical flaws, false assumptions and gaping holes riddle its landscape. Few authors have so clearly and decisively dissected these flaws as Sahotra Sarkar in his recent book, Doubting Darwin? Creationist Designs on Evolution.

Doubting Darwin is at once different from and superior to many of the newly popular books on atheism. It addresses the affront of Intelligent Design with patient clarity, covering thoroughly the various historical, biological, philosophical, and social perspectives of evolutionary theory. Sarkar begins by very succinctly outlining the assumptions and arguments, and providing clear definitions for discussion. ID creationism is defined as the fundamental claim that “complex adaptations could not have been produced by natural selection or any natural processes. Their emergence requires the intervention of an extra-natural designer” (Sarkar 2). The Central Argument of ID creationism is then divided into four parts: (1) Evolutionary theory allows only (i) the inheritance of traits, (ii) the occurrence of blind variation, and (iii) natural selection. (2) According to this argument, evolutionary theory cannot yet explain many natural phenomena, particularly, the emergence of biological complexity. (3) This failure is so great, that it demonstrates the lack of evolutionary theory’s conceptual resources to explain the emergence of complexity. (4) There is good reason to believe that the required conceptual resources must include some mechanism of intelligent design. These four points make up what Sarkar describes as the central argument of ID, and are the focus of his book. He proceeds to dismantle these points, and explain how such fallacies emerge. After decapitating the creationist argument, he provides a wealth of evidence – biological, historical, philosophical, and logical – for natural selection as the mechanism of evolution.

It might be interesting to note that Sarkar always refers to Intelligent Design as, “ID creationism,” clearly drawing no boundary between the two. This is justified by his explanation of their existence in the same metaphysical framework, thus subject to the same logical critiques. Sarkar addresses, importantly, the philosophical heart of the matter: ID creationists do not object to natural selection or evolution per se; they object to the entire naturalist framework in which it exists. Naturalism, Sarkar rightly claims, is the true target of ID creationism. Thus, Doubting Darwin is also an explanation and defense of naturalism, or the claim that “the methods of science and its extensions are enough to guide us through the enterprise of obtaining knowledge of the world” (Sarkar 3).

Sarkar explains that ID creationism, cannot survive so long as scientific thought depends upon naturalism – ID creationists do not want to merely get rid of evolution, they wish to eradicate naturalism altogether in order to allow their theory to survive.

Sarkar quotes Michael Ruse in his explanation of what naturalism is, distinguishing between methodological and metaphysical naturalism: “The methodological naturalist is the person who assumes that the world runs according to unbroken law; that humans can understand the world in terms of this law; and that science involves just such understanding without any reference to extra or supernatural forces like God… Metaphysical naturalism argues that the world is as we see it and that there is nothing more.” The difference, Sarkar argues, should be obvious: unlike the metaphysical naturalist, for the methodological naturalist, “whether or not there are supernatural forces or beings is another matter entirely and simply not addressed by methodological naturalism.” This is a strain of positivism in the philosophical environment itself; if it cannot be observed, it should not be commented upon. This approach was popularized by SJ Gould, and (expectedly, given their relationship) rejected forcefully by Richard Dawkins, in his recent and popular attacks on religion. Sarkar, however, brings much more to light about the philosophical troubles with ID creationism; while Dawkins takes a rather ad hominem approach, Sarkar describes exactly the difference in method between evolutionary science (naturalism) and ID creationism (teleology). He is careful to explain that naturalism is as much about the nature of epistemology as it is a thesis within epistemology.

Naturalism, Sarkar maintains, is as fallible as any other claim in science. Naturalism requires a minimal ontological commitment to the primacy of the physical world, and is accepted essentially because the laws of science, so far as we know, also assume the primacy of physical matter. Similarly, he points out that no philosophical or scientific theory will be a “theory of everything,” thus all correlations and connections in which things exist are contingent – not the embodiment of (logically) necessary links (Sarkar 145). A priori justification is not needed or desired; it is perhaps not even possible. Therefore, naturalism does not include other philosophical frameworks on a priori grounds. However, crucial to the defense of naturalism, the warrant for belief within this framework is derived exclusively from the evidence specific to the proposition – and evidence has been historically and generally effective in yielding reliable knowledge (Sarkar 145). Because ID creationism asserts that there is more than the primacy of material, they fit into a framework of super-naturalism, and so cannot contend with scientific ideas in the world of science.

Sarkar further distinguishes himself from many popular critiques of ID by explaining the history of metaphysical changes caused (or forced) by advances in science. Each generation feels as though its intellectual landscape has always been, or that the metaphysics they assume have always been held (at least by all “reasonable” people). We forgive historical figures for their strange views, but we do not always think about how their views came to be, and how they themselves helped dismantle the assumptions that led to those views. Sarkar provides us with a chance to hope for a permanent shift in metaphysics – a genuine end to ID creationism and super-naturalism. There is a likelihood, Sarkar maintains, that a metaphysical shift nearer to naturalism will be inevitable as evolutionary biology advances. He provides compelling historical parallels, from the initial response to revolutionary theories, to the last-ditch attempts to modify a dying metaphysics. He describes the response, for instance, to Newton’s laws of mechanics: laws such as gravity implied a strange sort of “action at a distance,” which was completely foreign to contemporary metaphysics. The mechanical philosophy of his time necessitated that all interactions were mediated by local contact between impenetrable particles of matter. Leibniz referred to Newtonian mechanics as “occult,” or “absurd.” However, it soon became clear that mechanical philosophy lacked the conceptual resources to explain phenomena such as gravity. There were several attempts to resuscitate the mechanical philosophy by slight changes in its central arguments, but eventually Newtonian mechanics forced a change in metaphysics. This is an obvious parallel to the shift from creationism to ID – an attempt to revive creationist theory through the supposedly more scientific Intelligent Design. The surest sign of a metaphysical shift is this last-ditch effort tweaking of the central argument – an argument that finds itself in an increasingly hostile environment must migrate (from the laboratory into the church), adapt (by modifying the explicitly Christian nature of creationism), or die (as Sarkar suggests has happened, and will happen, to dissonant metaphysics and their resultant thoughts).

Sarkar goes on to describe more empirically successful theories once deemed metaphysically impossible. The success of these theories forced changes in metaphysics – in addition to Newtonian mechanics, Sarkar describes general relativity and quantum mechanics, comparing the response to these theories to the response to natural selection. By putting evolutionary theory in its proper historical context, Sarkar enables the reader to envision a world where the teleology of ID creationists is as foreign as other dead metaphysical paradigms. To Sarkar, this is not a unprecedented or unexpected struggle; it was as inevitable as the change in metaphysical perspective that will someday be complete.

The arguments of two prominent ID creationists feature in Sarkar’s analysis. Michael Behe, a biochemist and author of Darwin’s Black Box, describes “irreducibly complex” biological systems, which he maintains could not have emerged through the processes of natural selection, and so must require a designer. Sarkar provides Behe’s definition of an irreducibly complex system (ICS): “A single system which is composed of several well-matched, interacting parts that contribute to the basic function, and where the removal of any one of the parts causes the system to effectively cease functioning.” Examples of such ICSs include the bacterial flagellum, the blood clotting cascade, and the complement cascade. Indeed, the flagellum is so popular with ID creationists that it features as the chosen emblem (on book covers and blog pages) of Sarkar’s next target: William Dembski. We will return to Sarkar’s critique of Behe’s argument, as well as an extensive look at one of the more serious charges against Behe – an insufficient command of cell and molecular biology. To do so, we will stray from a direct analysis of Sarkar’s criticism, as he could not possibly address the abundance of factual errors present in Behe’s argument in a single book. However, the elaborate dissection of one facet of Behe’s book is necessary to demonstrate the severity of its flaws. In the meantime, we will return to Sarkar’s discussion of William Dembski.

Dembski’s argument for ID begins with what he calls his “explanatory filter.” For Dembski, design is a “logical rather than causal” category, which he attempts to support using plenty of examples of design resulting from conscious human agency. If we ignore the flaw obvious in this logic, we can still be surprised at the flimsy nature of the filter itself. Sarkar breaks the filter down into seven parts: 1) Assume that 3 explanations, Regularity (R), Chance (C), and Design (D), are mutually exclusive and jointly exhaustive explanations of E. 2) Assume that we have a method for determining if E is specified or not. 3) Assume that we should only consider C and D after we reject R, and that we should only consider D if we reject C. 4) If E has a high probability, we should accept R; if not, we should consider C and D. 5) If C does not confer a low probability on E (or if E is not specified), we should accept C, otherwise we should reject C and consider D. 6) Since we have rejected both R and C, we should accept D as the explanation of E. In other words, we never reject D.

According to Dembski’s filter, design is supposed to be inferred if we cannot explain something by regularity or chance (Sarkar 51). The immediate problem is, we are never once invited to consider the probability that D attributes to E – we are never even told what design means, or what a design hypothesis says. Furthermore, Dembski’s filter never addresses the probability that R attributes to E; instead we look only at the probability of E itself. Moreover, the filter provides no threshold filter at which we must reject R, or what probability C must be in order to reject it. The filter never directly addresses the questions at hand.

With Dembski’s filter out of the way, Sarkar turns to one of his even more embarrassing arguments for Intelligent Design. Dembski, himself a mathematician, was very excited by the No Free Lunch (NFL) theorems, proved by David Wolpert and William Macready in 1997. These theorems state that no algorithm (given the set of all possible optimization problems) outperforms any other over the whole set. The first theorem establishes this result for the siuation in which an algorithm only tracks performance during the last generation (as is the case for many genetic/evolutionary algorithms). The second theorem establishes the same result when there is temporal change in the optimization problem and we average over all possible changes (Sarkar 82). In the proofs of these theorems, whether an algorithm is deterministic or stochastic is irrelevant.

The moral of these theorems is beautifully captured by Malcolm Foster’s “toy universe” model: consider a universe in which, on each day, only one of two possibly objects may exist: a sphere (S), or a cube (C). Suppose this universe lasts for exactly two days. If this is the case, the universe has exactly four possible histories: (S, C), (S, S), (C, S), and (C, C). The algorithm used here is supposed to predict what happens on the second day, given knowledge of the first. There are exactly four possible deterministic algorithms: 1) “Same” (same on both days), 2) “Different” (different on both days), 3) “Sphere” (sphere on the second day, regardless of the first), and 4) “Cube” (cube on the second day, regardless of the first). Since each history is equally probable (1/4), each algorithm is equally probable of predicting the second day correctly (1/2). This, when expanded to fit much more general scenarios than this toy universe, is what the NFL theorems mean. Essentially, Forster asserts that we can devise a better algorithm only if we know something empirical about the universe – there is no a priori path to a successful epistemology (Sarkar 84).

These are powerful theorems, and Dembski was certainly impressed, even entitling his book on the subject, No Free Lunch. Unfortunately, as Sarkar illustrates, he is far more impressed with his misinterpretation than their reality. Wolpert himself, who initially proved the NFL theorems, writes in his review that Dembski’s book “is written in jello. There is simply not enough that is firm in his text, not sufficient precision of formulation, to allow one to declare unambiguously ‘right’ or ‘wrong’ when reading through the argument” (Sarkar 86).

But let us ignore, for the moment, what others have said, and examine Dembski’s argument itself. In his own words, Dembski aims to demonstrate the inadequacy of the Darwinian mechanism to demonstrate complexity… By assimilating the Darwinian mechanism to evolutionary algorithms, [Darwinists] have invited a mathematical assessment of the power of their mechanism to generate life’s diversity. Such an assessment, begun with the No Free Lunch theorems of Wolpert and Macready, will be taken to their logical conclusion. The conclusion is that Darwinian mechanisms of any kind, whether in nature or in silico, are in principle incapable of generating specified complexity.

The problem with Dembski’s argument is, it lacks any mathematical or technical relevance at hand; the book, Sarkar claims, is “lacking in technical result, while replete with mathematical formalism well designed to impress the book’s likely readers, who are neither mathematicians nor evolutionary biologists” (85). To use the timeless words of Wolfgang Pauli, “It’s not right. It’s not even wrong.”

To achieve the result he claims to, Dembski would have had to establish that evolution can be viewed formally as an optimization problem (or else, the NFL theorems do not even apply). Since natural selection is very basically not the only factor involved in evolution, there is no optimization problem at hand. To this, Sarkar justifiably dismisses Dembski’s argument as “an exercise in irrelevance” (85).

Sarkar’s book is one of the best critiques of Intelligent Design available; he expertly and forthrightly cuts away at insufficient argument – his most remarkable feat is perhaps the comprehensiveness with which he calmly strips away the superfluous claims to reveal the untenable nature of the ID creationist position. There is little retort Dembski, Behe, or other ID creationist could make to put a dent in Sarkar’s analysis. There is little left to argue with, once Sarkar is through. However, there is one characteristic of ID creationism that Sarkar could not possibly have covered in a single book – the multiplicity of factual errors in – not just evolutionary logic – but in simple cell biology – made by the most prominent biological refutation of evolution by natural selection.

Behe, a biochemist by occupation, produced a biology-heavy work in 1996, claiming that the principles of cell biology did not support accepted theories of evolution. He returns, again and again, to the notion of “irreducible complexity” – although his book is stunningly full of both biological and logical errors and omissions. As Sarkar explains, “Many of [Behe’s] critics – though Johnson and Behe try to deny this – also questioned Behe’s command of the relevant biology. Behe’s recent criticisms of evolutionary theory have also been met with serious – and devastating – response from biologists” (Sarkar 96). Although the fallacies in Michael Behe’s Darwin’s Black Box are vast and easy to spot, there are still many who hail his work as proof of the Bible itself. The multiplicity of errors present in Behe’s work could not be properly responded to without the equivalent of another book. However, we may select one facet of his argument, and examine the biology itself a little more closely, in order to understand the quality of information – and alarmingly bland imagination – being supplied by ID creationists. Sarkar dismantles Behe’s discussions of the bacterial flagellum, the citric acid cycle, and the blood clotting cascade. We will now turn to a study of Behe’s discussion of the human immune system.

In chapter six of his anti-Darwinist crusade, Behe attempts to use immunological arguments to support ID creationism. He launches a three-pronged attack on the unlikely evolution of three complex immunological systems: clonal selection, V(D)J recombination, and the complement cascade. Behe amasses his evidence, carefully building his argument that the human body is filled with biochemical processes that are irreducibly complex, and therefore impossible to evolve. Recall his definition of an ICS: “By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively stop functioning^”(Behe 39). The only way such complicated systems could have arisen, Behe asserts, is through careful and Intelligent Design. Fortunately for Darwin, Behe’s analysis is filled with fatal mistakes and pitiful logic, exhibiting from a lack of background in evolutionary biology, and a tragic deficiency in critical thinking and reasoning skills.

He poses as one providing the reader with expert biological analyses, which are in fact filled with errors, omissions, and outright untruths. His careful misportrayal of the function of antibodies is as almost as convincing as it is inaccurate.

He compares antibodies to toy darts, claiming them to serve only as markers for macrophages, which will then know what to destroy. He goes on to describe the complement system, and the complex set of genes that make up the adaptive immune system’s massive repertoire. Each is dependent on the other, Behe argues; the system is irreducibly complex. Spanning several pages, Behe elaborates on his notion that antibodies serve no purpose other than to mark something for death, and can harm nothing on their own. The most amazing thing about this statement is, it’s just plain wrong. An counterexample coming immediately to mind is hemolin, a protein found in moths. It is almost identical in sequence to antibodies found in higher vertebrates. It binds, generically, to bacteria, causing lysis or precipitation out of the hemolymph (Beck 63). Furthermore, antibodies often serve as catalysts in biochemical reactions. These are widely-known facts that one assumes – for the sake of Behe’s dignity – have been intentionally ignored.

It is also the role of antibodies to neutralize toxins; by binding to the active site of a molecule of poison, the antibody can effectively deactivate it and render it harmless. This is the principle that allows the DPT vaccine to work; the vaccine stimulates the production of the antibodies that can neutralize the relevant toxins (Robison 8). Moreover, antibodies are capable of binding to and disabling viruses, by wedging themselves into the virus’s molecular “hinge” which allows it to infect a cell(Robison 5). Lastly, antibodies are well-known to precipitate targeted bacterial or viral proteins out of solution; if enough antibodies bind to a structure, it will lose its structure, and by extension, its function.

Behe is also not being entirely truthful when he claims that we have no hypotheses on how the enormous repertoire of antibody diversity could have possibly evolved. The V(D)J-C (Variable, Diversity, Joining - Constant) gene schematic is the mechanism for antibody assembly in gnathostomes through primates. In humans, antibody genes are mixed and matched; a little bit of each kind (V, D, and J) DNA is needed to be complete. An antibody gene consists of one V-segment, one D-segment, one J-segment, and one C-segment, each of which are drawn from huge pools of DNA segments. A human antibody can be labeled as V3(D2)J7-C, or V21(D17)J34-C.

