Demolishing a ‘vacuous’ argument for the RRW

The Reliable Replacement Warhead program (RRW) is a long-standing and controversial proposal that aims to replace aging plutonium pits and other parts in nukes to modernize the current US nuclear arsenal. Proponents of the RRW say that having nuclear weapons of dubious function and quality will defeat the basic purpose of a deterrent and therefore modernizing the arsenal and replacing worn out parts is essential for its very existence. In addition, Russia has indicated that it is modernizing its nuclear arsenal and this fact has put further pressure on implementation of the RRW. Opponents of the RRW say that by modernizing the arsenal the US will send out the wrong signals to the rest of the world, indicating that nuclear deterrence and weapons development is still an important part of US defense strategy. In any case, very recently the top government advisory group JASON which among others included Freeman Dyson) did a study on the central plutonium ‘pits’ in the nuclear weapons and concluded that these would last for at least half a decade if not more. Since then several arguments have continued to float around for the RRW. In the latest issue of The Bulletin, Jeffrey Lewis and Kingston Reif do a neat and clean job in demolishing the latest argument made by a General Chilton who, of all possible reasons, bases his argument on vacuum tubes, the point being that outdated vacuum tubes in nukes necessitate replacement. The last line is priceless and is not exactly BAS-like

Firstly, vacuum tubes are not used in the physics package of a single nuclear weapon design. Vacuum tubes are used only in the radar-fuse, which tells the firing system when the bomb is at the correct altitude for detonation, in some modifications (mods) of one warhead design, the B61 gravity bomb. In total, the B61 bombs that have vacuum tubes in their radar-fuses account for only about one in ten operationally deployed warheads. (Vacuum tubes are used in the radars of three B61 mods: 3, 4, and 7. Mods 10 and 11 have newer radars that use solid-state electronics.) The fuses in these weapons are old, but perfectly functional. To reiterate, vacuum tubes are not in use in any other warhead design, including the W76 warhead, a portion of which would be replaced by the first RRW warhead, the WR1, if it ever were funded and developed.

Secondly, the Energy Department has routinely replaced radars without nuclear testing or redesigning the physics package. In fact, during the 1990s, Sandia National Laboratories scientists developed the MC4033 common radar, which uses solid-state electronics, for planned refurbishments of the B61 and B83 gravity bombs. All B83 bombs now use the common radar, though similar plans to fit a new radar on all B61s have been repeatedly deferred.

Most recently, in 2006, Sandia planned to replace the remaining B61 vacuum tube radars as part of ALT 364/365/366. The National Nuclear Security Administration, which overseas the nuclear weapons complex, canceled these latest ALTs, which would have resulted in the removal of the last vacuum tubes from the U.S. nuclear stockpile, because the U.S. Air Force preferred replacement to life extension. Due to this absurd twist, one could say that vacuum tubes remain in the U.S. nuclear arsenal in part because of the RRW, contrary to Chilton’s insistence that the RRW is needed to get rid of them.

The bottom line is that vacuum tubes are used only sparingly in the U.S. nuclear arsenal and can be replaced on short notice if the need arises, independent of whether Congress funds the RRW Program. Of the many reasons that Defense and Energy officials have put forth to justify the RRW Program, the need to replace vacuum tubes is the worst and has no place in the debate about the RRW or modernizing the nuclear stockpile. General Chilton can stick that prop in his, um, pocket.

28 Apr, 2009 | No Comment

More hope on the horizon for Indian scientists

A while back, I had written a post about a new law due to be passed in India that could allow government scientists to own patents, a law similar to the Bayh-Dole act in the US that opened up lucartive fields like drug discovery and semiconductor technology to thousands of scientists. These scientists could then reap the benefits of the patents, start their own companies and not have to worry about the government appropriating these benefits. Now, mainly in an effort to lure Indian expatriates, the government is going to allow Indian scientists to start their own startup companies and reap the rewards of their discoveries, a mirroring of a tradition long-sustained and extremely fruitfully implemented by American universities like MIT. If this pulls together, it may potentially well be one of the most important policy advances in the history of Indian science, a development that could spur innovation in a way that was unprecedented. Let’s hope for the best. The entire article is worth quoting here.

India Allows Government Scientists to Own Companies
Pallava Bagla
NEW DELHI–In 2001, Swami Manohar and three colleagues at the Indian Institute of Science (IISc) in Bangalore invented the Simputer, a simple and cheap hand-held computer. But as civil servants, the computer scientists by law could not commercialize their invention. “I had no choice but to resign,” says Manohar, who is now chief of intellectual property and strategy at Geodesic Limited, a telecom firm that bought the company Manohar and his colleagues founded after leaving IISc in 2001.

Indian scientists will no longer be forced to make such a stark choice. On 24 February, the Department of Scientific and Industrial Research issued regulations that permit researchers at government-funded institutions to hold equity stakes in scientific enterprises and spinoff companies. The “historic decision,” says Science Minister Kapil Sibal, will “unleash the latent entrepreneurial potential of Indian scientists.”

