Monday, August 28, 2006

Cause and effect

I was planning to write a consise and insightful post on the concept of cause and effect, and then further describe necessary or sufficient causes. Sometimes in our desire to believe something, we want to ignore cause and effect.

But then, I remembered Carl Sagan’s description of cause and effect, re-read it, and it more than suffices to just quote him:

“Occationally someone remarks on what a coincidence it is that the Earth is perfectly suitable for life – moderate temperatures, liquid water, oxygen atmosphere, and so on. But this is, at least in part, a confusion of cause and effect. We earthlings are supremely well adapted to the environment of Earth because we grew up here. Those earlier forms of life that were not well adapted died......Organisms that evolve on a quite different world will doubtless sing its praises too.”


Now all that energy I was planning to spend writing that post on cause and effect can be saved and instead be used in something useful. Research perhaps.

Wednesday, August 23, 2006

Khayyam, Galileo, fundies and the finger salute

The present issue of Nature had a pithy editorial on the state of science in Iran and starts off with a nice historical story:
…… “In eleventh-century Persia, it is said that three school friends pledged to serve their country and share their fortunes. Very different fortunes, it turned out.
Nizam al-Mulk became prime minister to two consecutive Persian kings. …..and established the chain of 'Nizamiyya' schools, which taught theology, science and mathematics, adhering to a national curriculum…………………….

Hassan-i Sabbah became the head of a fanatical religious group, the Hashshashin, which operated an almost independent government, protected by a string of castles………

Omar Khayyam became the greatest astronomer and mathematician of his age. He invented, for example, the Khayyam triangle — better known as the Pascal triangle, after Blaise Pascal who described it hundreds of years later. Khayyam also provided his country with a solar calendar…….”

A rather typical but nice early example of typical conflict of politics, religion and science. As is usually the case, politics and religion slugged it out (and overlapped space) while the scientist was squeezed.

But this story is a good one. Nizam al-Mulk was a rather decent chap, and when he became prime minister, his two old pals came to him. Hassan-I-Sabbah was given a nice, cushy government post, got too ambitious, was dismissed, and then used religion to gain incredible power. His band of men (army, more likely) makes Osama pale in comparison, and his troops, high on Cannabis indica, better known as hashish or hash, went about their job of getting rid of the who’s who of the middle east, giving English a new word (assassin; from hashshashin). Khayyam though went up to Mulk, and all he asked for was a quiet place to study. The delighted prime minister packed Khayyam off with a small pension, and a little estate.

And there Khayyam produced some rather nice verse (in the form of the the Rubaiyat), but that was perhaps the least important of his contributions, since it was typical of a lot of excellent Farsi verse that was written between the borders of Turkey and Mughal India for 500 years or so. More importantly he went about answering some rather fundamental questions in mathematics and astronomy. Like a lot of mathematician astronomers, he tried to answer one of two questions (the other being the value of pi). He calculated the length of a year to be 365.24219858156 days (the Gregorian calendar estimate is 365.242190 days, and is less accurate). He went on to solve the cubic equation (ax3 + bx2 + cx + d = 0) by intersecting a parabola with a circle, and said that this couldn’t be solved by a rule and compass method, but needed conic sections. He did plenty of other interesting stuff, like contributing to non-Euclidean geometry, demonstrated the existence of equations with two solutions, and similar fun stuff [link]. But, like too many other scientists, he was skeptical and resistant to religious (in this case Islamic) dogma, particularly in divine intervention in daily life, as well as not believing in judgment day. That of course got him in to trouble, and he had to undertake the hajj to prove his faith.

And thus he joined a long list of scientists who got in to trouble with religious authorities.

While reading about Khayyam, I was reminded off the great Galileo Galilei, perhaps the first western scientist to quantitatively and mathematically analyze all data, and not relying solely on logic. He happily improved telescopes, discovered satellites of Jupiter, helped throw out the geocentric model of the earth as the center of the universe, studied sun spots, observed lunar craters, dropped spheres from the leaning tower of Pisa to show that the descent of an object was independent of mass, and determined laws of acceleration (to name just a few observations). And he got himself in to plenty of trouble with the Church, for not taking every word in the bible literally. His heliocentric model resulted in troubling the religious fundies so much that he died finally under house arrest.