But in sharks, the VDJ segments are already assembled; that is, the antibody genes are V5(D5)J5-C, or V21(D21)J21-C. The genes are prearranged in long strings of such assembled genes, called tandem arrays. Our understanding of tandem arrays and the genetic processes that can generate them is well-developed. From these tandem arrays, it is just a short step in evolutionary time to generate the arrangement found in man. Deletions, working in conjunction with secondary expansions caused by tandem duplication, can easily lead to the V(D)J system present in humans (Litman 73). And even if Behe were intelligent enough to argue that this arrangement is useless without the splicing machinery, the presence of a V(D)J system in sharks indisputably disproves Behe’s notion that antibody diversity requires splicing machinery in the first place.

There are many more fascinating clues to possible evolutionary origins to the adaptive immune system which are conveniently absent from Behe’s arguments. The intriguing similarities in molecular structure of antibodies to those involved in immune recognition, and especially those involved in cell-to-cell (non-immune) recognition. Why the resemblances? The recombination machinery which builds antibodies is, interestingly, active in vast regions of the brain; could antibodies have evolved from cell-to-cell recognition molecules? It certainly seems likely.

After reviewing Behe’s lack of immunological understanding, it is easy to conclude that his ideas about Intelligent Design are just as unsound. However, even if his biology was accurate, his central argument is hopelessly flawed, his logic doomed; even if his descriptions of the “irreducibly complex” systems were correct, even if there were no misleading omissions or subtle manipulation of the facts, his pretenses still, inevitably, collapse.

Sarkar reminds us that all of these cases are attempts by Behe to demonstrate the irreducible complexity of the immune system. Behe uses his favorite example, the mousetrap, to illustrate: a mousetrap has a clearly defined function (squashing mice), and is composed of several interacting parts (platform, spring, bait, metal bar for squashing, etc). Behe describes this system as irreducibly complex; if you remove any one of the interacting parts, the mousetrap will no longer be able to perform its function, and no mice will be squashed by that particular mousetrap.

This metaphor, Behe maintains, extends into the biochemical processes that keep us alive. Behe’s claim is that the adaptive immune system is so complex, with each antibody binding perfectly to its antigen, that there is no way it could have evolved. “There are billions of different kinds of antibodies… Could this system have evolved step-by-step? … In a simplified scheme, we are left with three critical ingredients: (1) the membrane-bound form of the antibody; (2) the messenger; and (3) the exported form of the antibody. If any of these parts is missing, the system fails to function” (Behe 124). As Behe rightly states, we gain nothing by replacing a problem with a miracle, so it is best to disregard statistically impossible explanations. In so doing, Behe rejects any possible Darwinian explanation for the evolution of such a complex system. This, however, is a fatal error: a solution does exist.

Ignoring the possible but highly unlikely chance that all genetic mechanisms to produce the immune system arose at the same time, or the idea that the parts of this “irreducibly complex” system evolved separately for other purposes and then joined together by accident to create adaptive vertebrate immunity, there is a very simple, and very Darwinian, explanation.

A system deemed irreducibly complex can be built step-wise, through the gradual addition of parts that are, initially advantageous, but become, because of later changes in the system or environment, essential for proper functioning. Sarkar quotes biologist H. Allen Orr’s response to irreducible complexity:

An irreducibly complex system can be built gradually by adding parts that, while initially just advantageous, become – because of later changes – essential. The logic is very simple. Some part (A) initially does some job (and perhaps not even very well). Another part (B) later gets added because it helps A. This new part isn’t essential, it merely improves things. But later on, A (or something else) may change in such a way that B now becomes indispensable. This process continues as further parts get folded into the system. And at the end of the day, many parts may all be required.

This applies also to the example at hand. Imagine that gene X encodes a protein that performs a certain function. Somehow, gene Y is acquired through mutation, and is selected for because it coincidentally helps with the function of gene X. Gene Y is not, at first, crucial, it simply improves upon what already occurs. Eventually, whether through changes in the organism or environment, gene Y becomes an essential part of the function initially only performed by gene X. This compounds over time, and can easily, over billions of years, become “irreducibly complex.” This step-wise refutation of irreducible complexity originates in 1918, refined later in 1939, with the writings of H. J. Muller, giant in genetics, and winner of the 1946 Nobel Prize in medicine for his work on artificially-induced mutations and genes.

This is also one of the thrusts behind the Red Queen Theory of Evolution, named after Lewis Carroll’s character in Through the Looking Glass. In her world where the landscape was a treadmill, the Red Queen said, “It takes all the running you can do, to keep in the same place.” It suggests that a species may have to evolve quickly just to hold on to its particular niche, which would plausibly explain the emergence of “irreducibly complex” systems.

Behe depends upon his “irreducibly complex” argument to attack biochemical cascades, in particular the blood-clotting and the complement cascades. He states, “Because of the nature of a cascade, a new protein would immediately have to be regulated. From the beginning, a new step in the cascade would require both a proenzyme and also an activating enzyme to switch on the proenzyme at the correct time and place. Since each step necessarily requires several parts, not only is the entire blood-clotting system irreducibly complex, but so is each step in the pathway” (Behe 87). This statement is earlier contradicted by Behe himself, when he describes how the blood-clotting cascade is capable of starting on its own: “it seems there is always a trace of thrombin in the bloodstream. Blood clotting is therefore auto-catalytic, because proteins in the cascade accelerate the production of more of the same proteins” (Behe 83). (Interestingly enough, it is often the hypothesis of an auto-catalytic set that would bolster the idea of our primordial soup origins, as complex systems analysis grows as a field, we uncover more and more data illuminating the evolution of auto-catalytic biophysical systems (Waldrop 87).)

Behe’s skill at manipulation is not to be underestimated; his gentle, confident tone and tactically humble encouragement of the reader to double-check the facts are handy tools to maintain the illusion of his authority. Behe does not hold a degree in evolutionary biology; he is a biochemist by education and practice. Evolutionary biologists have openly questioned his knowledge of basic evolutionary concepts such as soft selection, Muller’s ratchet, or the Fundamental Theorem of Natural Selection (Orr 7). The problem with his reasoning is that it is an “argument from ignorance”(Robison 2); Behe is saying that because we don’t know how the “irreducibly complex” immune system evolved, it didn’t evolve. This painful, pseudo-logic has led Behe to arrive at a conclusion based on a lack of information. It takes a remarkable lack of imagination to believe in irreducibly complex systems; any healthy mind with biological training may conceive of how these systems may have evolved.

Even if Behe had provided us with an interesting and valuable critique to evolution, which closer evaluation reveals is not the case, his reasoning falls apart when he tries to use arguments against evolution as support for intelligent design. This deceptive logic is another of Behe’s traps; it is like trying to argue for the health benefits of Coca-Cola, using evidence that Pepsi is unhealthy. This sort of negative argumentation is utterly useless without an alternative and testable hypothesis.

This trap, along with the deliberate omission of information about the function of antibodies, misleading metaphors, and unfounded assumptions, whether tactical or sincere, are quite suspicious when viewed alongside stunningly false statements, such as the one appearing on page 179: “There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems.” Ignoring papers such as the four published by a single lab (Melendez-Hevia) in 1985, 1988, 1990, and 1994 on the evolution of the pentose phosphate pathway, and a 1993 paper on glycogen biosynthesis, which cite other analyses of Krebs cycle evolution, published in 1981, 1981, 1985, 1987, 1987, and 1992. Furthermore, there were two entire books published on the subject within three years of his writing. Behe also decides to ignore the paper published a month before Darwin’s Black Box, entitled, “The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution” (Mendelez-Hevia 1996).

Behe’s brand of criticism consists of disregarding relevant facts, pretending that data does not exist, and claiming that the lack of the data he intentionally ignores proves his theory. Convinced of his own brilliance, Behe writes, of his own part in the “discovery” of intelligent design, “It is so significant that it must be ranked as one of the greatest achievements in the history of science… rivaling those of Newton and Einstein, Lavoisier and Schrodinger, Pasteur, and Darwin.” The rest of the scientific community can only shake their heads in amazement, wondering how a scientist with a clear creationist agenda, who is very untrained in evolutionary biology, can get such a fancy publication deal on a subject he clearly knows nothing about.

References:

1. Sahotra, Sarkar. Doubting Darwin? Blackwell Publishing. 2007.

2. Behe, Michael. Darwin’s Black Box: The Biochemical Challenge to Evolution. The Free Press. 1996.

3. Litman, Gary. “Sharks and the Origins of Vertebrate Immunity.” Scientific American. November 1996; 60-66.

4. Beck, Gregory. Habicht, Gail. “Immunity and the Invertebrates.” Scientific American. November 1996; 67-71.

5. Melendez-Hevia, Waddell & Cascante. “The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution.” Journal of Molecular Evolution, Sep 1996, 43: 293-303.

6. H. J. Muller, "Reversibility in Evolution Considered from the Standpoint of Genetics". Biological Reviews 14 (1939): 261–80.

7. Orr, Allen H. “Darwin v. Intelligent Design (Again)”. Boston Review. Jan 1997.

8. Robison, Keith. “Darwin's Black Box: Irreducible Complexity or Irreproducible Irreducibility?” Dec 11 1996.

9. Waldrop, Mitchell. Complexity: The Emerging Science at the Edge of Order and Chaos.

Simon & Schuster. 1992.

2008-07-25T05:40:00.000-07:00

There are an incredible number of things happening in the world, and we can read about them on the Internet. For instance, did you know that some Portuguese researchers created paper-based transistors? Yeah, pretty soon, we'll be writing code literally.

(Credit: CENIMAT)

There are also excellent comedians in the field of 12-tone music. Read what might have happened had Schoenberg had made cereal instead of compositions. Alternatively, re-live your favorite moments from the Second Viennese School. Music not your thing? Perhaps that's because it's witchcraft, plaguing our youth and disparaging our culture.

Welcome to the Internet, where insanity reigns.

2008-07-25T05:28:00.001-07:00

Whilst mopping the kitchen at 5:00AM on this lovely evening, I was struck by an idea so brilliant, so perfect -- so obviously the result of divine inspiration -- I simply had to share. It is possible that I've been inhaling too many cleaning products, but I've come across a way to reverse that unfortunate trend of everything looking hotter while you're drinking:

2008-07-24T06:58:00.000-07:00

I'd like to begin the day by asking the reader to take a moment and imagine all the potential abuses of this technology: slydial.com. "I don't understand, I called you in advance to tell you I was sick..." Will we ever trust voicemail again? This is akin to a real version of Google's Custom Time prank, sans the self-restraint even Google's prank squad displayed ("Our researchers have concluded that allowing each person more than ten pre-dated emails per year would cause people to lose faith in the accuracy of time, thus rendering the feature useless"). How long will it be before the upper echelons of the corporate hierarchy get wise to this scheme, this latest friend of the Internet-surfing slacker? How long will it be before we ourselves begin hating it? I'm glad I ignore all my voicemails anyway; now I can ignore them for a reason.

Before I hightail it over to the lab, I'd like to share something I'd buy if I had $25 that I needed to get rid of. They are tablet-versions of the Miracle Fruit (Synsepalum dulcificum) -- flavor-tripping berries. These berries, from West Africa, are supposed to make sour foods sweet, distorting your tongue's sour receptors for 20-30 minutes. Evidently, this results in a bunch of sophisticated people chugging hot sauce, remarking on its saccharine qualities. These tablets, however, are supposed to last up to six hours. Sadly, I have not yet tried these berries, but I just might have to throw an unusual (flavor-tripping) birthday party this year...

2008-07-23T04:21:00.000-07:00

2008-07-18T21:12:00.000-07:00

Louis Untermeyer, ed. (1885–1977).

Modern American Poetry. 1919.

GOD, though this life is but a wraith,
Although we know not what we use,
Although we grope with little faith,
Give me the heart to fight—and lose.

Ever insurgent let me be,	5
Make me more daring than devout;
From sleek contentment keep me free,
And fill me with a buoyant doubt.

Open my eyes to visions girt
With beauty, and with wonder lit—	10
But always let me see the dirt,
And all that spawn and die in it.

Open my ears to music; let
Me thrill with Spring's first flutes and drums—
But never let me dare forget	15
The bitter ballads of the slums.

From compromise and things half done,
Keep me with stern and stubborn pride;
And when at last the fight is won,
God, keep me still unsatisfied.

2008-07-18T08:33:00.000-07:00

Platform Planning Meeting: "This is Democracy"

This Saturday, July 19, 2008, from 2:00-4:00PM, come to an official Barack Obama Platform Planning Meeting in Hyde Park. Details and RSVP through this link. Hope to see you there!

2008-07-15T09:08:00.001-07:00

I has a kitteh!! And she is love.

Stopping by Digg on a Work-Filled Evening (with apologies to Robert Frost):

Whose dreams these are I think I know,
Her boss is on the campus, though;
He will not see me stopping here,
To bask in this screen's pale blue glow.

My little cat must think it queer
To ignore life year after year,
But between downtown and the lake,
All the world exists right here.

Her tranquil mind cannot partake
In hours spent alive-asleep;
Was ARPA's child a mistake?
This online world I cannot break.

The web is vast and talk is cheap,
But I have promises to keep,
And hours to go before I sleep,
And hours to go before I sleep.

2008-07-09T01:12:00.000-07:00

It's been over two years since this blog was born, and over five months since my last post. I should correct that... What shall I talk about? Ah, I know.

Religion. Religion is still as misguided as ever, but atheists have risen spectacularly to the task of proving that "reasonable" folk, too, can be utterly moronic. The point of atheism is to maintain a healthy skepticism, an honest humility, and an acceptance of what one does not and cannot know. The point is not to jump down the throat of those who are as ignorant of their views as you are of yours. A bad atheist is just as dangerous, just as pathetic, and just as stupid as a bad theist.

I'm reminded of a conversation I had just over a year ago with Leon Kass. As I tentatively made clear my transhumanist tendencies, he expressed -- to my surprise -- a form of relief, instead of the hostility I was expecting. He said he'd rather deal with people who were aware of technology's potential -- for good and for bad -- than those who were completely in the dark about the possibilities. This, I think, is a good stance to take. It's better to face an enemy who is educated in his weapon of choice; such people exhibit intelligence, caution, respect, and skill, and are far more worthy of triumph or defeat.

If you're a radical atheist, and believe me, I can be, remember your reasons for it. Remember why you became an atheist in the first place. Most atheists I know (e.g., atheists pre-Dawkins et al) became so independently, often secretly, because their intellectual paths forced them there. I, for one, did not want to stop believing in God. The idea of an all-knowing, all-loving, all-merciful God is a great concept -- our lives are guaranteed to mean something. There is an answer, and a fairly simple one at that. This sort of God may very well exist, although I'm inclined to doubt it. As a little girl, I wanted desperately to be like the God-loving heroines I read about in books; I valued very highly the virtues I read about, including the deep piety exhibited by all my childhood heroes. As an almost laughably spiritual kid, I'd skip classes in elementary school (sorry, Mom and Dad) to climb trees and tell God what was on my mind. I very much believed He was listening, although I never once expected him to talk back. I'd often feel guilty for wasting his time with my silly observations, and foolish laments (often over dead birds or wounded snails), so I instead spent hours praying for people I didn't know, generically hoping that everyone would be okay.

I remember finding a book on prayer in the back of a classroom (Mr. Marshall's room, in case anyone who reads this went to Highland Oaks Elementary in the early 1990's). Skimming it led me to believe that this was a secret method for actually communicating with God -- a hotline to the Deity himself! I remember furtively copying the Lord's Prayer into my own notebook, so that I could try it myself later that day. It became almost an obsession; I'd recite it in my head as I walked to school, to classes, as I fell asleep. It didn't matter that He never answered back; He's God, He's not supposed to respond to humans. We were supposed to accept our place happily, and I did. Knowing that God was real, that he was listening, and that I loved Him -- all of these things brought me almost constant elation.

Anyone who says that even theists aren't happy all the time is not a good theist -- if you truly believe, with every breath, that there is an all-forgiving God who loves you, you will always be happy. Moments of unhappiness are moments of weakness that are quickly corrected, when you remember how the universe truly works. This life is important, sure, but it's nothing compared to the totality of God and His plans. Hardships are merely opportunities for you to smile upwards and thank Him for giving you this test. If you are worried about yourself, ever, as a Christian, you're doing it wrong. Needless to say, elementary school was overwhelmingly the happiest time of my life.

I remember, even further back, my mother telling me as a toddler about Karma. I wildly misinterpreted the concept -- I believed that she was describing a physical law, and that there were actual, physical repercussions based on good and evil deeds. This, combined with being told that God and Christ were real, absolute figures, skewed my thinking for years. Of course, this is why most children brought up in a religious household are themselves religious; kids take everything literally, and parents are incapable of telling a lie. Parents are also incapable of not having an answer.