The policy shift is expected to have a profound impact in India: Some 400,000 scientists, about three-quarters of the scientific work force, are employed at public institutions. By bringing India in line with the United States and other Western nations, the new rules should create an attractive environment for talented expatriate scholars to return to India, says Samir Brahmachari, director general of the Council of Scientific and Industrial Research in New Delhi who helped shepherd the regulation through 18 ministries over 18 months.
The new rules also permit research institutes to hold equity stakes in commercial enterprises. To facilitate this process, the government will encourage the lateral mobility of researchers between institutes and industry. “Cross-fertilization between the academics and industry is very much necessary,” says Sibal. Although the regulations came too late for Manohar to keep his post at IISc, he applauds what he sees as a long-overdue change. “Scientists need the freedom to flourish, and now they have gotten it,” he says.

Perhaps capitalism will finally come to Indian science.

6 Mar, 2009 | 3 Comments

Year of Charles

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Two hundred years ago this day, Charles Darwin was born. The vision of life that he created and expounded on transformed humanity’s perception of its place in the universe. After Copernicus’s great heliocentric discovery, it was Darwin’s exposition of evolution and natural selection that usurped human beings from their favoured place at the center of the universe. But far from trivializing them, it taught them about the vastness and value of life, underscored the great web of interactions that they are a part of, and reinforced their place as both actor and spectator in the grand ball game of the cosmos. Not only as a guiding scientific principle but as an all-encompassing element of understanding our place in the world, evolution through natural selection has become the dominant idea of our time. As the eminent biologist Theodosius Dobzhansky put it quite simply, nothing in biology makes sense except in the light of evolution. Evolution is a fact. Natural selection is a theory that is now as good as a fact. Both evolution and natural selection happen. And both of them owe their exalted place in our consciousness to a quiet, gentle and brilliant Englishman.

Today, it is gratifying and redeeming to know how right Darwin was and how much his theory has been built upon, and extremely painful to know how those who wield religious power threaten to undermine the value of his and others’ careful and patient discoveries. Especially in the United States, evolution has become a bizarre battleground of extreme opinions and mudslinging, a development that seems to be in step with the tradition of coloring any and every issue with a political hue. In this country, it seems today that you can hardly utter an opinion without attaching a label to it. You cannot simply have an opinion or take a position; it has to be Republican, Democrat, Libertarian, Neo-Conservative, Socialist or Atheist. if none of these, it has to be Centrist then.

When it comes to evolution, attaching the label of “Darwinism” has completely obscured the importance and power of the theory of natural selection. On one hand, those who defend the label sometimes make it sound as if Darwin was the beginning and end of everything to do with evolution. On the other hand, those who oppose the label make it sound like all of us who “believe” in evolution and natural selection have formed a cult and get together every weekend to worship some Darwin idol.

Unfortunately both these positions and more obfuscate the life and times of the man himself, a simple, gentle and brilliant soul who was born two hundred years ago, who painfully struggled with reconciling his view of the world with religious ones and who thought it right to cast his religious views aside in the end for the simple reason that his findings agreed with the evidence while the others did not. Darwin Day should be a chance to celebrate the life of this remarkable individual, free from the burdens of religion and political context that his theory is embroiled in today. Because so much has been said and written about Darwin already, this will be more of a personal and selective exposition. Since I am a lover of both Darwin and books, I will tell my short story of Darwin as I discovered him through books.

When you read about his life for the first time, Charles Darwin does not evoke the label of “genius”, and this superficial incongruence continues to beguile and amaze. His famous later photographs show a bearded face with deeply set eyes. His look is gloomy and boring and is not one which elicits the image of a sparkling world-changing intellect and incendiary revolutionary taking on an establishment steeped in dogma. Darwin was not a prodigy by the standards of William Hamilton or Lord Kelvin, nor did he particularly excel in school and college. A Cambridge man who studied religion, Darwin had one overriding quality; curiosity about the natural world. He consummately nurtured this quality in field trips and excursions; as one famous story goes, Darwin once held two beetles in two hands and popped one of them in his mouth so that he could have one hand free for catching a third very attractive one which he had just noticed. He indulged in these interests much to the chagrin of his father who once said that he would not amount to anything and that he would be a disgrace to his family.

As is well-known, Darwin’s story really begins with his voyage of the Beagle when he accepted a position on a ship whose melancholic, manic-depressive captain Robert Fitzroy wanted an educated, cultured man to keep him company on a long and dangerous voyage that circumnavigated the world. For Darwin, this was a golden chance to observe and document the world’s flora and fauna. One of the best illustrated expositions of Darwin’s voyage is in Alan Moorhead’s “The Voyage of the Beagle” which is beautifully illustrated with original drawings of the wondrous plants, animals and geological formations that Darwin saw on the voyage. Darwin’s own account of the voyage is characteristically detailed and modest and depicts a man enthralled by the beauty of the natural world around him. By the time he set off on his historic journey, young Charles had already been inspired by his teacher Charles Lyell’s book on geology that talked about geological changes over time. As is also rather well-known, evolutionary ideas had been in the air for quite some time by then, and Darwin certainly was not the first to note the rather simple fact that organisms seem to have changed over time, a view that nonetheless and naturally flew in the face of religious dogma. Most importantly, Darwin was well-aware of Thomas Malthus’s famous argument about the proliferation of species exceeding the resources available to them, an idea whose logical extension would be to conjecture a kind of competition between species and individuals for finite resources. The “struggle for survival”, taught today in school textbooks, a phrase that became much maligned later, nonetheless would have been obvious to a man as intelligent and perceptive as Darwin when he set off on his voyage.