But I discovered that he did indeed have the last laugh. Tourists throng to Florence, and most spend their time staring at splendid art at the Uffizzi or running to the Accadamia to see the statue of David. But hidden close to the Uffizzi is a splendid museum of the History of Science. This superb museum has a fantastic collection of medieval scientific instruments (including navigational tools the Arabs used), maps and early electronic devices (including those used by another Tuscan, Volta!). It also pays tribute to two of Florence’s greatest sons, Galileo and Da Vinci, and has a superb collection of many of Galileo’s original telescopes and instruments.

And there I saw, in a little brass capped glass bottle, mounted on a little pedestal, Galileo’s ultimate snub to the fundies who got him. On that pedestal was mounted a preserved finger of Galileo.

Galileo remains immortal to this day, giving the great one finger salute to all those forgotten fundies who tormented him, as the earth continues to orbit the sun.

To quote Khayyam on the finger,
“The Moving Finger writes, and, having writ,
Moves on: nor all thy Piety nor Wit
Shall lure it back to cancel half a Line,
Nor all thy Tears wash out a Word of it.”

Now fundies, watch my finger wag.

Monday, August 21, 2006

Book review: Education of a wandering man

“If I were asked what education should give, I would say it should offer breadth of view, ease of understanding, tolerance for others, and a background from which the mind can explore in any direction”
-Louis L’amour

Many people think novels that fall under the “western” genre are rather trivial. To them, all there is to it are a bunch of cowboys, some shoot-outs, some cattle rustling, and a few Mexicans who get shot. The same people also do a great disservice to the genre, and cannot appreciate Clint Eastwood in Unforgiven. But I was drawn to the stories of the West by perhaps the best writer of them all, Louis L’amour.

His books fell in to two groups, the “classical western”, with the cowboys and fights (particularly the fistfights, that were always integral to the climax), and the second, his more detailed historical fictions. In this group are some wonderfully entertaining adventure historical fiction novels like The walking drum, Fair blows the wind, The warrior’s path, Jubal Sackett and many others. What made these books wonderful reading was that through his characters, L’amour painted a wonderfully descriptive picture of the times they occurred. And this, to me, was one of the most enjoyable ways of learning about the history of settlement and expansion in the Americas.

I chanced upon his memoirs, Education of a wandering man at a used bookstore, bought it, and ended up reading it over two days. It turned out to be, like the man himself (at least through his memoir), every bit as “out of the ordinary” as can be expected. In this book, instead of chronicling his life, which is what many writers do in their memoirs, L’amour unexpectedly presents us with an endless laundry list, of all the books he read over his life, sneaking in stories of his life in between lists. And from those stories we get snippets in to America through the depression, and the great war.

And the life was everything but mundane. He grew up in a family that loved to read, and books were a part of his every day life. And at the age of fifteen, he left home to go around the world, doing whatever work he could along the way. He spent many years as a hobo (carefully distinguishing a hobo from a tramp or a vagabond), working along the railroad, and all through those times, all he valued and carried with him were books. He spends time skinning cattle in Texas, and prizefighting across various towns (winning 50 of his 59 fights), and hops on ships as a merchant seaman, and in one incredible story talks of walking across the blazing Mojave desert without water, because he was spending time prospecting an old mine, and his wind-up car breaks down along the way back. Now, that would be true L’amour western style. But amazingly, that story comes as a backdrop, as L’amour describes his readings in the solitude of that mine, and his discovery of a small library there!