In fourth grade, I switched elementary schools, and had to do my first ever science project. (If this were a Christian blog, you'd insert ominous music here.) Terrified of looking stupid -- I had never done a science project before, and all the other kids had been doing them since first grade -- I tried to learn everything I could about doing science. I found a book on science projects, interestingly (or perhaps not) also in the back of Mr. Marshall's classroom.The first time I read the scientific method, I didn't understand it. The second time, something was involuntarily electrified in my thoughts -- this was a method of knowing truth! Truth! The most important thing possible! Previously, I had constant faith that truth existed, and that it was knowable -- but this was how to actually make it known! I was as excited as I was when I found the book on prayer -- this was a way to communicate with the absolutes, the only things that mattered. I thanked God almost constantly for months. I kept reading.

Thus began my career in science; a desire to learn the Truth at all costs (and let me tell you, being a nerd all your life has its costs. How many people will have to tell their grandkids that they missed their senior prom for an international science fair?). I kept reading, kept questioning, and kept familiarizing myself with increasingly nuanced scientific thought. For a long time, God and science were not incompatible; they were the same thing. And for a lot of people, this is still the case; they managed to understand in a way that I could not. The threads of positivism are so deeply and beautifully woven into the fabric of scientific thought, that I was at long last forced to reluctantly give up my all-consuming belief in the Christian God. This was not desired; it was merely necessary. I do not regret it.

Real revolutions are not those declared -- they are those resigned to, those forced upon the unwilling; they are the uprooting and often unpleasant changes brought to the door of the disinclined yet prepared. If you became an atheist because you consider yourself a rebel, or because your friends are, or because you think PZ Myers is cool, you are not an atheist. You are a child, or an idiot. You owe a great deal of historical debt to religion, whether you like it or not. You must cast off God with reluctance and acceptance of this debt. You must move forward only because you are compelled to, by your own independent and rational thought. You are not an atheist -- just as you are not a theist -- unless you've earned it.

2008-03-25T19:42:00.000-07:00

Okay, America is an oligarchic nation with an inbred aristocracy; I don't care what anyone says, a common man cannot be President. From BBC World News:

Mr Obama is the son of a white woman from Kansas and a black man from Kenya.

He has recently been identified as a tenth cousin of George W Bush. He was previously identified as a distant cousin of US Vice-President Dick Cheney.

His political lineage includes not just President Bush but also Gerald Ford, Lyndon Johnson, Harry S Truman, Dick Cheney and Winston Churchill.

The connection made with Hollywood star Brad Pitt adds a welcome splash of glamour to his family tree.

But Mrs Clinton's kin has much more of an exotic feel.

Her distant cousins include the singers Madonna, Celine Dion and Alanis Morisette, as well as the beatnik author Jack Kerouac and Prince Charles's wife, Camilla Parker-Bowles.

She and Angelina Jolie are ninth cousins, twice removed. They are both related to one Jean Cusson, who died in St Sulpice, Quebec, in 1718.

If the Hollywood couple, collectively known as "Brangelina", decide on a very extended family gathering, it could provide the perfect opportunity for the two Democratic presidential rivals to get together.

------

Unrelatedly, I think that Hillary's "mistake" about her arrival under sniper fire in Bosnia in 1996 is one of the worst lies in politics. Most lies are campaign promises; everyone expects those.

"I certainly do remember that trip to Bosnia, and as Togo said, there was a saying around the White House that if a place was too small, too poor, or too dangerous, the president couldn't go, so send the First Lady. That’s where we went. I remember landing under sniper fire. There was supposed to be some kind of a greeting ceremony at the airport, but instead we just ran with our heads down to get into the vehicles to get to our base." --HRC, 17 March 2008

"I did make a mistake in talking about it, you know, the last time and recently. So I made a mistake. That happens. It proves I'm human, which, you know, for some people, is a revelation." --HRC, 25 March 2008

But she insulted the careful intelligence and efforts of the US military to keep her safe (the Secret Service would *never* put the First Lady and her daughter in a situation of danger), in order to make herself look more experienced and more willing to face danger.

I mean, come on, how desperate is she getting? There is NOTHING WRONG with admitting that you were the First Lady, and thus everyone was making every effort to keep you safe at every moment. And they succeeded; there was no sniper fire. This is a *compliment* to the troops, Hillary, use it, like you use everything else, you deceitful bitch.

Very rarely am I ever actually offended by lies that politicians make. And I've been unnaturally sympathetic towards Hillary in recent weeks. However, she is insulting those who did everything they could to keep her safe, and that's not okay. I've seen first-hand how hard these guys work, I can't let that insult stand. Repent, Hillary, and give the nomination to Obama (...I can dream).

Plato once said that the rulers of states are the only ones who should have the privilege of lying. And Hillary, you're just not there yet.

2008-03-23T17:04:00.001-07:00

Warning: Potentially offensive speech ahead.

A happy Easter to all, except to Creationists, who are not worth their religion.

They are worth nothing. They are worth less than nothing. They do harm by existing. They are worse than worthless, because they spread such a dilute and empty form of vacant thought, mixed with such dangerously unguided passion. They are not misguided; they are unguided. They are confused.

Somewhere in history, religion branched off and freed itself from the shackles of logic and philosophical rigor, divorcing itself from science, reason, common sense, and eventually all sanity. This rogue strand of religion is now floundering out in the ocean of blind faith, clinging to driftwood and calling it Science. Ideas have no lungs, and so can scream loudly while thus drowning.

There is nothing worth saving about this cult of Creation; their intellect is fit for criminals and liars, their theology is fit for fantasy and fiction writers, their enthusiasm is fit for children and lunatics who get worked up into frenzies about nothing at all. Creationism exists for no purpose, extolling a hollow shell of Christianity while promoting fanaticism for its own sake. There is nothing unselfish about this movement; it is laughable, yet painful, because it robs so many of purpose and of life, this selfish meme. It is a crime to raise a child in such an environment, although such a crime shall not be punishable by any law other than natural selection. Of course, they don't believe in evolution...

I wish instead, to Creationists, the ability to understand, for instance, how lucky they are to have an Easter to celebrate. Or how lucky they are to have a brain cognizant of what Easter is, and what religion is, and what it all should be. If you're going to take the chance and assert that Christianity (or any religion) is true, you'd better be smart, and you'd better be aware of how absurd a thing it really is. Only then can you even pretend to have a right to believe it. Silly Creationists. Your IQ must be this high to believe in Jesus... ::smacks head against wall::

—– Added: —–

Ok, so I realize I’m a bit harsh, and that if I were a Creationist reading this I’d be upset. However, it is probably crucial for their own religion’s survival that they chill out and attempt to be reasonable. Perhaps they mistake their blind and pure faith for nobility and strength. Perhaps they think that God will forgive them for their inattention to intellect or theological rigor. Perhaps they really do think that Faith alone will save them. And that’s just pathetic.

I realize now that I am insulting most Christians in this country, but that’s the country’s fault, not mine. Perhaps this addition, intended to be apologetic, is in fact worse than the original post. Perhaps it will be unintentionally insulting in my attempt to further elaborate on my distaste for unfettered passion, where there should be calmly metered confidence in something you explore and attempt to understand.

See, even if you can’t prove something, you can attempt to display reason. You can exercise your head as well as your heart, and you can make full use of all the faculties your God gave you. While some seem to think laughably drastic claims are praise (see: http://spiritlessons.com/), there is an incredible appearance of insecurity in your God, if you have to lie about Him.

There exists a limit such that the plausibility of a claim approaches zero, as the fantasticalness of that claim approaches infinity. To avoid offending the sensibilities of, well, sensible people, it might be wise to display some sense in your argument.

In science, observations are considered “real” if they can be measured across multiple modalities (vision, hearing, mass spectrometry, etc). The more ways something can be observed, the more “real” it is considered.

God cannot be measured, as far as I know, across any modality (and if you know, please do tell me). But to seek Him through your mental as well as spiritual faculties, is to display an understanding of what reality is, and evidence of an attempt to move in that direction.

I honestly don’t think an atheist would have a problem with a theist who understood and was very passionate about reason and method and the logical objections most atheists have. If a theist understands all of these things, and can clearly demonstrate that, and still chooses to believe in God, well, that’s okay, I have no problem with that. They simply have some experience or understanding I lack. But since they have all the understanding that I do have as an atheist/skeptic, I will give them all the benefits of the doubt.

What skeptics hate about theists, specifically Creationists, is the confidence they have in being correct, while completely lacking an understanding for basic scientific theory (which includes degrees of empiricism and positivism), and seemingly lacking the courage or independence to question their tradition.

It is the kid who does not believe that 2+2=4, no matter how many times you explain it to him. And then, when he tells you he doesn’t believe 2+2=4, he hits you in the face and takes your lunch money, you damned offensive heathen, stop offending my religion. It’s truly offensive that people can use religion as a shield for stupidity. If I were a serious theist, I’d be angry.

If I were a Christian, I’d probably hate Creationists even more than I do now, for making my religion look bad, and for refusing to take the time to understand millennia of intellectual subtleties. Bastards… Giving a generation an excuse to be lazy, to be fanatics, to feel important, to feel safe, to feel saved. To think hard is to suffer doubt, and doubt is the greatest sin of all. So to avoid sin they avoid thought, but to avoid thought is to avoid understanding Christianity in the first place, and thus never capable of understanding or even committing a sin to begin with. I’m not sure how to respond to this, except to replace Creationism with some other sect of Christianity.

Religion is too deep a part of human nature, it will never go away. But I’ll take the better of two evils; I’ll take thought over ignorance any day. So, my Creationist brothers and sisters, I will respect you as Christians if you demonstrate a respect for reason and truth. You may not have to be atheists, but you should not be afraid of skepticism. In being afraid of skepticism, you doubt your God’s ability to overcome tiny atheists like me. Your God will not fail you, if he is as you think. So start here, and we’ll all get along just fine…

2008-02-12T04:31:00.000-08:00

Atrophy, Apathy: Only A's in the Dictionary

It has occurred to me that I cannot remember the last time I wrote down anything longer than an email address or phone number. Like many members of our modern society, everything I do is typed on a keyboard, calculator, or phone. Typing comes naturally as breathing; when I speak aloud, the words are typed on a mental keyboard in my head; I have recently discovered that I can text message faster than I can write with a pen.

The consequences?

Whilst reviewing for a midterm I have in several hours, I wrote less than half a page of notes before I developed an intense cramp in my left forearm. The question is now, how will I be able to sustain my terribly atrophied writing muscles for the duration of a 2-hour exam? Must I fail for lack of exercise? This would likely be the first time in UChicago history that an exam was failed out of physical, rather than mental, insufficiency.

I can do a decent 40 push-ups, several pull-ups, and climb elevator shafts without getting tired. But I failed to work out the muscles that really count. On an exam, that is.

For those of you who, like me, underestimated the importance of the pen and page, I give you this advice: try writing on a regular basis. Write at least a page or two a week -- draft your code on a paper instead of a whiteboard, outline an essay before typing away, bring a notebook instead of a laptop to class, even drawing or doodling for a bit should help.

This will one day be a major issue for the NIH, I suspect. Early-Onset Mogigraphia, Advanced Writer's Cramp Syndrome, they will call it. It will affect millions of Americans, who will be diagnosed only on the off-chance that they use a pen for an extended period of time. Instead of jogging, they will encourage us to unplug for an hour a day, and use the muscles designed for menial tasks.

Do not forget the pen and paper, my friends, even though our grandchildren may know of them only through legend. We might live in this future world, but our professors do not.

2008-01-27T23:04:00.001-08:00

So, an exciting piece of news to share with the world at large: Rhythm & Jews [under construction], my dearest a cappella group, will be singing an arrangement of "Still Alive" this Winter. For anyone who has not experienced the joy and GLaDness of this song, here it is:

2008-01-24T12:30:00.000-08:00

A very awesome video. Lyrics here.

~~~

Random blog related to this one.

2008-01-06T23:05:00.001-08:00

2008-01-02T11:00:00.000-08:00

To be able to study anything, and everything -- music, biology, philosophy, politics, psychology, language, cooking, chemistry, optics, EE, topology, what it feels like to jump out of a plane, you name it -- is the most wonderful feeling in the world. Why would anyone want to specialize? Why would anyone want to limit themselves to the confines of one field? It is true, as my father reminds me, that in branching out you run the risk of becoming the jack of all trades, but master of none. But it is a risk worth taking, because this game is something worth losing.

I'm reminded of the anxious mother of a high school student I once tutored; she was obsessed with getting her 9th grader into Harvard/MIT/Yale/[insert Ivy League school here]. She asked me, "Is he better off taking honors classes and getting A's, or taking AP's and getting B's?" I gave her the answer any honest admissions officer would give: "He's better off taking AP classes and getting A's." Why don't we hold the same standards for ourselves in Life? The college admissions rat race is not worth a thing if it stops once you're in the school of your dreams. It must go on, if anything, it must accelerate. Because we only have a limited time to gain all the knowledge we can ever know. As far as we can tell, we're all going to die, and this is it. How much will you have learned? Richard Feynman summed it up well, I think: "I was born not knowing, and have only a little time to change that here and there."

Many act as though it is not possible to be an expert in many and varying fields. And I say this is exactly the attitude which makes it true. A curiosity for everything will make widespread mastery inevitable, so long as we are not fettered by fear or shame at our own interests. So, to hell with those who say I can't learn that much in a lifetime; there is nothing better than thinking or learning; there is nothing else worth the time. Yes, there are infinite questions about any infinitely small specialization. Yes, it is unrealistic to desire all knowledge in a single lifetime. But there are also laws, generalizations, descriptions of reality, that teach us just as well: these are the Laws of Truth, and they are what we seek.

So have fun, go learn something. Happy New Year...

2007-12-28T15:24:00.000-08:00

Ritual Self-Mummification: The Strange Case of Japan's Auto-Deities

In a small mountainside temple overlooking the Sea of Japan on Japan's west coast, a Buddhist monk slowly chants a mantra and raises the small curtain above a dimly lit altar. The ornate curtain rises to reveal the preserved body of the fourteenth century priest Kochi. Enclosed in a small glass shrine, Kochi is worshipped as a form of living god, or sokushinbutsu—a priest who practiced ritual self-mummification, effectively starving himself to near-death over a period of years, before being entombed underground while still alive.

Sokushinbutsu

Kochi, Japan's oldest extant sokushinbutsu, mummified himself in 1363 at the age of 66. Today, his body is still reasonably well preserved, his fingers crooked talon-like, the darkened flesh drawn tight to his face. Dressed in ceremonial robes he sits curled in the lotus position in his hermetically sealed gilded shrine. The monks of Saishoji Temple, such as our guide, Ato-san, have tended their auto-deity for generations and are reasonably accustomed to visitors—Kochi was immortalized in Bokushi Suzuki's 1841 novel Snow Country Tales and is a minor celebrity to Japanese-culture mavens.

Saishoji Temple is a part of the Shingon sect, an Esoteric Buddhist school that was established in Japan in the ninth century. The sokushinbutsu—there are at least sixteen in Japan—are initiates who succeeded in mummifying themselves through a combination of lengthy ritualistic hermitage and extreme asceticism, as their name denotes: Sokushinbutsu means, literally, attaining Buddhahood while still alive. Though also known generically as miira (apparently a confusion of the foreign borrowings myrrh and mummy), sokushinbutsu is far more accurate as it captures the unique nature and purpose of these Japanese mummies, priests who undertook a lengthy ritualistic death in order to assist their communities and achieve enlightenment.

The mummies have always been something of an open secret in Japan—while there is no attempt to hide their existence, very few people are aware of them. They were first studied scientifically in the 1960s when researchers from Tokyo's Waseda University investigated the centuries-old rumours of indigenous mummies. Upon finding the mummies actually existed, scholars expected to discover signs of post-mortem mummification of the corpses, carried out in a similar fashion to their famous Egyptian, Aztec and Inca counterparts: the first step in any traditional mummification process is always the removal of the internal organs, for these quickly decay and release toxins throughout the body, hastening decomposition. When tests on the sokushinbutsu showed that the internal organs were still present, the researchers realised that these monks had not been preserved by their peers post-mortem. Rather, they had practised ritual self-mummification while still alive.

Self-Mummification for Dummies

The process of becoming a self-made mummy is long, slow and excruciatingly painful, taking from three to ten years. The procedure the monks followed developed over a 900 year period, and though there were different variations, it generally consisted of three equal states, each 1000 days long. For the first 1000 day period the monk adopted a strict diet that consisted of only small amounts of soba (buckwheat) dough and walnuts, hazelnuts, and nutmeg gathered from the surrounding forest. The diet served to reduce the ascetic's body fat dramatically, and as fat decomposes quickly after death, it increased the chances of successful mummification. In the second 1000 day period, the ascetic's diet became even more limited: only bark and the roots of pine tree were ingested. The monk became increasingly emaciated as his body fat reduced to nothingness and his body's water-content similarly declined. Though greatly weakened and increasingly skeletal in appearance, the monk continued to subject himself to long periods of prayer and chanting mantras.

Nearing the end of the second 1000 day period, the monk drank tea made from the juice of the Urushi, or Japanese Varnish tree. A caustic, extremely toxic sap—even its vapour can cause a rash—it is usually used to make a highly durable coating for Chinese and Japanese lacquerware. Drinking the tea caused the monk to vomit, perspire and urinate extensively, further reducing the fluids in his body, as well as causing a large build up of poisons. These poisons, however, played an important part of the mummification process, for they would also kill any organism that tried to consume the priest's flesh after death.

The monk, by then severely debilitated and, one assumes, in tremendous physical pain, was ready for the third and final stage in the process, described in a pamphlet from Kaikoji Temple: “When the priests were near death, stone shelters were constructed three metres underground. The priests were then put into wooden coffins and buried in the shelters with only a bamboo tube for air. In the coffins the priests continued their ascetic practices, sitting in meditation, reciting mantras, and maintaining their strict diet.”

Entombed in his subterranean chamber with only bark and roots to eat and a bell to signal their continued existence to the other monks, the initiate waited for death. “When the sounds of their prayers [or the bell] could no longer be heard, the priests were dug up to confirm their deaths and were then reburied. After three years and three months, they were again dug up, placed in shrines, and worshipped as living gods.” Unlike other mummies, the process finished with death: “No other methods were used in the mummification process”—hence the presence of internal organs that scholars were amazed to discover.

Having successfully attained Buddahood, the mummies were usually taken to a particular temple, where generations of monks such as Ato-san tended for them. In the hilltop Kaikoji Temple in Sakata, Yamagata Prefecture, we found two very well preserved sokushinbutsu, Chukai and Enmyokai, who are enshrined side by side in their quiet suburban temple. The two gods today sit in the same position in which they were lowered into the ground to die, in 1755 and 1822 respectively, and face the three holy mountains of Dewa Sanzan where they undertook their rites.

Dying to Help

It is still something of a mystery why these priests would submit themselves to what must have been extraordinarily drawn out and painful deaths. As followers of Esoteric Buddhism, the monks already led lives of prayer, fasting, asceticism and pilgrimage. A ritual death would therefore be the culmination of a lifelong spiritual quest. A number of the temples stress that the priests did it for the benefit of the local populous. Whether to prevent droughts, or illness among their communities, the monks believed that their deaths would help alleviate the suffering of the populace. It is for this reason a number of the sokushinbutsu have only one eye—as eye disease was widespread, it was not uncommon for devout monks to remove an eye to help prevent the illness striking others.

Robes

The Dainichi temple, deep within Dewa Sanzan—the three holy mountains of Yamagata Prefecture—played a central role in the mummification process. The majority of the monks who mummified themselves did so near this temple on the slopes of Mount Yudono, one of Japan's three most sacred mountains and long regarded by the Shingon sect as a residence of the gods, or kami. On this mountain is a sacred spring that local monks still believe holds special medicinal powers, and drinking its water assumed a special role for the monks seeking to become sokushinbutsu. The spring, tests have revealed, contains dangerously high levels of arsenic. When ingested, arsenic causes organ failure and cell death. It is also, however, a strong preservative—Napoleon Bonaparte's body was found to be extraordinarily well-preserved when it was exhumed 20 years after his death as a result of the high levels of arsenic in his system. Monks who drank from the spring on Mount Yudono would have had a far greater chance of success in their quest to be mummified, and the legendary slopes of the mountain assumed the favoured place for the practice for this reason.

Nevertheless, the mummification process was far from reliable, and often the body simply decomposed during the three year burial. In these cases, the priest had failed to become sokushinbutsu, and was reburied permanently in a ordinary grave. It is uncertain how many monks attempted to obtain living godhood, but literature from the temples makes it clear that the vast majority failed, indicating that hundreds of initiates may have committed ritual suicide over the last 1000 years. The process itself was outlawed in 1909 by the Meiji government, which carried out a sustained national campaign in favour of Shinto, Japan's indigenous religion.

An Obscure Godhood

There are twenty-eight known sokushinbutsu in Japan, achieving godhood over a nine century period between the first in 1081 and last in 1903. The majority of the sixteen still viewable are in temples in northern Honshu, Japan's main island, although not all are sokushinbutsu. There are also cases of more standard mummification, such as that of Yasuhira Fujiwara in Chusonji Temple, whose head had been decapitated by sword blows prior to death. The four auto-deities visited for this article were, however, all sokushinbutsu.

The temples are often small, unassuming affairs that are, unsurprisingly, scattered around the sacred mountains of central Yamagata. Nangakuji temple, the resting place of Tetsuryo-kai, sits quietly in the blandly anonymous suburbs of Tsuruoka. When we asked the monk—who was loading crates of empty beer bottles into his car as we arrived—if we were at the correct temple, he simple opened the door behind us, revealing the mummy. The attractive yet unassuming Kaikokuji temple, which hosts two sokushinbutsu, is located within a veritable maze of suburban Buddhist temples and Shinto shrines in the small city of Sakata.

The mummies were all revealed with a minimum of fuss and are regarded by their wards as a normal feature of the temple, although of the ones we visited, there is usually a small ceremony as the mummy is unveiled. The temples and their unique inhabitants are not well known and—with the exception of the famous Dainichi temple on Mount Yudono—are largely unvisited. None of the mummies are on open display in the main temple, it was only after a specific request to see them that their shrines were revealed. Most Japanese, although they partially understand the title 'sokushinbutsu' (particularly in its written form), are unaware of the existence of these auto-deities—until they are told by foreigners who can't believe what they've stumbled upon, that is. Located far off any tourist trails, the sokushinbutsu enjoy a surprising anonymity in their obscure temples, quietly hiding their extraordinary history in the suburbs and mountains of Japan.

Fate Magazine, May 2007

Some notes on this article:

It has been noted that the use of Buddhist terms and concepts within this article are not used in accordance with more familiar forms of Buddhism. No, they are not. They are, however, used in exactly the way the monks use them to describe their beliefs in their literature and in person, both in English and Japanese. The sects described in the article follow the esoteric teachings of Kukai (774-835) who sought to 'attain enlightenment in this existence' (sokushin jobutsu).

Furthermore, please bear in mind that the boundary between Buddhist and Shinto belief collapses completely at a number of these sites, with Shinto and Buddhist elements frequently evident side by side. This is particularly true of Shugendo, the native Japanese religion that combines Shingon Buddhist, Shinto, and Taoist elements. In Japan, the forceful separation of the these religions in favor of State Shinto only occurred during the Meiji period (1868-1912), when the process described above was outlawed. Again, this results in a form of Buddhist belief and practice that may strike many as strange.

Since writing this article in January, I have discovered from the staff at one of the temples that at least one of the sixteen extant mummies is a fake. His 'corpse' actually decayed long ago, but the monks replaced his flesh and covered it with lacquer to preserve it. This finding does not imply that the other Sokushinbutsu are fake, but it does deepen the mystery somewhat. Clearly, it's best to regard this article as an introduction to a very interesting topic, with further investigation pending.

The pronunciation is: soh-koo-shin-boo-tsu ('tsu' as in 'tsunami'), but said fast.

- Chris Mathews, July 4, 2007 (Minor revisions to original article made on July 11, 2007)

All content copyright 2006-2007, Chris Mathews.

2007-12-09T20:07:00.001-08:00

Lord, make me a channel of thy peace;
That where there is hatred, I may bring love;
That where there is wrong, I may bring the spirit of forgiveness;
That where there is discord, I may bring harmony;
That where there is error, I may bring truth;
That where there is doubt, I may bring faith;
That where there is despair, I may bring hope;
That where there are shadows, I may bring light;
That where there is sadness, I may bring joy.
Lord, grant that I may seek rather to comfort than to be comforted;
To understand, than to be understood;
To love, than to be loved.

I thought this was nice... Happy holidays from the road...

2007-11-29T01:11:00.000-08:00

Stupid creationist ideas
--Joe Meert

I've heard a lot of young earth creationist ideas in my life and so compiling the top 10 most idiotic claims/research by the YEC crowd is not easy. So here they are (in no real particular order)

1. Catastrophic plate tectonics- John Baumgardner, an otherwise decent geodynamicist, has proposed a jelly-like mantle during the flood. In this scenario, continents are zooming around like jet-airplanes while the mantle releases tremendous amounts of heat in a global flood. The story of Noah fails, of course, to mention any of this and also to avoid the obvious buoyancy issues of underwater volcanic eruptions with large gas emissions. Noah, in his floating structure never even noticed any of this! So desperate are the creationists to explain all of geology in a flood framework that they've abandoned all reason.

2. Noah's Ark- It's not so much a claim as it is a blind following of a borrowed myth (from the Sumers) about a man building a boat because his god is pretty pissed off. The obvious problems of 8 people caring for all of the created kinds on the boat (food, water, excrement) are all hidden away in some dark 'feasibility analysis' by evolutionist cum creationist Jan Peczkis (aka John Woodmorappe). Woody claims that each of the 16,000 animals on the ark require only 7.2 seconds to care for (that's shoveling a lot of ---- literally and figuratively) John's wonderful statistical analysis manages to convince the brethren that the median size animal on the ark is a rat in order to solve the space problem. Woodmorappe probably borrowed the statistical analysis from his 1995 evolutionary article in the Journal of Vertebrate Palentology (written under his real name Jan Peczkis). There is so much wrong with this story that the mind boggles that anyone would try to show its feasibility.

3. Baraminology- This half-hearted attempt by creationists to develop a Linnean classification scheme for 'created' (bara) 'kinds' (min) was used to make young earth creation sound more scientific. In reality, this is a way in which they can place humans in a distinct classification in order to make them special (the apobaramins).

4. Vegetarian Carnivores- Yes, Virginia, t-rex was a vegetarian along with all the other meat-eaters! Here's what Mark Looy had to say about the T-rex:

"We call him our 'missionary lizard,' " Looy says. "When people realize the T. rex lived in Eden, it will lead us to a discussion of the gospel. The T. rex once was a vegetarian, too."

The Original "Salad Shooter"?

5. Rapid Radioactive Decay: In order to rescue a young earth something had to be done with radioactive decay. The obvious choice is to make radioactive decay not constant! So, the RATE group has worked hard to show that decay rates are not constant and may have been faster in the past. No one seems to wonder that if decay rates can change to be faster, they may also have been slower in the past. Rapid radioactive decay also presents a heat problem. Interestingly, a creationist by the name of Robert Gentry claims that decay rates are constant and therefore the short half-life of Polonium shows that some rocks were created instantaneously!

6. Wedge Plan: Often dubbed 'creationists trojan horse' or 'creationism lite', Intelligent Design is an attempt by creationists to establish a theocracy in America via scientific sounding publications. The Wedge Document, originally a private communique between the ID groups main politicians was leaked onto the web back in the 1990's. The ID folk have since tried to play down its importance, but the poor handling of this document (and the fact that they wrote it at all) has got to be one of the stupidest things the intelligent design creationists have ever done.

7. Evolution is the root of all evil: This argument has various permutations within the creationist community. Creationist Carl Wieland gives us the 'mild connection' argument in the following quote:

Creationists are often accused of making a false connection between evolution and the various social evils of our modern world.

The charge is that we are claiming evolution causes immoral behaviour, holocausts, and the like. Is this AiG’s stance? Do we think evolution causes such things? Not directly; sin is of course responsible. But evolutionary thought permeating a culture will inevitably lead to a magnification of the effects of sin in one form or another. For one thing, it weakens the shared cultural restraints that arise out of a commonly adhered-to basis for morality.