Biology, unlike mathematics or physics, is a science more akin to astronomy that relies on extensive tabulation and observation. Unlike a theoretical physicist, a biologist would be hard-pressed to divine truths about the world by armchair speculation. Thus, painstakingly collecting and classifying natural flora and fauna and making sense of its similarities and differences is a sine qua non of the biological sciences. Fortunately, Darwin was the right man in the right place; endowed with a naturally curious mind with an excellent memory for assimilation and integration, he was also unique and fortunate to embark on a worldwide voyage that would enable him to put his outstanding faculties to optimum use. Everywhere he went, he recorded meticulous details of geology, biology, anthropology and culture. His observation of earthquakes and rock formations in South America and his finding of fossils of giant mammals lend credence to his beliefs about organisms being born and getting extinguished by sometimes violent physical and planetary change. His observation of the Pacific and Atlantic islanders and their peculiar customs underscored the diversity of human life along with other life in his mind. But perhaps his best known and most important stop came after several months of traveling, when the ship left Ecuador to dock at the Galapagos Islands.

Again, much has been written about the Galapagos Islands and Darwin’s Finches. The truth is more subtle, sometimes simpler and more interesting than what it is made out to be. Darwin’s had mistook his famous finches for other species of birds. It was only after coming back that his friend, the ornithologist John Gould, helped him to identify their correct lineage. But finches or not, the birds and the islands provided Darwin with a unique opportunity to study what we now know as natural selection. The islands were separated from each other by relatively small distances and yet differed significantly in their geography and flora and fauna. On each island, Darwin observed similar plants and animals that were yet distinct from each other. As in other places, he also observed that species seemed to be adapted to their environment. Geographic isolation and speciation were prominent on those hot, sweaty and incredibly diverse land masses.

After five years of exhaustive documentation and sailing, Darwin finally returned home for good, much changed both in physical appearance and belief. His following life has been the subject of much psychological speculation since he settled down with his cousin Emma and never ever left the British Isles again. He also seemed to have been stricken with what today is noted by many authors as a kind of psychosomatic illness because of which he was constantly ill with abdominal and other kinds of pains. After living in London for some time, Darwin retired to Down’s House in Kent where he peacefully lived the rest of his life with a kind and loving wife, playing with his children, taking walks along the path at the back of his house named the “Sandwalk”, corresponding with intellectuals around the world and constantly interrupting his research with salutary visits to spas and resorts for “natural” treatments that were sometimes of dubious value.

But peaceful as his life was, psychologically Charles Darwin was fomenting a maelstrom of revolution that was to have earth-shaking implications. Another fact that is frequently emphasized is his hesitation to not publish his ideas for another twenty five years in the form of the famous “The Origin of Species”. Darwin was planning to write it for a while, but was finally jolted into writing it when he received a letter from an obscure young naturalist named Alfred Russell Wallace who was living a hard life of science and natural history exploration in Indonesia. Wallace had read some of Mr. Darwin’s papers and manuscripts and had been struck by the similarity of his ideas to his own. Would Mr. Darwin comment on them? Darwin finally realized that he had to act to prevent getting scooped but characteristically credited Wallace in his published work.

In my mind however, Darwin’s procrastination and its story sounds much simpler than the mystique and psychological speculation that sometimes envelops it. As we noted earlier, Darwin was a highly trained biologist and scientist of the first caliber. He knew that he would have to exhaustively document and classify the windfall of creatures, plant and rock specimens that he had collected on his voyage. Apart from thinking and writing about his Beagle collections, Darwin also maintained an astonishingly comprehensive and detailed research program on marine invertebrates and barnacles. More tellingly, he did experiments to find out if seeds are viable even when dispersed over long distances over salt-water. He visited gardens and zoos, and quizzed pigeon breeders about their profession. Much of this was in preparation for the grand act that was to follow. In case of the barnacles and marine creatures, Darwin’s research was second to none. He published several extremely detailed books on the minutiae of these organisms; some of these had titles which would have put anyone to sleep. And yet the level of details in them reflects the extraordinary patience, power of observation and meticulous hard work that characterized the man, characteristics crucial for developing the theory of natural selection. Darwin was also very fortunate to have had several friends and colleagues who were experts in areas that he was not, who helped him classify and name all the material. Foremost among his correspondents were Charles Lyell and Joseph Hooker to whom he confided not just his scientific questions but also his emerging convictions about the interconnections and implications that were emerging from his research and writing. Also as noted above, John Gould accomplished the crucial task of reminding Darwin that his Galapagos birds were finches. With help from these collaborators and his own studies and thoughts on his observations, thoughts that filled literally dozens of rough drafts, scribblings and private diaries, Darwin finally began to glimpse the formation of a revolutionary chain of thought in his mind.