Some one telling a story needs to love stories for what they are. That person needs to love to listen to stories as much as s/he loves to write them, and L’amour repeatedly talks about his love for stories. That was his education; books and people. His mind remained ever curious, eager to know what ever it could find. And “old timers” in little towns, whom most people thought were senile, told most of his own stories to him. In between his laundry list, L’amour talks of his passion for writing stories. Though he went on to write over a hundred novels, he started off writing short stories, and most of them were rejected (in the book there’s a nice photo of one of his lists of his own stories, with “rejected” written next to most of them). Here we get a wonderful insight in to the world of publishing, with the top rung magazines, like the New Yorker which were really hard to publish in, and the bottom rung, of small town publishers, who couldn’t pay much. But the money was in pulp paperbacks, a phenomenon, which L’amour observes, revolutionized writing, writers and most importantly, readers, forever.

L’amour also talks of his passion for history, of the ancient world, as well as the west. After all, westerns are a little piece of history, and his love for detail makes him research the smallest aspect of the country he writes about, the peoples, the plants, the mountains. This we see in his novels, which are never “churned out” westerns, where Indians and cowboys shoot it out. Instead it’s a complex mix of grey, of different tribes and their own rivalries or friendships, pioneers, slavers, profiteers, Quakers, and the rest. L’amour appears to be remarkably open constantly to learning of lands and times that are not his own. He reminds readers of history in the west being western-centric, starting in Babylon and moving west to Egypt, Greece and Rome. But there was a world beyond, far East, where great civilizations once rose. And he credits his love for the east to an Arab boy he met when he was on a ship in Indonesia. He asked the Arab what an Arab was doing that far east, and the boy replied that the Arabs were sailing those seas for 500 years. And that lead L’amour to learn of the civilizations of the East, of great ocean expeditions of Chinese navies, of great ports in Tamil Chola country, of civilizations of Cambodia, of history little appreciated in the west. And all this through his collection of books, starting with the Shahnama.

L’amour considered himself an old-fashioned storyteller, a teller of yarns around a campfire. This we see in all his novels and stories. But the memoirs reveal a man who was constantly in search of stories, from history and people. A remarkably open mind, curious to know, and with a desire to learn. And that is the best part of the laundry list of books that become his memoirs. It tells us that there is joy and learning in all written words.

Land of the scientific mind (where science means miracle)

First we have droves of people in Mumbai, right by Mahim, going out to drink the miracle sea water that had turned sweet

“………………….Several people who drank the muddy water from the Arabian Sea said it had been changed by a miracle and could now cure illnesses……."This water is definitely sweet. We see it as a blessing from Baba (Holy Saint)," a man called Rafique told news agency AFP..”

All hail the holy saint. There was absolutely no chance that the torrential rains of the recent past, which left the Mithi river (amongst others) that dumps fresh (not clean) water in to the Mumbai bay by Mahim at spate had any thing to do with the miracle.

But shame, this was right by a Muslim dargah. When stupidity rules, the rest can’t be that far behind.

Here’s more now.

“………………The faithful continued to flock to temples since the morning as word got around of idols of Hindu deities drinking milk while scientists ascribed it to soaking of liquid by dry clay and some leaders on Monday asked people to use reason instead of going by superstition.
Long queues of men, women and children were seen in front of Durga, Shiva and Ganesha temples in several parts of Madhya Pradesh as people offered spoons full of milk to the idols. Many went there out of curiosity…….”

Great. No chance of course that the clay can even possibly absorb milk. Those fools shouting for logic and reason will rot in hell.

Now watch as some Christians come up with some miracles. There’ll be pigeons flying around with halos around them.

Truly we live in such scientific times.

Friday, August 18, 2006

Books, books, books

Arunn of Nonoscience has an excellent and extensive list of books of his choice, and has tagged me for my own choices. A nice way to collect reading material suggestions!

One book that changed your life?
Don't know about changing my life, but one "book" I keep going back to again and again is the Indian epic, the Mahabharata, in its various forms (from comic book through Rajagopalachari, Buck, Narasimhan and other versions). Not for any religious significance, but always for new insights in to human nature each time I read it. Marvellous.