Invariably, this argument always leads to discussions about Hitler, Stalin or any other megalomaniac. Evolution is always blamed for the evil perpetrated by these individuals. The argument is so nonsensical that I always make the point that when creationists trot out this canard, they have already lost the argument.

8. Evolution leads to Atheism: This one is so silly, but the idea is deeply embedded in the creationist mind. The minute someone begins to discuss evolution in a positive way, the creationist will assume (more often than not) that the evolutionist is an atheist. The plot is all to familiar. The creationists with some knowledge of creation literature will try to argue the problems with evolution and those with no knowledge will simply offer to pray for you and tell you about hell.

2007-11-28T00:19:00.000-08:00

Grape Microwave Plasma:

2007-11-23T20:44:00.001-08:00

Ere Time began, from flaming Chaos hurl'd
Rose the bright spheres, which form the circling world;
Earths from each sun with quick explosions burst,
And second planets issued from the first.
Then, whilst the sea at their coeval birth,
Surge over surge, involv'd the shoreless earth;
Nurs'd by warm sun-beams in primeval caves
Organic Life began beneath the waves.

First HEAT from chemic dissolution springs,
And gives to matter its eccentric wings:
With strong REPULSION parts the exploding mass,
Melts into lymph, or kindles into gas.
ATTRACTION next, as earth or air subsides,
The ponderous atoms from the light divides,
Approaching parts with quick embrace combines,
Swells into spheres, and lengthens into lines.
Last, as fine goads the gluten-threads excite,
Cords grapple cords, and webs with webs unite;
And quick CONTRACTION with ethereal flame
Lights into life the fibre-woven frame. --
Hence without parent by spontaneous birth
Rise the first specks of animated earth;
From Nature's womb the plant or insect swims,
And buds or breathes, with microscopic limbs.

--Erasmus Darwin, The Temple of Nature* (1802) Canto I.IV lines 227-250

ORGANIC LIFE beneath the shoreless waves
Was born and nurs'd in ocean's pearly caves;
First forms minute, unseen by spheric glass,
Move on the mud, or pierce the watery mass;
These, as successive generations bloom,
New powers acquire and larger limbs assume;
Whence countless groups of vegetation spring,
And breathing realms of fin and feet and wing.

--Erasmus Darwin, The Temple of Nature* (1802) Canto I.V lines 295-302

From thus meditating on the great similarity of structures of the warm-blooded animals, and at the same time of the great changes they undergo both before and after their nativity; and by considering in how minute a portion of time many of the changes of animals above described have been produced, would it bee too bold to imagine, that in the great length of time, since the earth began to exist, perhaps millions of ages before the commencement of the history of mankind, would it be too bold to imagine, that all warm-blooded animals have aristen from one living filament, which the Great First Cause endued with animality, with the power of acquiring new parts, attended with new propensities, directed by irritations, sensations, volitions, and association; and thus possessing the faculty of continuing to improve by its own inherent activity, and of delivering down those improvements by generation to its posterity, world without end!

--Erasmus Darwin, Zoomania** (1794)

*Written 57 years before his grandson, Charles, published his Origin of Species.
**Written 65 years before his grandson, Charles, published his Origin of Species.

Was somebody stealing granddaddy's ideas?

It's not stealing if it's family... That's evolution :-)

2007-11-17T22:05:00.001-08:00

This post is in response to blog-trawler Mitchell’s fairly extensive comment on my previous post on AGI, which brings up some excellent points. It’s fantastic to know that others are thinking about this sort of thing. Because this allows me to address points in a more expansive manner, this is not a comment, but a full-blown post. Wow… Let's get started.

____________________________________

Mitchell: “1. We need big new ideas to understand consciousness, but not to achieve AGI. Some patchwork combination of already known algorithms and architectures will be sufficient for the latter.”

What you said is (unfortunately for AI researchers) largely true, because, IMHO, intelligence and consciousness are only incidentally related. The fact that we are self-aware is only a tiny part of the picture. There are many processes considered intelligent of which we are only vaguely aware; for instance, when I run to catch a Frisbee, I do not consciously perform the necessary calculations that allow me to know the exact velocity and direction I need to take to catch it, however, I (usually) catch the Frisbee. I’m fairly sure dogs don’t perform these calculations, either. However, we can catch and throw things with ease, with no explicit awareness of our inherent mathematical ability to do so. (This is likely because mathematics is a man-made abstraction, complicating otherwise simple phenomena, but that’s another story.) It’s significantly easier to build an intelligent system than a conscious one, which is why AGI is a realistic goal for the next 25 years, whereas artificial general consciousness (AGC... I just copyrighted that) is likely not going to be.

Mitchell: “2. The natural sciences, as presently constituted, cannot explain consciousness, because they are reducible to physics, and you cannot even get basic sensory qualities like color out of existing physics, which is conceived only in geometric and algebraic terms.”

Agreed. Well, we’re screwed on this one for now, aren’t we? The existence of metamers, etc., makes this pretty irrefutable.

Mitchell: “3. This can be overcome if the quest for the neural correlates of consciousness is combined with the study of consciousness as it presents itself to the individual. Phenomenology is a guide to ontology - whatever entities and relationships do exist in reality, we know that those which show up in consciousness must be among them. Conversely, physics can be reduced to a mathematics largely independent of ontology - all we need is for some part of the mathematics to relate to observations. Therefore, a phenomenological ontology of conscious states has a unique ability to tell us what physics is really about, by telling us what NCCs, physically described, really are. The relationships between ontology and physical formalism established in the case of NCCs could then, one hopes, be extended to the rest of physics.”

Well, wouldn’t this just solve everything? If I knew the answer to this one, I would be rich, successful, and my robot would be doing lines of coke with my Nobel Prize certificate. The problem with this, obviously, is that no matter what, we’ll probably never know it if we’re right. Unless, if we’re lucky enough, these radical changes and breakthroughs are made.

Mitchell: “4. The key to understanding consciousness (which I take to be an aspect of your concept of sentience) thus turns out to be something which must come, at least in part, from within. I might go further and suggest that the key is to be found in the concept of self. The intuitive pre-scientific experience of the world can be roughly described as an experience of things through the senses and an experience of the self through thought. The scientific experience of the world focuses very much on things, even though it employs thought to make progress. When science attempts ontology, it attempts to explain everything using concepts developed on the thing side of the thing/self dichotomy. But in fact a whole other set of concepts - such as 'sensation' and 'thought'! - can be developed by making the self the object of investigation. The synthesis of physics and ontology will lie in knowing some NCC-like thing, formally described in the sense-originated language of physics, to be the very same "thing" known introspectively as the self.”

To clarify, consciousness is *not* a part of sentience. Several definitions that might be necessary for this type of talk are:

Sentience (sentire, "to feel"): refers to utilization of sensory organs, the ability to feel or perceive subjectively, not necessarily including the faculty of self-awareness

Sapience (sapere, "to know"): usually defined as wisdom since it is the ability of an organism or entity to act with judgment

Self-awareness: is the explicit understanding that one exists. Furthermore, it includes the concept that one exists as an individual, separate from other people, with private thoughts

Intelligence: a property of mind that encompasses many related abilities, such as the capacities to reason, to plan, to solve problems, to think abstractly, to comprehend ideas, to use language, and to learn. There are several ways to define intelligence. In some cases, intelligence may include traits such as: creativity, personality, character, knowledge, or wisdom. However, some psychologists prefer not to include these traits in the definition of intelligence.

Consciousness: a characteristic of the mind generally regarded to comprise qualities such as subjectivity, self-awareness, sentience, sapience, and the ability to perceive the relationship between oneself and one's environment

So despite all the talk of “sentient machines”, consciousness is not a necessary component. To a degree, motion sensors are sentient. However, this is just easy enough to be no fun (unless you’re DARPA). I’m personally a fan of not only sentience and intelligence, but fully sapient, self-aware, *conscious* machines.

Science does indeed focus on “things”; that is the long-established aim of science. While Big Science gets all the headlines now, it will only lay the foundations for AGI (AGC?), once we’ve done all the major steps, like reverse engineer the brain, etc. Luckily, increasing numbers of philosophically-minded rogue cognitive scientists (at least at the Univ of Chicago) are wandering in this direction.

Mitchell: “5. However, it is not likely that this degree of insight is necessary in order to achieve AGI, nor do I think it likely that an entity must actually possess consciousness to have intelligence as presently understood - because intelligence is presently understood in terms of functional competence, the ability to solve problems or achieve goals. Earlier, I distinguished between experience of things and experience of the self, though they are both just aspects of experience as a whole. Similarly, one could talk about intelligence regarding things and intelligence regarding the self - meaning a capacity to get the facts right, solve problems, etc., involving things or self, as the case may be.”

Agreed. AGI is likely to be significantly easier to work on or understand than consciousness, if only for the extreme lack of tools we have to determine whether or not something is self-aware.

Mitchell: “6. In AI it is sometimes argued that self-intelligence is the key to consciousness - the day when Cyc knows that propositions about "Cyc" are about itself, will be the day when Cyc wakes up. I do not agree, and until one has an ontological theory of selfhood, this is actually just mysticism. I can certainly exhibit a toy ontology in which this would not be so: simply suppose that consciousness is always and only monadic (i.e., that the only things which truly have consciousness are elementary in some sense), but that we assemble groups of these elementary things into causal aggregates which have the ability to report correctly on their own properties as an aggregate. Functionally this is self-intelligence, but ontologically it is not.”

Hm. I’d agree at first glance, but I’m uncertain as to how parallel the situations are. If the monadic “things” can report only on the properties of the aggregate, the point stands. However, I don’t think that any AI researcher – well, okay, Minsky doesn’t count – would seriously assert this. If so, well, no wonder we haven’t got intelligent machines running around already – they’re complicating the issue wildly. AGI is not the hardest goal. Consciousness is.

Mitchell: “7. Revisiting proposition 1: we don't need big new ideas to achieve AGI, but we do need big new ideas if we are to understand what we are doing when we do it. We know enough to copy it functionally, but not enough to understand it ontologically. This has to be a dangerous situation, because even the most benevolently programmed AGI will still be capable of making a mess if its ontology is wrong.”

This is indeed the consensus when it comes to AGI/AGC. Is it possible that we will create a conscious machine and not realize it? Entirely. Is it smart to take steps to try and prevent such a discovery from falling through the cracks, or to refute the religious fanatics who will swear that a machine can never be conscious? Absolutely.

The situation will indeed be dangerous; no doubt the first AGI’s we create will be utterly, completely, fantastically insane. God help the poor thing when they first hit the “Run” button. Why? Because we’re bad programmers. However, after much vision and revision, we may well have a genuinely generally intelligent machine. The functional approach is likely to be the most successful, but it is also, unfortunately, the one we are least likely to understand.

What, then, do we do? We will likely need to pour more of our mental resources into understanding such things as consciousness overlap, abstraction theory of intelligence, ontologies of self and unified theories of mind. The biggest obstacle is that we have no concept of what consciousness is, in our own minds or anyone else’s. We can try to think out of the box on this one, but we haven’t even found the box, nor do we know if one exists.

Opinion Statements:

- Programmers will not approach this the right way for at least another generation; the stigma in the hard sciences against such things as psychology, phenomenology, etc, will prevent this from occurring, until people stop caring.

- People are likely to get discouraged and quit; the more we learn about the brain, the further and further away an understanding begins to seem.

- There are most likely “laws” of the mind; we should not underemphasize unified theories of cognition.

- Everyone should read Aristotle. With a grain of salt handy.

- Think about the Fox and the Crow. You know, the fable your mom read to you when you were little. Why are we impressed by the Fox? Modules, prediction, and abstraction theory. It’s as old as time.

____________________________________

I leave you with an encouraging quote, from that fantastic and popular (in 1997) book, Darwin Among the Machines:

“In the game of life and evolution, there are three players at the table: human beings, nature, and machines. I am firmly on the side of nature. But nature, I suspect, is on the side of the machines.”

--George Dyson, Darwin Among the Machines

2007-11-14T23:41:00.000-08:00

So... Artificial Intelligence. An outdated term, perhaps, but a recognizable one nonetheless, and will be used here in its original sense. I tend to prefer artificial general intelligence (AGI), to maintain the distinction between the search for genuine sentience and strong artificial intelligence, and the desire for limited (but unquestionably useful) applications of AI.

Where does artificial intelligence stand today? Surely it has become more of a fanciful term, a sci-fi author's meal ticket, a crazy scientist's late-night obsession. The grand promises of the 1950's have yet to be realized, for the mind is a complicated game.

Sure, there has been progress. In October of this year, the simplest universal Turing machine was proved (by a 20-year-old undergraduate, no less). Government agencies such as DARPA are pouring millions into both general and specific AI, from the Integrated Learner, to DARPA's Grand Challenge. Ray Kurzweil and Ben Goertzel are shouting news of the Singularity from every street corner. Silicon Valley's prematurely-rich are getting bored and doing AI research of their own (see Jeff Hawkins' Redwood Neuroscience Institute). Social networking sites such as Second Life are becoming foster homes for baby AI's. Google is the new Bell Labs. Roboticists and computer scientists are finally beginning to collaborate with neuroscientists and cognitive scientists. Throw developmental biologists and philosophers into the mix, and we've got something serious beginning to cook. Could the age of strong AI be here at last?

The problem with progress in this field, I think, lies not with our ability to create intelligent machines -- not yet. We must first transcend the disciplines we divide our science into; it is almost shameful for a person to admit to being interested in philosophy or psychology... at least to anyone involved in mathematics, computer science, computational biology, or physics. The arrogance with which those in the "hard sciences" assert themselves is not only unseemly, it is dangerously counterproductive. The tension between disciplines is aggravated by this behavior, and the knowledge and wisdom of each is neatly sectioned into membranes as exclusive as the disciplines themselves.

May I be forgiven for all the time I looked down my nose at those in the social sciences or the humanities. May we hubristic scientists somehow prove ourselves worthy of the knowledge possessed by those immersed in the study of the human mind. May we somehow overcome our need for labels, our desperate desire to climb the scientific hierarchy, our need to satisfy ourselves with the knowledge that our work takes the most math or processing power to complete.

May we overcome the desire for the latest fashion in science: interdisciplinary teams of researchers, churning out papers with 20+ authors, treating scientific knowledge like a cheap, trendy accessory. Do take a moment, if you've got one, to read this spectacular article by Sean Eddy, a scientist who refuses to conform to one discipline. Some choicier quotes from the article:

"Progress is driven by new scientific questions, which demand new ways of thinking. You want to go where a question takes you, not where your training left you."

"Molecular biologists even worried about what to call themselves, like we argue over whether we're computational biologists or bioinformaticians. Any revolution needs to find the right slogan to unify under. Francis Crick explained, 'I myself was forced to call myself a molecular biologist because when inquiring clergymen asked me what I did, I got tired of explaining that I was a mixture of crystallographer, biophysicist, biochemist, and geneticist, an explanation which in any case they found too hard to grasp' [4]."

"Perhaps the whole idea of interdisciplinary science is the wrong way to look at what we want to encourage. What we really mean is "antedisciplinary" science—the science that precedes the organization of new disciplines, the Wild West frontier stage that comes before the law arrives. It's apropos that antedisciplinary sounds like "anti-disciplinary." People who gravitate to the unexplored frontiers tend to be self-selected as people who don't like disciplines—or discipline, for that matter.

One can't deny that science is getting more complex, because the sheer amount of knowledge is growing. But the history of science is full of ideas that seemed radical, unfathomable, and interdisciplinary at the time, but that now we teach to undergraduates. Every generation, we somehow compress our knowledge just enough to leave room in our brains for one more generation of progress. This is not going to stop.

It may take big interdisciplinary teams to achieve certain technical goals as they come tantalizingly within view, but someone also needs to synthesize new knowledge and make it useful to individual human minds, so the next generation will have a taller set of giants' shoulders to stand on. Computer science mythologizes the big teams and great computing engines of Bletchley Park cracking the Enigma code as much as we mythologize the Human Genome Project, but computer science rests more on the lasting visions of unique intellectual adventurers like Alan Turing and John von Neumann. Looking around my desk at the work I'm trying to build on, I do see the human genome paper, but even more, I see the work of individual pioneers who left old disciplines and defined new ones—writing with the coherence, clarity, and glorious idiosyncrasy that can only come from a single mind."

Amen, amen...

2007-11-11T04:02:00.000-08:00

The greatest of all things we treasure
Is time spent alone and at leisure;
No joy can supplant it --
No breath gone for granted --
Sweet solitude heals without measure.