But Darwin did not rush forth to announce his ideas to the world, again for reasons that are obvious; Victorian England was a hotbed of controversy between science and religion, with many distinguished and famous scientists there and in other countries not just fervently believing in God, but writing elegant tomes that sought a supernatural explanation for the astounding diversity of life around us. Cambridge was filled with intellectuals who sought a rational framework for God’s intervention. Darwin would have been quite aware of these controversies. Even though Darwin’s grandfather himself had once propounded an evolutionary view, Darwin was finely attuned to the sensitive religious and social debate around him. Not only did he not want to upset this delicate intellectual and spiritual balance and get labeled as a crackpot, but he himself had not started his voyage as a complete non-believer. One can imagine the torment that he must have faced in those early days, when the evidence pointed to facts that flew in the face of deeply-held or familiar religious beliefs. One of the factors that dispossessed Darwin of his religious beliefs was the stark contradiction between the observation of a cruel and ruthless race for survival that he had often witnessed first hand, and the image of an all-knowing and benign God who kindly reigned over his creations. As the evidence grew to suggest a relationships between species and their evolution by the forces of natural selection that preserved beneficial characteristics, Darwin could no longer sustain two diametrically opposite viewpoints in his mind.

Opponents of evolution who want to battle the paradigm not from a scientific viewpoint (because they can’t) but from a political one frequently raise a smokescreen and proclaim that evolution itself is too complex to be understood. The charlatans who propagate intelligent design further attest to the biochemical complexity of life and then simply give up and say that only an omniscient God (admittedly more complex than the systems whose complexity they are questioning) could have created such intricate beauty. The concept of a struggle for survival has also been hijacked by these armies of God who proclaim that it is this philosophy that would make evolution responsible for genocide, fascism and the worst excesses of humanity. This is a deeply hurtful insult to natural selection and evolution as only the most dogmatic believers can deliver. Stripped down to its essentials, the “theory” of evolution can be understood by any school child.

1. Organisms and species are ruthlessly engaged in a constant struggle for survival in which they compete for finite resources in a changing environment.

2. In this struggle, those individuals who are more adapted to the environment, no matter how slightly, win over other less adapted individuals and produce more offspring.

3. Since the slight adaptations are passed down to the offspring, the offspring are guaranteed to preserve these features and therefore are in a position to survive and multiply more fruitfully.

4. Such constant advantageous adaptive changes gradually build up and, aided by geological and geographical factors, lead to the emergence of new species

In my mind, the beauty of evolution and natural selection is two-fold; firstly, as Darwin emphasized, the slightest adaptation leads to a reproductive advantage. Such slight adaptations are often subtle and therefore sometimes can sow confusion regarding their existence. But the confusion should be ameliorated by the second even more striking fact; that once a slight adaptation exists, it is guaranteed to be passed on to the offspring. As Gregor Mendel hammered the mechanism for natural selection in place a few years after Darwin with his discovery of genetic inheritance, it became clear that not every one of the offspring may acquire the adaptation. The exact pattern may be complex. But even if some of the offspring acquire it, the adaptation is then guaranteed to confer reproductive fitness and will be passed on. This fact should demolish a belief that even serious students of evolution and certainly laymen have in the beginning; that there is something very uncertain about evolution, that it depends too much on “chance”. The key to circumvent these misgivings is to realise the above fact, that while adaptations (later attributed to mutations) may arise by chance, once they arise, their proliferation into future generations is virtually certain. Natural selection will ensure it. That in my mind is perhaps Darwin’s greatest achievement; he finally found a mechanism for evolution that guarantees its existence and progress. As for the struggle for survival, it certainly does not mean that it results in non-cooperation and purging of other individuals. As examples in the living world now document more than convincingly, the best reproductive fitness can indeed come about through altruistic leanings and cooperative behaviour.

Every one of these factors and facts was detailed and explained by Darwin in “The Origin of Species”, one of the very few original works of science which remain accessible to the layman and which contained truths that have not needed to be modified in their basic essence even after a hundred and fifty years. It was readable even when I picked it up as a callow young college student. No one who approaches it with an open mind can fail to be taken with its simplicity, elegance and beauty. Its essential arguments are as true today as they were then. One of the most extraordinary things about Darwin and something that continues to stupefy is how right the man was even when he lacked almost all the modern tools that have since reinforced basic evolutionary ideas. As one of Darwin’s intellectual descendants, the great biologist E O Wilson says, it is frustrating for a modern biologist to discover an evolutionary idea through his work, and then go back a hundred and fifty years and discover that the great man had hinted at it in his book.