One book you have read more than once?
Let's see now, if I had to pick only one, I'll pick Dawkins' The Selfish Gene. Not without its flaws, but always raising questions. A classic.

One book you would want on a desert island?
Hypothetically, "How to build a boat with no tools and a single coconut tree". Realistically, The SAS survival handbook. Get me out of there!

One book that made you laugh
Almost all of P.G. Wodehouse's books and Terry Pratchett's books. A particular recent favorite is Pratchett's Small Gods.

One book that made you cry
Haven't really cried after reading a book. But one book that left me really depressed was The scavenger's son.

One book you wish had been written?
Heh...this must be the sequel to Louis L'amour's historical fictionThe walking drum. The hero, Kerbochard, was well on his way to India. Wonder what would have happened after he reached "Hind".

One book you wish had never been written?
A book is a book. It always has some place.

One book you are currently reading?
I'm usually reading two or three books at a time. Just finished the memoirs of Louis L'amour, The Te of Piglet, a collection of Nobel lectures.

Now go and spread some book love, and tell me about new and wonderful books. I'll be happy to link to your post here if you let me know.

Sunday, August 13, 2006

The Astonishing X-Men: Desi unleashed

A little late, but better than never, I finally got down to reading Joss Whedon’s Vol. 3 of The Astonishing X-Men, with more of the Cyclops-Emma Frost distraction, but more importantly, the description of the cure for the “mutant disease”.

The recent X-Men: The last stand got a little carried away with the special effects, and lost out a little on the superior screenplay the earlier movies had. But it was based on the concept of the “mutant cure vaccine”, and the description of mutants as diseased humans. I just love the quasi-science in the X-men, with a blending of atrocious rot with rather well researched science. There’s an effort to describe mutants and revertants, while flooding the mind with improbable rapid mutations resulting in superpowers. Irregular readers of the comic books though might still remember the female doctor in the movie, who was the scientist behind the mutant cure vaccine.

Shohreh Aghdashloo appeared in a blink-and-you’ll-miss-it role as the Indian doctor, Kavita Rao. The comics do a much better job of fleshing out her character.

She’s very desi in the comics, clad in sari (with white lab coat, reminding me of labs in India), and a prominent bindi. A colleague respected by my favorite mutant, Dr. Hank McCoy (the Beast), she’s the world’s foremost geneticist, employed by Benetech Corp, and truly believes that mutants are just diseased humans, who need help, and the vaccine will help them lead “normal” lives. But she’s also strongly against the taking of any life, or discrimination. The ethical problems she faces remain in grey areas, and lead to some interesting conversations with the Beast. (Something on the lines of “…so, you think homosexuality is a disease?”, “no, and we could debate the ethics of this endlessly, but homosexuals aren’t a threat to society, mutants have harmed humans.”)

And she’s using the help of super-alien-villain, Ord of Breakworld, who has captive another rather mutant X-man (I won’t be a spoiler here, go read the comic), and has used him to find the cure.

Now, with Virgin comics and Devi, Snakewoman and Ramayana Reborn, there’s a veritable deluge of desi in the comic world.

Go read them all.

(You can read the first issue of Virgin comics for free here, while you’ll have to dish out hard earned chips for X-men, but it’s worth it.)

Friday, August 11, 2006

Happy hour: Peer review accountability

Peer review still remains the best available way for journals to review and accept papers, though this system has some limitations and problems. There have been some exciting changes though in how journals are viewing their reviewing process. Nature is beginning to debate about it, and PLoS now has a new, community peer review system, with PLoS ONE. All very cool trends.

But there was something else that the significant other and I ended up discussing about, and it was what we thought was a rather simple but required step. The present system of peer review is anonymous peer review, where you submit your paper to a journal, and then it is sent off to a couple of experts in your area, who review the paper. But neither you nor any one else in the world (apart from the editors and the reviewers) know who these people are. Though a majority of the reviewers take their job of reviewing papers very seriously (the only two papers I’ve reviewed thus far, I spent hours analyzing. That we can dismiss as early enthusiasm, but still), many do not. They end up doing a rather sloppy job of reviewing papers (usually due to reminders or phone calls from editors). They sometimes pass on their decision without reading all the details of the paper, sometimes basing it on the author reputations, or where the paper’s from (sad, but sometimes true). Or else, they base it on how “cool” the story seems to be (without looking out for appropriate controls in the experiments). These papers slip through the cracks, and get published, even in so called “premier” journals.