~~~

01000010 01100101 01100011 01100001 01110101 01110011 01100101 00100000 01001001 00100000 01101011 01101110 01100101 01110111 00100000 01111001 01101111 01110101 00101100 00100000 01001001 00100000 01101000 01100001 01110110 01100101 00100000 01100010 01100101 01100101 01101110 00100000 01100011 01101000 01100001 01101110 01100111 01100101 01100100 00100000 01100110 01101111 01110010 00100000 01100111 01101111 01101111 01100100 00101110

~~~

And had it been, it would have been,
a most extraordinary day.
That day, that Once, so long ago,
the day that never was.

2007-11-02T09:42:00.000-07:00

Overexpression of the Cytosolic Form of Phosphoenolpyruvate Carboxykinase (GTP) in Skeletal Muscle Repatterns Energy Metabolism in the Mouse

Parvin Hakimi , Jianqi Yang , Gemma Casadesus , Duna Massillon¶, Fatima Tolentino-Silva||**, Colleen K. Nye , Marco E. Cabrera||**, David R. Hagen , Christopher B. Utter , Yacoub Baghdy , David H. Johnson||, David L. Wilson||, John P. Kirwan , Satish C. Kalhan , and Richard W. Hanson 1

From the Departments of Biochemistry, ¶Nutrition, **Pediatrics, Neuroscience, and ||Biomedical Engineering, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106-4935 and the Department of Gastroenterology/Hepatology and Pathobiology, Cleveland Clinic Foundation, Cleveland, Ohio 44195

Transgenic mice, containing a chimeric gene in which the cDNA for phosphoenolpyruvate carboxykinase (GTP) (PEPCK-C) (EC 4.1.1.3 [EC] 2) was linked to the -skeletal actin gene promoter, express PEPCK-C in skeletal muscle (1-3 units/g). Breeding two founder lines together produced mice with an activity of PEPCK-C of 9 units/g of muscle (PEPCK-Cmus mice). These mice were seven times more active in their cages than controls. On a mouse treadmill, PEPCK-Cmus mice ran up to 6 km at a speed of 20 m/min, whereas controls stopped at 0.2 km. PEPCK-Cmus mice had an enhanced exercise capacity, with a VO2max of 156 ± 8.0 ml/kg/min, a maximal respiratory exchange ratio of 0.91 ± 0.03, and a blood lactate concentration of 3.7 ± 1.0 mM after running for 32 min at a 25° grade; the values for control animals were 112 ± 21 ml/kg/min, 0.99 ± 0.08, and 8.1 ± 5.0 mM respectively. The PEPCK-Cmus mice ate 60% more than controls but had half the body weight and 10% the body fat as determined by magnetic resonance imaging. In addition, the number of mitochondria and the content of triglyceride in the skeletal muscle of PEPCK-Cmus mice were greatly increased as compared with controls. PEPCK-Cmus mice had an extended life span relative to control animals; mice up to an age of 2.5 years ran twice as fast as 6-12-month-old control animals. We conclude that overexpression of PEPCK-C repatterns energy metabolism and leads to greater longevity.

Received for publication, July 25, 2007, and in revised form, August 21, 2007.

For details see the article by Hakimi et al., pages 32844–32855.

2007-10-06T17:58:00.001-07:00

THE EMPEROR'S NEW CLOTHES

by Hans Christian Anderson

Once upon a time there lived a vain Emperor whose only worry in life was to dress in elegant clothes. He changed clothes almost every hour and loved to show them off to his people.

Word of the Emperor's refined habits spread over his kingdom and beyond. Two scoundrels who had heard of the Emperor's vanity decided to take advantage of it. They introduced themselves at the gates of the palace with a scheme in mind.

"We are two very good tailors and after many years of research we have invented an extraordinary method to weave a cloth so light and fine that it looks invisible. As a matter of fact it is invisible to anyone who is too stupid and incompetent to appreciate its quality."

The chief of the guards heard the scoundrel's strange story and sent for the court chamberlain. The chamberlain notified the prime minister, who ran to the Emperor and disclosed the incredible news. The Emperor's curiosity got the better of him and he decided to see the two scoundrels.

"Besides being invisible, your Highness, this cloth will be woven in colors and patterns created especially for you." The emperor gave the two men a bag of gold coins in exchange for their promise to begin working on the fabric immediately.

"Just tell us what you need to get started and we'll give it to you." The two scoundrels asked for a loom, silk, gold thread and then pretended to begin working. The Emperor thought he had spent his money quite well: in addition to getting a new extraordinary suit, he would discover which of his subjects were ignorant and incompetent. A few days later, he called the old and wise prime minister, who was considered by everyone as a man with common sense.

"Go and see how the work is proceeding," the Emperor told him, "and come back to let me know."

The prime minister was welcomed by the two scoundrels.

"We're almost finished, but we need a lot more gold thread. Here, Excellency! Admire the colors, feel the softness!" The old man bent over the loom and tried to see the fabric that was not there. He felt cold sweat on his forehead.

"I can't see anything," he thought. "If I see nothing, that means I'm stupid! Or, worse, incompetent!" If the prime minister admitted that he didn't see anything, he would be discharged from his office.

"What a marvelous fabric,” he said then. "I'll certainly tell the Emperor." The two scoundrels rubbed their hands gleefully. They had almost made it. More thread was requested to finish the work.

Finally, the Emperor received the announcement that the two tailors had come to take all the measurements needed to sew his new suit.

"Come in," the Emperor ordered. Even as they bowed, the two scoundrels pretended to be holding large roll of fabric.

"Here it is your Highness, the result of our labour," the scoundrels said. "We have worked night and day but, at last, the most beautiful fabric in the world is ready for you. Look at the colors and feel how fine it is." Of course the Emperor did not see any colors and could not feel any cloth between his fingers. He panicked and felt like fainting. But luckily the throne was right behind him and he sat down. But when he realized that no one could know that he did not see the fabric, he felt better. Nobody could find out he was stupid and incompetent. And the Emperor didn't know that everybody else around him thought and did the very same thing.

The farce continued as the two scoundrels had foreseen it. Once they had taken the measurements, the two began cutting the air with scissors while sewing with their needles an invisible cloth.

"Your Highness, you'll have to take off your clothes to try on your new ones." The two scoundrels draped the new clothes on him and then held up a mirror. The Emperor was embarrassed but since none of his bystanders were, he felt relieved.

"Yes, this is a beautiful suit and it looks very good on me," the Emperor said trying to look comfortable. "You've done a fine job."

"Your Majesty," the prime minister said, "we have a request for you. The people have found out about this extraordinary fabric and they are anxious to see you in your new suit." The Emperor was doubtful showing himself naked to the people, but then he abandoned his fears. After all, no one would know about it except the ignorant and the incompetent.

"All right," he said. "I will grant the people this privilege." He summoned his carriage and the ceremonial parade was formed. A group of dignitaries walked at the very front of the procession and anxiously scrutinized the faces of the people in the street. All the people had gathered in the main square, pushing and shoving to get a better look. An applause welcomed the regal procession. Everyone wanted to know how stupid or incompetent his or her neighbor was but, as the Emperor passed, a strange murmur rose from the crowd.

Everyone said, loud enough for the others to hear: "Look at the Emperor's new clothes. They're beautiful!"

"What a marvellous train!"

"And the colors! The colors of that beautiful fabric! I have never seen anything like it in my life!" They all tried to conceal their disappointment at not being able to see the clothes, and since nobody was willing to admit his own stupidity and incompetence, they all behaved as the two scoundrels had predicted.

A child, however, who had no important job and could only see things as his eyes showed them to him, went up to the carriage.

"The Emperor is naked," he said.

"Fool!" his father reprimanded, running after him. "Don't talk nonsense!" He grabbed his child and took him away. But the boy's remark, which had been heard by the bystanders, was repeated over and over again until everyone cried:

"The boy is right! The Emperor is naked! It's true!"

The Emperor realized that the people were right but could not admit to that. He though it better to continue the procession under the illusion that anyone who couldn't see his clothes was either stupid or incompetent. And he stood stiffly on his carriage, while behind him a page held his imaginary mantle.

The Courtier's Reply

by PZ Myers

I have considered the impudent accusations of Mr Dawkins with exasperation at his lack of serious scholarship. He has apparently not read the detailed discourses of Count Roderigo of Seville on the exquisite and exotic leathers of the Emperor's boots, nor does he give a moment's consideration to Bellini's masterwork, On the Luminescence of the Emperor's Feathered Hat. We have entire schools dedicated to writing learned treatises on the beauty of the Emperor's raiment, and every major newspaper runs a section dedicated to imperial fashion; Dawkins cavalierly dismisses them all. He even laughs at the highly popular and most persuasive arguments of his fellow countryman, Lord D. T. Mawkscribbler, who famously pointed out that the Emperor would not wear common cotton, nor uncomfortable polyester, but must, I say must, wear undergarments of the finest silk.

Dawkins arrogantly ignores all these deep philosophical ponderings to crudely accuse the Emperor of nudity.

Personally, I suspect that perhaps the Emperor might not be fully clothed — how else to explain the apparent sloth of the staff at the palace laundry — but, well, everyone else does seem to go on about his clothes, and this Dawkins fellow is such a rude upstart who lacks the wit of my elegant circumlocutions, that, while unable to deal with the substance of his accusations, I should at least chide him for his very bad form.

Until Dawkins has trained in the shops of Paris and Milan, until he has learned to tell the difference between a ruffled flounce and a puffy pantaloon, we should all pretend he has not spoken out against the Emperor's taste. His training in biology may give him the ability to recognize dangling genitalia when he sees it, but it has not taught him the proper appreciation of Imaginary Fabrics.

2007-09-27T12:30:00.000-07:00

Richard Dawkins

at the University of Chicago

A preeminent scientist -- and the world's most prominent atheist -- asserts the irrationality of belief in God and the grievous harm religion has inflicted on society, from the Crusades to 9/11.

With rigor and wit, Dawkins examines God in all his forms, from the sex-obsessed tyrant of the Old Testament to the more benign (but still illogical) Celestial Watchmaker favored by some Enlightenment thinkers. He eviscerates the major arguments for religion and demonstrates the supreme improbability of a supreme being. He shows how religion fuels war, foments bigotry, and abuses children, buttressing his points with historical and contemporary evidence. The God Delusion makes a compelling case that belief in God is not just wrong but potentially deadly. It also offers exhilarating insight into the advantages of atheism to the individual and society, not the least of which is a clearer, truer appreciation of the universe's wonders than any faith could ever muster.

Time: Thursday, October 4, 2007 6:00 PM
Location: International House, 1414 E 59 St

2007-09-24T10:14:00.001-07:00

From www.uscampaignforburma.org:

Over 200,000 March in Burma

NATIONAL STRIKE BEGINS

Courageous people of Burma, under the leadership of Buddhist monks, began a national strike today. Over 200,000 people, monks, nuns, students, actors, journalists, doctors, housewives, elders, people from all walks of life join in the national strike in Rangoon today and many other cities through out the country.

Please do something if you can. The situation in Burma has reached a boiling point. Yesterday, 200,000 people marched throughout Burma calling for human rights and democracy. The marches were led by Buddhist monks, the most revered people inside Burma. The last time people marched in these numbers the regime gunned down 10,000 peaceful demonstrators. We have received credible news that the regime is ordering some of its soldiers to shave their heads so they can impersonate monks and incite violence, which would be used to justify a crackdown by military troops. Please donate as much as you can today. Donations of $5,000 --- $1,000 -- or $500 are needed: http://www.uscampaignforburma.org/join/joinnow.html

2007-09-19T19:38:00.000-07:00

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taminylserylleucyllysylisoleucylaspartylthreonylleucylisoleucylglutamylalanyl-
glycylalanylaspartylalanylleucylglutamylleucylglycylisoleucylprolylphenylala-
nylserylaspartylprolylleucylalanylaspartylglycylprolylthreonylisoleucylgluta-
minylasparaginylalanylthreonylleucylarginylalanylphenylalanylalanylalanylgly-
cylvalylthreonylprolylalanylglutaminylcysteinylphenylalanylglutamylmethionyl-
leucylalanylleucylisoleucylarginylglutaminyllysylhistidylprolylthreonylisoleu-
cylprolylisoleucylglycylleucylleucylmethionyltyrosylalanylasparaginylleucylva-
lylphenylalanylasparaginyllysylglycylisoleucylaspartylglutamylphenylalanyltyro-
sylalanylglutaminylcysteinylglutamyllysylvalylglycylvalylaspartylserylvalylleu-
cylvalylalanylaspartylvalylprolylvalylglutaminylglutamylserylalanylprolylphe-
nylalanylarginylglutaminylalanylalanylleucylarginylhistidylasparaginylvalylala-
nylprolylisoleucylphenylalanylisoleucylcysteinylprolylprolylaspartylalanylas-
partylaspartylaspartylleucylleucylarginylglutaminylisoleucylalanylseryltyrosyl-
glycylarginylglycyltyrosylthreonyltyrosylleucylleucylserylarginylalanylglycyl-
valylthreonylglycylalanylglutamylasparaginylarginylalanylalanylleucylprolylleu-
cylasparaginylhistidylleucylvalylalanyllysylleucyllysylglutamyltyrosylasparagi-
nylalanylalanylprolylprolylleucylglutaminylglycylphenylalanylglycylisoleucylse-
rylalanylprolylaspartylglutaminylvalyllysylalanylalanylisoleucylaspartylalanyl-
glycylalanylalanylglycylalanylisoleucylserylglycylserylalanylisoleucylvalylly-
sylisoleucylisoleucylglutamylglutaminylhistidylasparaginylisoleucylglutamylpro-
lylglutamyllysylmethionylleucylalanylalanylleucyllysylvalylphenylalanylvalyl-
glutaminylprolylmethionyllysylalanylalanylthreonylarginylserine, n.:
     The chemical name for tryptophan synthetase A protein, a
     1,913-letter enzyme with 267 amino acids.

2007-09-11T19:17:00.000-07:00

Synthetic Biology is just computer scientists screaming at biologists, "Enough already! We'll organize it all..."

While I'm at it, the basic ideas underlying synthetic biology are really quite simple, for those of you who are interested:

Automated (DNA) Construction
Standards of Abstraction

We want to move from an ad-hoc research approach to a scalable engineering framework. If anyone is interested in joining the UChicago research group, and preferably isn't an idiot, let me know...

2007-09-08T19:28:00.000-07:00

Like Borat, But Not As Funny

Full (not-that-poorly translated) transcript of latest OBL video:

All praise is due to Allah, who built the heavens and earth in justice, and created man as a favor and grace from Him. And from His ways is that the days rotate between the people, and from His Law is retaliation in kind: an eye for an eye, a tooth far a tooth and the killer is killed. And all praise is due to Allah, who awakened His slaves’ desire for the Garden, and all of them will enter it except those who refuse. And whoever obeys Him alone in all of his affairs will enter the Garden, and whoever disobeys Him will have refused.

As for what comes after: Peace be upon he who follows the Guidance. People of America: I shall be speaking to you on important topics which concern you, so lend me your ears. I begin by discussing the war which is between us and some of its repercussions for us and you.

To preface, I say: despite America being the greatest economic power and possessing the most powerful and up-to-date military arsenal as well; and despite it spending on this war and its army more than the entire world spends on its armies; and despite it being the being the major state influencing the policies of the world, as if it has a monopoly on the unjust right of veto; despite all of this, 19 young men were able - by the grace of Allah, the Most High - to change the direction of its compass. And in fact, the subject of the Mujahideen has become an inseparable part of the speech of your leader, and the effects and signs of that are not hidden.

Since the 11th, many of America’s policies have come under the influence of the Mujahideen, and that is by the grace of Allah, the Most High. And as a result, the people discovered the truth about it, its reputation worsened, its prestige was broken globally and it was bled dry economically, even if our interests overlap with the interests of the major corporations and also with those of the neoconservatives, despite the differing intentions.

And for your information media, during the first years of the war, lost its credibility and manifested itself as a tool of the colonialist empires, and its condition has often been worse than the condition of the media of the dictatorial regimes which march in the caravan of the single leader.

Then Bush talks about his working with al-Maliki and his government to spread freedom in Iraq but he in fact is working with the leaders of one sect against another sect, in the belief that this will quickly decide the war in his favor.

And thus, what is called the civil war came into being and matters worsened at his hands before getting out of his control and him becoming like the one who plows and sows the sea: he harvests nothing but failure.

So these are some of the results of the freedom about whose spreading he is talking to you. And then the backtracking of Bush on his insistence on not giving the United Nations expanded jurisdiction in Iraq is an implicit admission of his loss and defeat there.

And among the most important items contained in Bush’s speeches since the events of the 11th is that the Americans have no option but to continue the war. This tone is in fact an echoing of the words of neoconservatives like Cheney, Rumsfeld and Richard Pearle, the latter having said previously that the Americans have no choice in front of them other than to continue the war or face a holocaust.

I say, refuting this unjust statement, that the morality and culture of the holocaust is your culture, not our culture. In fact, burning living beings is forbidden in our religion, even if they be small like the ant, so what of man?! The holocaust of the Jews was carried out by your brethren in the middle of Europe; but had it been closer to our countries, most of the Jews would have been saved by taking, refuge with us. And my proof for that is in what your brothers, the Spanish, did when they set up the horrible courts of the Inquisition to try Muslims and Jews, when the Jews only found safe shelter by taking refuge in our countries. And that is why the Jewish community in Morocco today is one of the largest communities in the world. They are alive with us and we have not incinerated them, but we are a people who don’t sleep under oppression and reject humiliation and disgrace, and we take revenge on the people of tyranny and aggression, and the blood of the Muslims will not be spilled with impunity, and the morrow is nigh for he who awaits.

Also, your Christian brothers have been living among us for 14 centuries: in Egypt alone, there are millions of Christians whom we have not incinerated and shall not incinerate. But the fact is, there is a continuing and biased campaign being waged against us for a long time now by your politicians and many of your writers by way of your media, especially Hollywood, for the purpose of misrepresenting Islam and its adherents to drive you away from the true religion. The genocide of people and their holocausts took place at your hands: only a few specimens of Red Indians were spared, and just a few days ago, the Japanese observed the 62nd anniversary of the annihilation of Hiroshima and Nagasaki by your nuclear weapons.

And among the things which catch the eye of the one who considers the repercussions of your unjust war against Iraq is the failure of your democratic system, despite it raising of the slogans of justice, liberty, equality and humanitarianism. It has not only failed to achieve these things, it has actually destroyed these and other concepts with its weapons - especially in Iraq and Afghanistan - in a brazen fashion, to replace them with fear, destruction, killing, hunger, illness, displacement and more than a million orphans in Baghdad alone, not to mention hundreds of thousands of widows. Americans statistics speak of the killing of more than 650,000 of the people of Iraq as a result of the war and its repercussions.

People of America: the world is following your news in regards to your invasion of Iraq, for people have recently come to know that, after several years of the tragedies of this war, the vast majority. of you want it stopped. Thus, you elected the Democratic Party for this purpose, but the Democrats haven’t made a move worth mentioning. On the contrary, they continue to agree to the spending of tens of billions to continue the killing and war there, which has led to the vast majority of you being afflicted with disappointment.

And here is the gist of the matter, so one should pause, think and reflect: why have the Democrats failed to stop this war, despite them being the majority?

I will come back to reply to this question after raising another question, which is:

Why are the leaders of the White House keen to start wars and wage them around the world, and make use of every possible opportunity through which they can reach this purpose, occasionally even creating justifications based on deception and blatant lies, as you saw Iraq?

In the Vietnam War, the leaders of the White House claimed at the time that it was a necessary and crucial war, and during it, Rumsfeld and his aides murdered two million villagers, And when Kennedy took over the presidency and deviated from the general line of policy drawn up for the White House and wanted to stop this unjust war, that angered the owners of the major corporations who were benefiting from its continuation.

And so Kennedy was killed, and al-Qaida wasn’t present at that time, but rather, those, corporations were tie primary beneficiary from his killing. And the war continued after that for approximately one decade, but after it became clear to you that it was an unjust and unnecessary war, you made one of your greatest mistakes, In that you neither brought to account nor punished those who waged this war, not even the most violent of its murderers, Rumsfeld. And even more incredible than that is that Bush picked him as secretary of defense in his first term after picking Cheney as his vice-president, Powell as secretary of state and Armitage as Powell’s deputy, despite their horrific and blood history of murdering humans. So that was clear signal that his administration - the administration of the generals didn’t have as its main concern the serving of humanity, but rather, was Interested in bringing about new massacres. Yet in spite of that, you permitted Bush to complete his first term, and stranger still, chose him for a second term, which gave him a clear mandate from you - with your full knowledge and consent - to continue to murder our people in Iraq and Afghanistan.

Then you claim to be innocent! This innocence of yours is like my innocence of the blood of your sons on the 11th - were I to claim such a thing. But it is impossible for me to humor any of you in the arrogance and indifference you show for the lives of humans outside America, or for me to humor your leaders in their lying, as the entire world knows they have the lion’s share of that. These morals aren’t our morals. What I want to emphasize here is that not taking past wars criminals to account led to them repeating that clime of killing humanity without right and waging this unjust war in Mesopotamia, and as a result, here are the oppressed ones today continuing to take their right from you.

This war was entirely unnecessary, as testified to by your own reports. And among the most capable of those from your own side who speak to you on this topic and on the manufacturing of public opinion is Noam Chomsky, who spoke sober words of advice prior to the war, but the leader of Texas doesn’t like those who give advice. The entire world came out in unprecedented demonstrations to warn against waging the war and describe its true nature in eloquent terms like "no to spilling red blood for black oil," yet he paid them no heed. It is time for humankind to know that talk of the rights of man and freedom are lies produced by the White House and its allies in Europe to deceive humans, take control of their destinies and subjugate them,

So in answer to the question about the causes of the Democrats failure to stop the war, I say: they are the same reasons which led to the failure of former president Kennedy to stop the Vietnam war. Those with real power and influence are those with the most capital. And since the democratic system permits major corporations to back candidates, be they presidential or congressional, there shouldn’t be any cause for astonishment - and there isn’t any - in the Democrats’ failure to stop the war. And you’re the ones who have the saying which goes, "Money talks." And I tell you: after the failure of your representatives in the Democratic Party to implement your desire to stop the war, you can still carry anti-war placards and spread out in the streets of major cities, then go back to your homes, but that will be of no use and will lead to the prolonging of the war.

However, there are two solutions for stopping it. The first is from our side, and it is to continue to escalate the killing and fighting against you. This is our duty, and our brothers are carrying it out, and I ask Allah to grant them resolve and victory. And the second solution is from your side, it has now become clear to you and the entire world the impotence of the democratic system and how it plays with the interests of the peoples and their blood by sacrificing soldiers and populations to achieve the interests of the major corporations.

And with that, it has become clear to all that they are the real tyrannical terrorists. In fact, the life of all of mankind is in danger because of the global warming resulting to a large degree from the emissions of the factories of the major corporations, yet despite that, the representative of these corporations in the White House insists on not observing the Kyoto accord, with the knowledge that the statistic speaks of the death and displacement of the millions of human beings because of that, especially in Africa. This greatest of plagues and most dangerous of threats to the lives of humans is taking place in an accelerating fashion as the world is being dominated by the democratic system, which confirms its massive failure to protect humans and their interests from the greed and avarice of the major corporations and their representatives.

And despite this brazen attack on the people, the leaders of the West - especially Bush, Blair, Sarkozy and Brown - still talk about freedom and human rights with a flagrant disregard for the intellects of human beings. So is there a form of terrorism stronger, clearer and more dangerous than. tills? This is why I tell you: as you liberated yourselves before from the slavery of monks, kings, and feudalism, you should liberate yourselves from the deception, shackles and attrition of the capitalist system.

If you were to ponder it well, you would find that in the end, it is a system harsher and fiercer than your systems in the Middle Ages, The capitalist system seeks to turn the entire world into a fiefdom of the major corporations under the label of "globalization" in order to protect democracy.

And Iraq and Afghanistan and their tragedies; and the reeling of many of you under the burden of interest-related debts, insane taxes and real estate mortgages; global warming and its woes; and the abject poverty and tragic hunger in Africa: all of this is but one side of the grim face of this global system.

So it is imperative that you free yourselves from all of that and search for an alternative, upright methodology. in which it is not the business of any class of humanity to lay down its own laws to its own advantage at the expense of the other classes as is the case with you, since the essence of man- made positive laws is that they serve the interests of those with the capital and thus make the rich richer and the poor poorer.

The infallible methodology is the methodology of Allah, the Most High, who created the heavens and earth and created the Creation and is the Most Kind and All-informed and the Knower of the souls of His slaves and the methodology that best suits them.

You believe with absolute certainty that you believe in. Allah, and you are full of conviction of this belief, so much so that you have written this belief of yours on your dollar.

But the truth is that you are mistake in this belief of yours. The impartial judge knows that belief in Allah requires straightness in the following of His methodology, and accordingly, total obedience must be to the orders and prohibitions of Allah Alone in all aspects of life.

So how about you when you associate others with Him in your beliefs and separate state from religion, then claim that you are believers?!

What you have done is clear loss and manifest polytheism, And I will give you a parable of polytheism, as parables summarize and clarify speech.

I tell you: its parable is the parable of a man who owns a shop and hires a worker and tells him, "Sell and give me the money," but he makes sales and give the money to someone other than the owner. So who of you would approve of that?

You believe that Allah is your Lord and your Creator and the Creator of this earth and that it is His property, then you work on His earth and property without His orders and without obeying Him, and you legislate in contradiction to His Law and methodology.

This work of yours is the greatest form of polytheism and is rebellion against obedience to Allah with which the believer becomes an unbeliever, even if he obeys Allah in some of His other orders. Allah, the Most High, sent down His orders in His Sacred Books like the Torah and Evangel and sent with them the Messengers (Allah’s prayers and peace be upon them) as bearers of good news to the people.

And everyone who believes in them and complies with them is a believer from the people of Garden. Then when the men of knowledge altered the words of Allah the Most High, and sold them for a paltry price, as the rabbis did with the Torah and the monks with the Evangel, Allah sent down His final Book, the magnificent Quran, and safeguarded it from being added to or subtracted from by the hands of men, and in it is a complete methodology for the lives of all people.

And our holding firm to this magnificent Book is the secret of our strength and winning of the war against you despite the fewness of our numbers and materiel.

And if you would like to get to know some of the reasons for your losing of your war against us, then read the book of Michael Scheuer in this regard.

Don’t be turned away from Islam by the terrible situation of the Muslims today, for our rulers in general abandoned Islam many decades ago, but our forefathers were the leaders and pioneers of the world for many centuries, when they held firmly to Islam.

And before concluding, I tell you: there has been an increase in the thinkers who study events and happenings, and on the basis of their study, they have declared the approach of the collapse of the American Empire.

Among them is the European thinker who anticipated the fall of the Soviet Union, which indeed fell. And it would benefit you to read what he wrote about what conies after the empire in regard to the United States of America. I also want to brine your attention that among the greatest reasons for the collapse of the Soviet Union Was their being afflicted with their leader. Brezhnev, who was overtaken by pride and arrogance and refused to look at the facts on the ground. From the first year of the Afghanistan invasion, reports indicated that the Russians were losing the war, but he refused to acknowledge this, lest it go down in his personal history as a defeat, even though refusal to acknowledge defeat not only doesn’t do anything to change the facts for thinking people, but also exacerbates the problem and increases the losses. And how similar is your position today to their position approximately two decades ago. The mistakes of Brezhnev are being repeated by Bush, who - when asked about the date of his withdrawing of forces from Iraq - said in effect that the withdrawal will not be during his reign, but rather, during the reign of the one who succeeds him. And the significance of these words is not hidden.

And here I say: it would benefit you to listen to the poignant messages of your soldiers in Iraq, who are paying - with their blood, nerves and scattered limbs - the price far these sorts of irresponsible statements. Among them is the eloquent message of Joshua which he sent by way of the media, in which he wipes the tears from his eyes and describes American politicians in harsh terms and invites them to join him there for a few days. Perhaps his message will find-in you an attentive ear so you can rescue him and more than 150,000 of your sons there who are tasting the two bitterest things:

If they leave their barracks, the mines devour them, and if they refuse to leave, rulings are passed against them. Thus, the only options left in front of them are to commit suicide or cry, both of which are from the severest of afflictions. So is there anything more men can do after crying and killing themselves to make you respond to them? They are doing that out of the severity of the humiliation, fear and terror which they are suffering. It is severer than what the slaves used to suffer at your hands centuries ago, and it is as if some of them have gone from one slavery to another slavery more severe and harmful, even if it be in the fancy dress of the Defense Department’s financial enticements.

So do you feel the greatness of their sufferings?

To conclude, I invite you to embrace Islam, for the greatest mistake one can make in this world and one which is uncorrectable is to die while not surrendering to Allah, the Most High, in all aspects of one’s life - ie., to die outside of Islam. And. Islam means gain for you in this first life and the next, final life. The true religion is a mercy For people in their lives, filling their hearts with serenity and calm.

There is a message for you in the Mujahideen; the entire world is in pursuit of them, yet their hearts, by the grace of Allah, are satisfied and tranquil. The true religion also puts peoples’ lives in order with its laws; protects their needs and interests; refines their morals; protects them from evils and guarantees for them entrance into Paradise in the hereafter through their obedience to Allah and sincere worship of Him Alone.

And it will also achieve your desire to stop the war as a consequence, because as soon as the warmongering owners of the major corporations realize that you have lost confidence in your democratic system and begun to search for an alternative, and that this alternative is Islam, they will rue after you to please you and achieve what you want to steer you away from Islam. So your true compliance with Islam will deprive them of the opportunity to defraud the peoples and take. their money under numerous pretexts, like arms deals and so on.

There are no taxes in Islam, but rather there is a limited Zakaat [alms] totaling only 2.5%. So beware of the deception of those with the capital. And with your earnest reading about Islam from its pristine sources, you will arrive at an important truth, which is that the religion of all of the Prophets (peace and blessings of Allah be upon them) is one, and that its essence is submission to the osiers of Allah Alone in all aspects of life, even if their Shari’ahs [Laws] differ.

And did you know that the name of the Prophet of Allah Jesus and his mother (peace and blessings of Allah be on them both) are mentioned in the. Noble Quran dozens of times, and that in the Quran there is a chapter whose name is "Maryam," i.e. Mary, daughter of Imran and mother of Jesus (peace and blessings of Allah be upon them both)? It tells the story of her becoming pregnant with the Prophet of Allah Jesus (peace and blessings of Allah be upon them both), and in its confirmation of her chastity and purity, in contrast to the fabrications of the Jews against her. Whoever wishes to find that out for himself must listen to the verse of this magnificent chapter: one of the just kings of the Christians - the Negus - listened to some of its verses and his eyes welled up with tears and he said something which should be reflected on for a long time by those sincere in their search for the truth.

He said, "verily, this and what Jesus brought come from one lantern": i.e., that the magnificent Quran and the Evangel are both from Allah, the Most High; and every just and intelligent one of you who reflects on the Quran will definitely arrive at this truth. It also must be noted that Allah has preserved the Quran from the alterations of men. And reading in order to become acquainted with Islam only requires a little effort, and those of you who are guided will profit greatly. And peace be upon one who follows the Guidance.

2007-09-04T09:26:00.000-07:00

This week is the week of the long-awaited SENS conference; Aubrey de Grey's Strategies for Engineered Negligible Senescence conference takes place from September 6-10.

This week also marks the release date of Aubrey's new book, "Ending Aging":

From Aubrey's website, www.sens.org:

SENS is a detailed plan for curing human aging. SENS is an engineering project, recognising that aging is a medical condition and that medicine is a branch of engineering. Aging is a set of progressive changes in body composition, at the molecular and cellular level, which are side-effects of essential metabolic processes. Many of these changes are eventually bad for us -- they are an accumulation of damage, which becomes pathogenic above a certain threshold of abundance.

The traditional gerontological approach to life extension is to try to slow down this accumulation of damage. This is a misguided strategy, firstly because it requires us to improve biological processes that we do not adequately understand, and secondly because it can even in principle only retard aging rather than reverse it. An even more short-termist alternative is the geriatric approach, which is to try to stave off pathology in the face of accumulating damage; this is a losing battle because the continuing accumulation of damage makes pathology more and more inescapable.

Instead, the engineering (SENS) strategy is not to interfere with metabolism per se, but to repair or obviate the accumulating damage and thereby indefinitely postpone the age at which it reaches pathogenic levels. This is practical because it avoids both of the problems with the other approaches: it sidesteps our ignorance of metabolism (because it does not attempt to interfere with metabolic processes and their production of side-effects) but also it pre-empts the chaos of pathology (because it repairs the precursors of pathology, rather than addressing the pathology head-on).

2007-09-02T10:03:00.001-07:00