And yet, as Darwin himself would have acknowledged, there is much in the book that needed to be modified, there was much that did not explain. Darwin had no inkling of genes and molecular biology. The exact mechanism of passing on adapted characteristics was unknown. Major fossils of primates and humanoid ancestors had yet to be discovered. Quite importantly, random genetic drift which is completely different from natural selection was later discovered as another process operating in evolution. The development of viral and bacterial resistance in causing diseases like AIDS finally brought evolution to the discomfort of the masses. It was only through the work of several evolutionary biologists and geneticists that Darwin finally became seamless integrated with the understanding of life in the middle twentieth century. But in the absence of all these developments, it is perhaps even more remarkable how many of Darwin’s ideas still ring true.

There is another factor that shines through in “The Origin”; Darwin’s remarkable modesty. One would have to search very hard in history to find a scientist who was both as great and as modest. Newton may yet be the greatest scientist in history, but he was nothing if not a petty, bitter and difficult man. Darwin in contrast was a symbol of kindly disposition. He doted on his children and told them stories. He loved and respected his wife even though their religious views gradually grew more distance. His written correspondence with her was voluminous and fond. His correspondence with his collaborators, even those who disagreed, was cordial and decent. Never one for contentious public debates, he let his “bulldog” Thomas Henry Huxley fight his battles; one of them with Bishop Samuel Wilberforce ended in a famous showdown when the Bishop inquired whether it was through his father or mother that Huxley had descended from an ape, and Huxley countered that he would rather descend from an ape than from the Bishop. Darwin stayed away from these delicious confrontations; as far as he was concerned, his magisterial work was done and he had no need for public glory.To the end of his life, this kind and gentle man remained a wellspring of modest and unassuming wonder. His sympathetic, humane and sweet personality continues to delight, amaze and inspire reverence to this day.

In the later stages of his life, Darwin became what he himself labeled as an agnostic but what we today would probably call an atheist. His research into the progression of life and the ruthless struggle that it engenders made it impossible for him to justify a belief in a paternal and loving deity. He was also disillusioned by popular conceptions of hell as a place where non-believers go; Darwin’s father was a non-believer and yet a good doctor who treated and helped hundreds of human beings. Darwin simply could not accept that a man as kind as his father would go to hell simply for not believing in a version of morality, creation and life trotted out in a holy book. Probably the last straw that convinced Darwin of the absurdity of blind faith was the untimely death of his young daughter Annie who was his favourite among all the children. According to some accounts, after this happened, Darwin stopped even his cursory Sunday trips to church and was satisfied to take a walk around it while not at all minding his wife and children’s desire to worship inside. The second fact is also in tune with Darwin’s kind disposition; he admittedly had no problem reconciling the personal beliefs of other people with his conviction about their falsity. Darwin’s tolerance of people’s personal faith and his unwillingness to let his own work interfere in his personal life and friendships is instructive; to the end he supported his local parish and was close friends with a cleric, the Reverend John Innes. Darwin’s example should keep reminding us that it is actually possible to sustain close human bonds while having radically different beliefs, even when one of these is distinctly true while the other one is fantasy. Nurturing these close bonds with radical scientific ideas that would change the world for ever, Charles Darwin died on April 19, 1882, a content and intellectually satisfied man.

To follow, nourish and sustain his legacy is our responsibility. In the end, evolution and Darwin are not only about scientific discovery and practical tools arising from them, but about a quest to understand who we are. Religions try to do this too, but they seem to satisfied with explanations for which there is no palpable evidence and which seem to be often contradictory and divisive. It is far better to imbibe ourselves with explanations that come from ceaseless exploration and constant struggle; the very means that constitute these explorations are then much more alluring and quietly fulfilling than any number of divergent fantasies that can only promise false comfort. And these means promise us a far more humbling and yet grand picture of our place in this world. Especially in today’s age when the forces of unreason threaten to undermine the importance of all the beautiful simplicity in the fabric of life that Darwin and his descendants have unearthed, we owe it to Charles Darwin to continue to be amazed at the delightful wonder of the cosmos and life. We owe it to the countless shapes and forms of life around us with whom we form a profoundly deep and unspoken connection. And we owe it to each other and our children and grandchildren to keep rationality, constructive skepticism, freedom and questioning alive.

LITERATURE ON DARWIN:

I don’t often write about Darwin and evolution here for a simple reason; there are scores of truly excellent authors and now bloggers who pen eloquent thoughts about these subjects. There is enough literature on Darwin and evolution to fill up an encyclopedia of its own. His original work as stated above is still very readable. Every aspect of his life and work; the scientific, the psychological, the social, the political and the personal has been exhaustively analyzed. I have certainly not sampled more than a fraction of this wealth of knowledge, but based on my long interest in Darwin and selected readings, I can recommend the following.

For what it’s worth, if you want to have the best overview of Darwin’s life after he came home from his voyage on the Beagle, I think nothing beats the elegance of language and wit of David Quammen’s “The Reluctant Mr. Darwin”. Quammen has exhaustively researched Darwin’s post-Beagle life and work, and no one I have come across tells the story with such articulate enthusiasm, fondness and attention to detail in a modest sized book.

Janet Browne’s magisterial biography of Darwin is definitely worth a look if you want to get all the details of his life. Browne pays more attention to the man than the science, but her work is considered the authoritative work, and there are nuggets of eloquence in it.