So, and idea we had a couple of nights ago was to make the reviewers and editor responsible for the publication of a paper a little more accountable. For this, an obvious solution could be to have anonymous peer review during the process of review, but after a paper has been accepted for publication, the reviewers names should be mentioned in print when the paper is published. In addition, it could be easily possible to include a paragraph at the end of each paper published, where the reviewer(s) can say what they liked about the paper, and what else they would have liked to see. That way, it seems to me that reviewers will strive to do a better job with reviews, since their reputations will (in a way) be at stake. This step should go a long way in ensuring fair but rigorous reviews of papers, with a little more responsibility for the reviewer to do a good job.

(Interestingly, I mentioned this to my advisor, who thought it wasn’t a bad idea. So perhaps it may have some support amongst academics after all (there’s an n of one here, I need two more people supporting this, and this idea becomes practically publishable in itself J)).

Update: More from PLoS One "9. Anonymity
Although reviewers may remain anonymous during the review process, we strongly urge them to relinquish this anonymity to promote open and transparent decision-making."
, and "If published, papers will be accompanied by comments from the handling Editorial Board member and will be made available for community-based open peer review involving online annotation, discussion, and rating.". Read about it here. All more than excellent. In addition though, I would like to see the reviewers comments too in the published paper, and their names being made pubic, just like the handling Editorial Board member's comments. Adds incentive to review well.

Wednesday, August 02, 2006

Can do anything nation

When I take a cab alone (which is not something that happens often), I usually sit up in front with the driver, so that I can chat. I’ve found most cab drivers love chatting, especially if you ask them about themselves. And I’ve heard some very interesting stories from them.

But here’s a good story.

A couple of days ago I was in a cab, and as is my habit, sat up in front and struck a conversation with the cab driver. He asked me about my own work, and I told him a little about my research, and then I asked him about himself. And that got him started on his incredible story.

“I understand how you work”, he said. “I’m an inventor myself, you see.”

Intrigued, I sat up to listen. He needed little prompting.

“I worked for many years for oil and steel companies, in Saudi Arabia, in Africa, all over. I’ve done due diligence or studied manufacturing practices in companies in forty countries. Over the years, it got me and some friends thinking. There’s so much industrial growth in the world, in China, in India, in the Far East. They all need steel, lots of steel. And steel making is amongst the most polluting industries in the world. Iron’s easy to get, but mining’s harsh, and making iron in to steel’s really polluting. So I thought the answer to all this is silica glass fiber. Silica’s the second most common substance on earth, you can get it anywhere. And so we took out a patent for some technology to make these fibers. It’s as hard as steel, as strong as steel, lasts longer, and is easier to make.”

“But we know it’s not going to be easy to launch it in the States, or in a big market, to make something mainstream, like cars. But I have it all figured out. We’ll make specialized boats, and we won’t do it in the States.”

“We’ll do it in Africa. Most of that continent is a mess, but Ghana, it’s stable, and safe, and you can do business there. I’ve been there a dozen times on work myself.”

And I sat back and remembered a little phrase from what I think is the best book written on globalization, Tom Friedman’s The lexus and the olive tree, where he said the thing that made America is the fact that this country has amongst the lowest barriers to entry in the world, and anyone with an idea, good or bad, can run with it, and find some one to fund that idea, and then try to sell it. You don’t need to push paperwork for years, you don’t need to bribe any one, you don’t need a thousand middlemen, and you can just do something you dream about.

You might fail, but you can still try, and you’ll never say it didn’t happen. And that, to me, is the greatest thing that can happen to any nation.