~~~

Taoism
Shit happens.
Buddhism
If shit happens, it's not really shit.
Islam
If shit happens, it's the will of Allah.
Protestantism
Shit happens because you don't work hard enough.
Judaism
Why does this shit always happen to us?
Hinduism
This shit happened before.
Catholicism
Shit happens because you're bad.
Hare Krishna
Shit happens rama rama.
T.V. Evangelism
Send more shit.
Atheism
No shit.
Jehova's Witness
Knock knock, shit happens.
Hedonism
There's nothing like a good shit happening.
Christian Science
Shit happens in your mind.
Agnosticism
Maybe shit happens, maybe it doesn't.
Rastafarianism
Let's smoke this shit.
Existentialism
What is shit anyway?
Stoicism
This shit doesn't bother me.

2007-08-29T10:02:00.001-07:00

I need castles again, castles! Great stone towers, sheets of snow, driving wind, painful cold, drafty lecture halls, dark basements, old libraries, fireplaces, dusty books, winding stairwells, mugs of coffee, steaming soups, used book stores, thick carpets, high ceilings, stone gargoyles, hard work, long hours, and the sense of power and mystery that surrounds the place I most rightly call home. I miss the University of Chicago; I wish I never had to leave.

"Lying in bed would be an altogether perfect and supreme experience if only one had a colored pencil long enough to draw on the ceiling."
--GK Chesterton

2007-08-28T15:41:00.000-07:00

"Biology is a technology for processing information, materials, and energy. As a technology platform, biological systems provide access to artifacts and processes across a range of scales (e.g., the ribosome is a programmable nanoassembler, a bamboo shoot can grow 12” a day). Biology also forms the basis for human welfare (e.g., modest amounts of memory and logic, implemented as genetically encoded systems, would directly impact biological research and medicine). However, our ability to deploy biology as a technology and to interact internationally with the living world is now limited; the charge to our study was to begin to specify enabling technology that, if developed, would provide a general foundation for the engineering of biology and make routine the creation of synthetic biological systems that behave as predicted.”
--Drew Endy, 2003

2007-08-25T03:18:00.001-07:00

:-(

2007-08-08T00:47:00.000-07:00

What do I want most?

01110000 01101111 01110111 01100101 01110010

2007-07-28T16:41:00.000-07:00

What an interesting week. Attending the TransVision 07 conference was certainly a fantastic experience. There is a lot to say about it, but for the moment I'd like to comment on the state of Artificial Intelligence, and the fact that I disagree with many experts in the field.

Marvin Minsky, who, incidentally, is one of the most hilarious wise-asses I've ever met, said I have "physics envy", because I think that the key to AI is a simple but powerful theoretical basis to consciousness. Sort of a variant on Newton's Laws of Mechanics, or Maxwell's Laws of Electromagnetism. The "Laws of the Mind", so to speak. Minsky feels that there are a lot of complex mechanisms at work, and that we just need to get building them. This may be true, but I can't help but feel that the theoretical basis for true strong AI is lacking, and that the focus must change before we can truly succeed.

I would also like to comment that I think it is most likely that a woman will be the one to create true strong AI. We are, after all, the Mothers of our race. The first AI will be a virgin birth, and will change mankind forever, for better or for worse. An artificial Anti-Christ... How's that to piss off our religious brethren? ;-)

Cheers!

2007-07-18T00:25:00.000-07:00

For some, studying the mind and all its glory brings them to heights unparalleled. The altitude at which you fly when you overlook the intelligence and very reality of man is otherwise unattainable. To fathom intelligence, and indeed, to reproduce it, has been the goal of our species since its inception. We have succeeded in the blind recreation of intelligence with every generation, but we still fail to explain how -- or why -- the intelligence itself exists. There is only one way to get to the top of this, the highest mountain on which we can stand. These theories, these glimpses of consciousness, have ensnared the greatest minds ever to walk the earth. They are incredible, wonderful, and inspiring. Pondering the concepts involved certainly does lead to the greatest highs the mind can experience. But what if you're afraid of heights?