As a student in high school, I was inspired by Alan Moorehead’s “The Voyage of the Beagle” noted above which combines an account of Darwin’s life and voyage with beautiful and full page illustrations.

Geting to evolution now, there’s an even bigger plethora of writings. Several books have captured my attention in the last many years. I don’t need to extol the great value of any (and indeed, all) of Richard Dawkins’ books. If you ask me which ones I like best, I would suggest “The Selfish Gene”, “The Extended Phenotype”, “Climbing Mount Improbable” and “The Blind Watchmaker”. For a journey into our ancestral history, Dawkins’ strikingly illustrated “The Ancestor’s Tale” is excellent. Speaking of ancestral history, a wonderful book published recently by Neil Shubin, “Our Inner Fish”, charts a fascinating course that details how our body parts come from older body parts that were present in ancient organisms. Shubin talks for instance about how hernias are an evolutionary remnant. This is one of the best books around for understanding our evolutionary history. Another great general introduction to evolution is Carl Zimmer’s “Evolution”

No biologist- not even Dawkins- has had the kind of enthralling command over the English language as Stephen Jay Gould. We lost a global treasure when Gould died at age sixty. His books are relatively difficult to read and for good reason. But with a little effort, they provide the most astonishing synthesis of biology, history, culture and linguistic exposition that you can ever come across. And all of them are meticulously researched. Out of all these, I personally would recommend “Wonderful Life” and “The Mismeasure of Man”, and if you want to challenge yourself with a really difficult unedited original manuscript written just before he died, “The Hedgehog, the Fox and The Magister’s Pox”. In general, pick up any Gould book and you would have access to an extraordinary writer and mind. His collections of essays are also outstanding.

I don’t want to really write about books which criticize creationism, because for me it’s extremely painful to see how and why such a bizarre fallback to antiquated ideas keeps rearing its head in this country. But if you want to read one book about the controversy that rips apart intelligent design proponents’ arguments, read Ken Miller’s “Finding Darwin’s God” which makes mincemeat out of the usual “arguments from complexity” trotted out by creationists which are actually “arguments from personal incredulity”. He also has a new book which covers the 2005 Dover Trial. I have only browsed it but it seems to be equally good read. What makes Miller intriguing and puzzling is that he is also an ardent Christian.

There are others, but I will end with recommending a book published less than a month back which is getting great reviews and which I am currently reading- Jerry Coyne’s “Why Evolution is True”. The simple title says everything that is to be said about evolution.

12 Feb, 2009 | 1 Comment

Black Swans, Models and Reality

And Nassim Nicholas Taleb

Nassim Nicholas Taleb’s two books, Fooled by Randomness and The Black Swan, are undoubtedly two of the most provocative and interesting books I have come across in my life. While I am still ploughing through them, especially the second book, The Black Swan, has made waves and is apparently now (as usual in retrospect) cited as required reading on Wall Street. The books are highly eclectic and traverse a remarkably diverse landscape that includes psychology, finance, evolution, mathematics, philosophy, history, sociology, economics and many other disciplines. It would be impossible to review them in a limited space. But if I wanted to capture their essence, it would be by saying that Taleb alerts readers to the patterns that human beings see in the randomness inherent in the world, and the models, both mental and practical, that they build to account for this randomness.

Since his book came out, Taleb has become a mini celebrity and has been interviewed on Charlie Rose and Stephen Colbert. His books sell in large numbers in the far corners of the world. The reason why Taleb has suddenly become such a big deal is in part because he at least philosophically seems to have predicted the financial crisis of 2008 which occured two years after The Black Swan came out. One of the firms he advised turned out a profit of more than a 100 million dollars in 2008 when others were close to losing the clothes on their back. Taleb now has emerged as one of the most profound soothsayers and philosophers of our times, a “scholar of randomness”, although his message seems to be more modest; models are not designed to account for rare or Black Swan events which may have monumental impact. The analogy deals with the assured belief that people had in the past about all swans being white. When the continent of Australia was discovered and black swans were observed in flocks (a fact which my dad who is currently in Australia corroborated), there was a paradigm shift. Similarly a model, any model, that is built on the basis of White Swan events will fail to foresee Black Swans.

Unfortunately as Taleb explains, it’s the Black Swans that dictate the direction that the world proceeds in. It’s the rare event that is the watershed, the event that changes everything. And it’s exactly the rare event that models don’t encapsulate. And this fact spells their doom.

To augment his theory, Taleb cites many Black Swan events from history and politics. For example if you lived in 1913, you would hardly foresee the gargantuan event of 1914 which would forever change the world. If you lived in 1988, you would scarcely comprehend the epoch-making events of 1989. One of my favourite parts of the book concerns The Turkey Analogy. Imagine you are a turkey who is being constantly fed by the butcher 364 days a year. You are happy, you know the butcher loves you, your economics and accounts departments are happy, they start to think this is the way of the world for you. Now comes the 365th day. You die. Just when your expectations levels reach their most optimistic, your destiny reaches its lowest point. But right before day 365 on day 364, you were 100% certain that you had a lifetime of bountiful happiness ahead of you. Day 365 was exactly contrary to the expectations of your finance department. Day 365 was the Black Swan which you did not anticipate. And yet it was that single Black Swan day that proved fateful for you, and not the earlier 364 days of well-fed bliss. According to Taleb, this is what most of us and especially the derivatives wizards on Wall Street are- happy, deluded turkeys.

In any case, one of the most important discussions in Taleb’s books concerns the fallacy of model building. He claims that the models that Wall Streets used, the models that raked in billions and Nobel Prizes, were fundamentally flawed, in part because they were not built to accommodate Black Swans. That made me think about models in science and how they relate to other models. Science has always progressed through model building; some models such as relativity or quantum theory have come as close to modeling “reality” as anything else, in spite of us still not understanding what they actually mean. As in the case of other models, more data helps to validate or reject the model hypothesis. However, it is dangerous to use the model if you are not sure how it works. In some ways we are always playing a high-risk game. In Taleb’s mind, the derivatives and other frameworks that the genius quants used were like a plane whose workings they did not understand. When you build a plane, you should always keep the possibility of a storm, a rare event, in mind. Aerospace engineers do this. The quants apparently did not.

Since my own field crucially involves building and investigating models, I can vouch for the fact that model building is always a tricky exercise and can always become seductive and misleading. We all, irrespective of the fields we work in, want models that will help us to predict the next important data point. And yet models are always elusive, always leave us with an uncomfortable, or falsely comfortable feeling, that our thing is the real thing. Several factors contribute to this problem, not to mention an inadequate exposure to statistics courses in college. But two things for me have especially stood out as common flaws in any kinds of models.

1. Correlation does not mean causation:
I believe that children should be taught to recite this 10 times in the evening the way they are taught to recite multiplication tables. Mistaking correlation for causation is the one of the biggest mistakes that all of us all too commonly make. This fallacy pervades our thinking in science, philosophy, politics, and every single day we see it running rampant in our daily conversations, in our sermons to our children, and in the newspaper articles. Even if many of us are aware of it in theory, we cannot avoid it in practice. The correlation vs causation problem is so omnipresent that it keeps serving us generous doses of what may be completely unreal but what we would construe as reality. There are several examples of mistaking correlation for causation; for instance the correlation between the number of breeding storks in Germany and the number of new births might readily provide credence to children’s beliefs. Mistake correlation with causation and you are off on a trajectory orthogonal to that of reality.

But let’s face one big truth about models that attempt to correlate and explain; most of them in fact are not designed to represent “reality”. In fact models don’t care as much about causation as they do about accurate correlation and prediction. While this may sound like shooting ourselves in the foot, it often saves us a lot of time, not to mention philosophizing. We use models not because they are “real” but because they work. This is a very important point, and I believe that most human beings who mistake correlation for causation nevertheless keep on operating in everyday life under the fallacy because it saves them time and allows them to make quick decisions, even if many of them are wrong. Part of this gut reaction probably stems from our evolutionary history in which our mind was essentially programmed to seek patterns. This pattern finding quality would have been indispensable in our cave-dwelling days; it’s probably safe to always assume that a dark forest means the presence of wild creatures who can easily attack and eat you. People who paused to take their time and tried to distinguish between correlation and causation may well have been weeded out of the gene pool. However, the quality is less than useful in an increasingly information-driven complex world full of quick multitasking, money management and unconscious data processing. In such a world, those who will carefully reflect on the fallacy and use it to temper their decisions might seem slow, but might prosper more in the long term.

2. The Problem of Overfitting:
Models can always fit data if arbitrary changes are made to their parameters and enough number of parameters are used. As a friend once quoted the great mathematician John Von Neumann in a past comments thread, “Give me five parameters and I can fit an elephant to a curve. Give me six and I can make him dance”. This is overfitting. In overfitting, models can do a stellar job of accounting for known data, but miserably fail to predict new data which is after all what they should be able to do. Modelers are frequently misled by high correlation coefficients that may not mean much and may well lead them down the wrong path. There are several methods to avoid overfitting, none of which however always works. One way is to leave out some of the data used for fitting the model and look at the resulting modified fit. Another one is to do a careful study and actually determine the minimal number of parameters necessary to fit the model to the data, and no more. Bishop Occam’s Razor is quite handy in such circumstances. Statistics is another, a simple remedy being to try to assert if whatever result you are getting is due to chance alone (p values, F tests and all that).