How do people continually deal with the existential vertigo inherent to studying the mind? Are preconceptions that successful in their salvation? How can people stand on the edge for hours, days, weeks at a time, looking into the abyss, hoping that -- for a moment -- the abyss will, indeed, stare back. For me, the most frightening and overwhelming moments are those spent staring into the nebulous concepts of consciousness, the ever unreachable comprehension of comprehension itself. The incredible distance between myself and this Invisible Hand, this Theory of Mind, is at once unavoidable and insurmountable. This is a battle that must be fought, although it will most certainly be lost. Perhaps it will be my downfall, but I maintain that it is a battle worth losing...

~~~

On an entirely different note, I'd like to start nominating the best lines from Harry Potter and the Deathly Hallows, starting with this one:

“Ooh, you look much tastier than Crabbe or Goyle, Harry,” said Hermione, before catching sight of Ron’s raised eyebrows and blushing slightly. –HP 7, Pg 50

**Note: I do not support or condone copyright infringement in any form, and am including this quote as a hideous example of terrible people who would actually do something so horrible as photograph and upload the entire 7th Harry Potter book.

As a further demonstration of my commitment to protecting the rights of Bloomsbury Publishers, I would like to remark upon how disgusting it is that I received the complete 7th Harry Potter book in jpg format. Email me for the link...

2007-07-13T23:19:00.003-07:00

It's 11:30 on a Friday night, and I'm still at work... why??

Happy Friday the Thirteenth...

2007-07-13T16:02:00.001-07:00

2007-07-11T19:18:00.001-07:00

2007-07-11T09:24:00.000-07:00

Life's Bigger Questions

To PhD or not to PhD...
That is the question.
Whether tis saner in the mind
To suffer the slights and putdowns
Of outrageous faculty...
Or to take data despite advisor grumbles,
And by graduating, end them?
To graduate: to sleep, once more,
And by a PhD to say
We end the back-ache
And thousand financial debts that we are heir to.
Tis a commencement devoutly to be wish'd.
To graduate, to sleep...
To nap: perchance to dream...
Ay, there's the rub!
For in that PhD what dreams may come,
When we have shuffled off this campus soil?
For who would bear the whips and scorns of time,
The professor's wrong, the undergrad's contumely.
The pangs of dispriz'd love, the experiment's delay,
But that the dread of something after graduation,
The undiscovered country from whose bourn no slacker returns,
Puzzles the will and makes us rather bear those ills we have,
Than fly to others that we know not of?
Thus cowardice does make procrastinators of us all,
And lose the name of action.

-PhD Comics

2007-07-10T09:53:00.001-07:00

The $300 Linux-Powered 'iPhone Killer' Arrives

By Michael Calore July 09, 2007 | 1:41:33 PMCategories: Linux, iPhone

After seemingly endless delays, the OpenMoko phone is here. The first version of the NEO 1973 mobile phone, which carries the Linux kernel inside and is not locked to a specific network, is available for purchase from OpenMoko.com. It's not as jaw-droppingly pretty as the iPhone, but it shares a design philosophy -- no buttons, just a screen -- and it's ready to be loaded with any number of open-source software applications. (Though, according to Gadget Lab, so is the iPhone).

The base version of the NEO sells for $300. It has a 2.8" VGA touch screen, a micro SD card slot, a USB port and 2.5G GSM quad band capability.

Keep in mind that this unit (the GTA01) was pushed out early so developers could begin writing device drivers, custom GUIs and some cool apps for the phone. The next revision (GTA02), which will be available starting at $450 in October, will be ready for the mass market. It will have wi-fi, 3-D motion sensors and added graphics accelerators. So this phone isn't exactly an iPhone killer -- the next one will be a contender. AptUsTech has a nice comparison of the NEO 1973 and the iPhone.

When it comes to devices, more choice is almost always "a good thing." But will consumers respond to the NEO? We all know developers are going to dig this phone. But what's more important to consumers -- a super-sexy status item that's locked to one carrier and one set of functions, or a less sexy look-alike with a fully free and open software system?

2007-07-10T00:34:00.001-07:00

Oh, life...

2007-07-08T04:42:00.000-07:00

Things I Learned from Die Hard 4:

- In the future, we will have biological transistors that allow us to download an entire server onto a PDA. And by future, I mean now.
- Palms, Treos, and Sidekicks are all you need to hack into NSA and save the world. As long as you don't get shot. (No iPhone necessary.)
- A bullet in the kneecap doesn't really impair your ability to walk.
- Contrary to the work we do in the lab, BioWatch sensors actually react instantly, setting off big red alarms within moments. I've gotta tell Slezak about this on Monday; at this point he's just wasting his time.
- Move over, Chuck Norris. Bruce Willis cannot die.

~~~

The sequence is that of a gene on chromosome 6p22, involved in neuronal migration and intelligence in humans. If you're interested in being on Chicago's SynBio team next year, contact me.

~~~

Semi-Protect the Constitution: Wikipedian Protester

2007-07-04T00:28:00.001-07:00

Happy Independence Day!

On an entirely unrelated note, I must at length describe how much I am fascinated with and impressed by the writing of Friedrich Nietzsche. Cliche, I'll admit, but true nevertheless. Everytime I pick up work by that man, I am absorbed for hours, almost without exception. There is such good in that evil, it's really quite delightful. Nietzsche was a man who loved to shock and anger, but believed he was doing the right thing by going about it. His outright rejection of the Christian (or any) God was the first step, he felt, on the path to morality. The famous quote from The Gay Science (see below) describes the death of the concept of God; modern man no longer finds God convincing. Science has no use for that hypothesis.

While this quote is frequently and annoyingly misconstrued as a sign that Nietzsche is just pure evil, it signifies, to him, the loss of something necessary. With the death of God, man lost morality; with the advance of science and rational thought, Western civilization lost its defining and uniting approach to life, as a shared cultural set of belief fully within which people had lived their lives.

To Nietzsche, this was just bad news. Hear the wonderfully articulated anguish in his tone:

Have you not heard of that madman who lit a lantern in the bright morning hours, ran to the market-place, and cried incessantly: "I am looking for God! I am looking for God!"
As many of those who did not believe in God were standing together there, he excited considerable laughter. Have you lost him, then? said one. Did he lose his way like a child? said another. Or is he hiding? Is he afraid of us? Has he gone on a voyage? or emigrated? Thus they shouted and laughed. The madman sprang into their midst and pierced them with his glances.

"Where has God gone?" he cried. "I shall tell you. We have killed him - you and I. We are his murderers. But how have we done this? How were we able to drink up the sea? Who gave us the sponge to wipe away the entire horizon? What did we do when we unchained the earth from its sun? Whither is it moving now? Whither are we moving now? Away from all suns? Are we not perpetually falling? Backward, sideward, forward, in all directions? Is there any up or down left? Are we not straying as through an infinite nothing? Do we not feel the breath of empty space? Has it not become colder? Is it not more and more night coming on all the time? Must not lanterns be lit in the morning? Do we not hear anything yet of the noise of the gravediggers who are burying God? Do we not smell anything yet of God's decomposition? Gods too decompose. God is dead. God remains dead. And we have killed him. How shall we, murderers of all murderers, console ourselves? That which was the holiest and mightiest of all that the world has yet possessed has bled to death under our knives. Who will wipe this blood off us? With what water could we purify ourselves? What festivals of atonement, what sacred games shall we need to invent? Is not the greatness of this deed too great for us? Must we not ourselves become gods simply to be worthy of it? There has never been a greater deed; and whosoever shall be born after us - for the sake of this deed he shall be part of a higher history than all history hitherto."

Here the madman fell silent and again regarded his listeners; and they too were silent and stared at him in astonishment. At last he threw his lantern to the ground, and it broke and went out. "I have come too early," he said then; "my time has not come yet. The tremendous event is still on its way, still travelling - it has not yet reached the ears of men. Lightning and thunder require time, the light of the stars requires time, deeds require time even after they are done, before they can be seen and heard. This deed is still more distant from them than the distant stars - and yet they have done it themselves."

It has been further related that on that same day the madman entered divers churches and there sang a requiem. Led out and quietened, he is said to have retorted each time: "what are these churches now if they are not the tombs and sepulchres of God?"

This is, again, bad news for Nietzsche, who feels that people behaving decently is more important than any sort of rational thought, and also feels that people are most likely to behave decently when they have some sort of uniting goal for which to strive. Hence, the Ubermensch. By replacing the far-fetched concept of God with something he felt was easier and more desirable, Nietzsche felt he was doing his part to help that detested mankind.

"I teach you the Overman. Man is something that shall be overcome. What have you done to overcome him? All beings so far have created something beyond themselves; and do you want to be the ebb of this great flood and even go back to the beasts rather than overcome man? What is the ape to man? A laughingstock or a painful embarrassment. And man shall be just that for the Overman: a laughingstock or a painful embarrassment..."

In his literary masterpiece, Thus Spake Zarathustra, Nietzsche gives us a protagonist who contends that "man is something which ought to be overcome" (sounds a little bit like House, MD). Zarathustra thus announces the coming of the Ubermensch (Overman, Superman, Homo superior), which must succumb to nihilism in order to defeat it. Zarathustra charges his followers to prepare for the Superman, in three quick and easy steps: 1) Use your will to power destructively, in the rejection of societal ideals and moral codes, 2) Use your will to power creatively, by overcoming nihilism and the re-evaluation of old ideals and creation of new ones, 3) Undergo a continual process of self-overcoming.

Nietzche, as can be imagined, really didn't like silly ideas such as the soul, personal consciousness, or the ego. He destroys arguments that use metaphysics, and hates individualistic societies that would view the Superman as a hero. It always seemed to me that Nietzsche loved Buddhism, but hated Buddhists.

However, the Superman is generally not interpreted as a person (Nietzsche hates people, remember), but as a state or occurrence of multiple wills to power undergoing the existential process of overcoming both oneself and nihilism. Naturally, Nietzsche also hated free will (what a silly concept in the first place! Free will! Ha!), so his instructions were, he knew, just general advice that would or wouldn't be followed. No one, he claimed, can choose to be the Superman; it's just something that will happen when the time is right.

Given the proper conditions, man will transcend himself.

2007-07-03T01:37:00.000-07:00

To: parijata@gmail.com
From: berke@mit.edu
Subject: Things to amuse you while you're at work and I'm not

1. Cadaver Dissection Videos
http://www.lawrencegaltman.com/Naugbio/CADAVER/GALLERY.htm

2. Very Old Anatomy Drawings
http://www.nlm.nih.gov/exhibition/dreamanatomy/da_gallery.html

3. Predictably, Scientists are much better than writers at Explaining Science
http://observer.guardian.co.uk/review/story/0,,2115569,00.html

~~~

Thanks, Ally, very cool :-)

Jean-Paul Sartre is sitting at a French cafe, revising his draft of Being and Nothingness. He says to the waitress, "I'd like a cup of coffee, please, with no cream." The waitress replies, "I'm sorry, monsieur, but we're out of cream. How about with no milk?"

2007-07-01T00:59:00.000-07:00

Candy for Thought

or Chicken Soup for the Scientist's Brain

2007-06-29T07:36:00.000-07:00

Science 29 June 2007:
Vol. 316. no. 5833, p. 1827
DOI: 10.1126/science.316.5833.1827a

Prev | Table of Contents | Next

News of the Week

GENETICS:
Replacement Genome Gives Microbe New Identity

Elizabeth Pennisi

For decades, molecular biologists have genetically modified microbes and other kinds of cells by adding short DNA sequences, whole genes, and even large pieces of chromosomes. Now, in a feat reported in a paper published online by Science this week (www.sciencemag.org/cgi/content/abstract/1144622), one group has induced a bacterium to take up an entire 1.08-million-base genome in one gulp. In doing so, microbiologist John Glass and his colleagues at the J. Craig Venter Institute in Rockville, Maryland, have transformed one bacterial species into another.

"This is a significant and unexpected advance," says molecular biologist Robert Holt of the Michael Smith Genome Sciences Centre in Vancouver, Canada. But the advance remains somewhat mysterious. Glass says he doesn't fully understand why the genome transplant succeeded, and it's not clear how applicable their technique will be to other microbes. Nonetheless, "it's a necessary step toward creating artificial life," says microbiologist Frederick Blattner of the University of Wisconsin, Madison.

Glass and his colleagues are among several groups trying to build a microbe with the minimal gene set needed for life, with the goal of then adding other useful genes, such as ones for making biofuels. In anticipation, Glass and colleagues wanted to develop a way to move a complete genome into a living cell.

As a proof of principle, they tried transplanting the single, circular chromosome of Mycoplasma mycoides large colony (LC) into a close relative, M. capricolum. Both of these innocuous goat pathogens lack the cell walls typical of many other bacteria, eliminating a possible impediment to genome transfer.

At the Venter Institute, Carole Lartigue and her colleagues first added two genes to M. mycoides LC that would provide proof if the transfer of its genome worked. One gene conferred antibiotic resistance, and the other caused bacteria expressing it to turn blue. Lartigue removed the modified chromosome from M. mycoides LC, checked to make sure she had stripped off all proteins from the DNA, and then added the naked genome to a tube of M. capricolum. Within 4 days, blue colonies appeared, indicating that M. capricolum had taken up the foreign DNA. When they analyzed these blue bacteria for sequences specific to either mycoplasma, the researchers found no evidence of the host bacterium's DNA.

Microbial geneticist Antoine Danchin of the Pasteur Institute in Paris calls the experiment "an exceptional technical feat." Yet, he laments, "many controls are missing." And that has prevented Glass's team, as well as independent scientists, from truly understanding how the introduced DNA takes over the host cell.

Glass suspects that at first, both genomes are present in M. capricolum. But when one of those double-genomed microbes divides, one genome somehow goes to one daughter cell and the other to the second. By exposing the growing colony to an antibiotic, the researchers selected for cells that contain only the M. mycoides LC genome.

Species makeover. Blue signals successful genome transfer in these bacterial colonies.
CREDIT: NACYRA ASSAD-GARCIA/JCVI

Other researchers are not sure the strategy will work on bacteria with cell walls. And Danchin expects it will be difficult to swap genomes among bacteria that aren't as closely related. Regardless, George Church of Harvard University questions the need for genome transplantation; instead of starting with a minimal genome, he's making useful chemicals by simply adding customized genes to existing species' genomes.

Nonetheless, Markus Schmidt of the Organisation for International Dialogue and Conflict Management in Vienna, Austria, predicts that the mycoplasma genome swap will force more discussions about the societal and security issues related to synthetic biology. "We are one step closer to synthetic organisms," he says.

READ ARTICLE HERE [PDF]

2007-06-28T14:54:00.000-07:00

US holds rare meeting with Burma

Ms Suu Kyi has been in detention for most of the last 18 years

A senior US diplomat has held talks with Burmese government ministers in Beijing, in the first such high-level meeting since 2003.

The US pressed for the release of the democracy activist, Aung San Suu Kyi.

Ms Suu Kyi, 61, has spent 11 of the last 18 years in detention. Her latest period of house arrest began in 2003.

Washington described the discussions as frank but that there was no sign the Burmese military government had changed its basic opinions.

Fight for democracy

Eric John, a deputy assistant secretary of state, met Burma's ministers of foreign affairs, culture and information in the Chinese capital, Beijing.

US state department spokesman Tom Casey said it was "a very frank discussion of our concerns about the regime, about its behaviour".

"It gave us an opportunity to express our opinions directly," he said.

Last month members of Ms Suu Kyi's National League for Democracy marked the 17th anniversary of their party's landslide election victory.

However, the victory was never recognised by the junta.

They have ruled the country - which it calls Myanmar - since a coup in 1962.

In 1991, Ms Suu Kyi was awarded the Nobel Peace Prize for her efforts to bring democracy to Burma.

2007-06-26T23:39:00.000-07:00

Entire CIA MKULTRA Collection (Source: The Black Vault)

Project MKULTRA (also known as MK-ULTRA) was the code name for a CIA mind-control research program that began in the 1950s.^[1]^[2] There is much published evidence that the project involved the use of many types of drugs to manipulate peoples' mental state and to alter brain function.^[3]

It was first brought to wide public attention by the U.S. Congress (in the form of the Church Committee) and a presidential commission (known as the Rockefeller Commission) (see Revelation below) and also to the U.S. Senate.

On the Senate floor in 1977, Senator Ted Kennedy said:

The Deputy Director of the CIA revealed that over thirty universities and institutions were involved in an 'extensive testing and experimentation' program which included covert drug tests on unwitting citizens 'at all social levels, high and low, native Americans and foreign.' Several of these tests involved the administration of LSD to 'unwitting subjects in social situations.' At least one death, that of Dr. Olson, resulted from these activities. The Agency itself acknowledged that these tests made little scientific sense. The agents doing the monitoring were not qualified scientific observers.^[4]"
^--Wikipedia
^~~~~~

The following directories contain .tif images of the released MKULTRA documents, and two other files. The .txt file is a poor excuse for a OCR (optical character recognition) of the document, which means they put the documents through a software title to make it text. You will see these are usually useless, because the process does not work on poorly photocopies documents. The .dat file in these directories is the one line description, as found in the index.

Please Note: If you need a FREE .TIF viewer - you can download Brava!® Reader. Brava!® Reader is a free application that opens, views, and prints TIFF files.

MKULTRA CIA Document Index - Start here! This will list the contents of the following links, which are the documents on the CD-ROMs. Or, you can just start browsing the CD's below - it's up to you!

CD-ROM #1: ( DOC_0000017481 - DOC_0000149499 | DOC_0000149500 - DOC_0000197284 )

CD-ROM #2 ( DOC_0000017352 - DOC_0000017437 )

CD-ROM #3 ( DOC_0000017392 - DOC_0000148094 )

Discuss MKULTRA documents

Mind Control

Communist Control Techniques [123 Pages]

Parapsychology in Intelligence [12 Pages]

Project MKUltra, The CIA's Program of Research in Behavioral Modification [172 Pages]

Related Documents of Interest

Interrogation: Science and Art [371 Pages] - U.S. military personnel and intelligence officers in particular are expected to gain accurate information from detainees or prisoners and thus need to know “what works” in “educing” information through interrogation, strategic debriefing and information elicitation. This book presents the work of 13 specialists in law, psychology, military intelligence, neuroscience, computer science, conflict management and library science. The authors review what is known and not known about educing information.

Adventures of a Wetware Hacker

Objective:

The $300 Linux-Powered 'iPhone Killer' Arrives

News of the Week

GENETICS:Replacement Genome Gives Microbe New Identity

GENETICS:
Replacement Genome Gives Microbe New Identity