So how can all this affect our perception of Black Swans, of rare events that shake the whole foundation? Well, let’s say if I want to model the digestive process in my stomach and assume that food in my stomach is digested by little dwarves shuttling food to one another, breaking it down with hammers and chisels, and finally passing it on to goblins who open the gates to my blood supply and let it in. While this model might sound completely nonsensical, it could make perfect sense if I tweak the assumptions to explain observed facts. In fact religious people use exactly the same strategy; invoke assumptions to explain known facts. If facts don’t follow from assumptions, simply modify the assumptions to explain the new facts. Using these potentially ad infinitum set of assumptions, the dwarf-goblin model I constructed for digestion could work perfectly. One of the most important lessons I learnt from my advisor in graduate school is to always question the assumptions in any study. If the assumptions themselves are suspect, then all the conclusions that follow from them may be necessarily wrong, no matter how elegant or logical the train of thought sounds. In all of the above scenarios, we have neglected the one annoying factor that could help to disillusion us of the entire edifice- evidence. Hard facts found from observation, interrogation and experiment. That is in fact what prevents science and in fact most of everyday life from going down the same road as religion, and that is why anything goes in religion and therefore eventually nothing goes. In science and most of everyday life, one can do experiments to test assumptions. These experiments will then shed light on the ground reality of assumptions. Cut open a stomach, and my fantasy of dwarves and goblins playing with each other will come crumbling down in an instant. Needless to say, because of its pronounced emphasis on and indeed essential adherence to assumptions that cannot be tested, religion is the ultimate bad model.

And now we should understand that this is precisely the reason why models that don’t model reality carry the dangerous liability of not being able to predict monumental rare events. Because let’s say you have a model that has simply ignored a real factor operative under the circumstances. The model works pretty well when the contribution of that factor is marginal. But now, suddenly, the marginal factor becomes a factor of overriding importance. Since we don’t even know that the factor exists, it is as much of an outlier in our model as anything can ever be. We fail to predict it. And if it is a Black Swan, it may then negate the importance of everything that we apparently predicted well before. We can forget about prediction; at this stage we will be left with our head spinning, completely clueless about what went wrong because of our obliviousness to a factor whose existence we are not aware of. We won’t even be able to do retrospective explanation.

But finally, as much as we know these pitfalls, in practice we are much less careful since we want to get practical, applicable results and could care less if our model represented conditions on Mars. The bottom line is, all of us are playing a game when we use models, in science, finance or any other discipline. As in other games, we are fine as long as we win. One of Taleb’s messages is that we should at least be able to assess the impact of losing, something which he asserts the quants have significantly underestimated. If the impact is a complete game changer, then we should know when to get out of the game. We tend to forget that the models that we have don’t represent reality. We use them because they work, and it’s the reality of utility that produces the illusion of reality. Slightly modifying a quote by the great Pablo, models are the lies that help us to conceal the truth.

Note: The short Charlie Rose interview with Taleb is worth watching:

5 Feb, 2009 | 2 Comments

The Wrath of Lithium

If you are a chemist, there’s some things you would rather avoid. Making quantities of nitrogen triiodide is something that’s strongly discouraged for example, as I can tell from my own experience. When I was a bathroom chemist during my middle school days, I used to experience oodles of glee in dissolving my mother’s copper-containing safety pins in nitric acid and watching the resulting wisps of nitrogen dioxide float away in the small unventilated room with a single window. I kept up this activity for a long time, primarily because I wanted to make laughing gas- nitrous oxide. The trick as it turned out was very simple; use dilute instead of concentrated nitric acid with copper.

It was when I entered graduate school that I was startled to read in the Merck Index about the deadly properties of nitrogen dioxide. Apparently the gas shows no immediate effects, but one fine morning you can just fall to the ground and die of edema. In addition it can initially numb your nose, precluding further detection. Maybe the insidious brute has already shaved off a few years off my life. I won’t really know. The point is that lab work in chemistry is a deadly serious activity, even though its routine nature gradually makes it seem rather casual. It was dumb luck that my gungho bathroom explorations did not at least take out an eye.

A coterie of methods for careful use of lab reagents have developed over the years to handle such volatile beasts. One such method consists of carefully drawing out a highly toxic or flammable liquid from a bottle using a syringe whose needle is inserted into the bottle through an airtight rubber septum. Before you insert the needle, you insert another needle connected to a tube that delivers an inert gas- usually nitrogen or argon- through a cylinder. As the bottle fills up with this gas, positive pressure is developed that makes it easier for the liquid to enter your syringe.

But even this well-trodden technique used by hundreds of students can results in a disaster, as was tragically demonstrated a few days ago by the death of a 22-year old lab assistant who was trying to suction some tertiary-butyl lithium into a syringe. In the list of “things that you won’t work with”, this would probably figure high. It instantaneously ignites upon contact with air and almost nothing can put out the resulting fire. Unfortunately it’s a rather useful reagent that can do things that other regents won’t accomplish. Nobody knows what quantity of this hideous substance the assistant was siphoning out. She had even worn the all-important safety goggles and gloves, although not a lab coat. Somehow the lithium squirted out onto her arms and hands and instantly caught fire. Her sweater caught fire too. She did manage to get to a shower, but after two agonizing weeks, she is now dead. I think it must have been her sweater that spelt her doom and not the lithium itself.

But this incident demonstrates that no matter how much scientists might jest about lab procedures, they should please take them very seriously. The loss of a single student with all her life ahead of her is not remotely worth all the merry tales about daredevil reagent handling.

Link: Mitch

21 Jan, 2009 | 2 Comments
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