Degrees of knowledge

The recent announcement of the winners for the Nobel Prize in Physics reminded me of this post on the status of "junk" DNA where the author obliquely compares economics to genetics and physics:

Economists are sometimes chided for disagreeing about the importance of such basic questions as the relative role of aggregate demand and aggregate supply but physicists can’t even find most of the universe and microbiologists don’t agree on whether the human genome is 80% functional or 80% junk. Is disagreement a result of knaves and fools? Sometimes, but more often disagreement is just the way the invisible hand of science works.

In one of my more sensitive (i.e. irritable) moments I leaped to the conclusion that the author was tying to put economics on the same pedestal as genetics and physics. After all, if physics and genetics can only know 5% and 20% respectively of their fields are these fields any more scientific than economics?

Pshaw, and I am probably arguing against a straw man here - but since I'm getting old and grouchy I'll just go ahead and pile into the straw man. Economics is nowhere near physics and in physics the proof is in its ability to predict the existence and characteristics of particles at the quantum level. At a more aggregate level consider Einstein's prediction on the orbit of Mercury based on GR. There is NOTHING even close in economics that can make any statement with such quantitative accuracy. At the most economics can say that on one hand stock prices will go up or on the other it might go down and if he had three hands he might even through in unchanged as another option. Macroeconomics has vacillated from one fad to another (New Keynesian, classical revival, real business cycles -- you name it) without ever coming close to even having a decent understanding of the economy.* If you don't believe this statement then ask yourself whether an increase in government spending will increase aggregate demand and what are its quantitative effects.

The debate on junk DNA will continue as will the definition of its "function" but one measure of science is the amount of knowledge that is gained as scientists continue to peel back the layers. No doubt in physics, the question already being studied is "what generates this Higgs field" whereas in economics, the process is more like "er, er, er, hmm... on one hand...".

*One possible advancement in economics is in auctions and the evidence is in the success of the FTC auction of the spectrum. However, my reading of the implementation of the auctions in the US and UK lead me to conclude that at best it is still an inexact science. (After all, we aren't dealing with particles, we're dealing with people, which is the famous economists' excuse for knowing very little.)

Origins of us?

I had the opportunity to read Delta Willis’ Hominid Gang (now out-of-print) as well as Don Johanson’s Lucy: The Beginnings of Humankind a few months ago. Without a doubt Johanson’s book is more readable and I felt that Willis’ book was written as a sort of a obtuse rebuttal to Johanson although if it were a rebuttal it wasn’t clear what it was. Despite claiming to be a book about the group of Kenyans (the so-called Hominid Gang) that were instrumental in unearthing archaeological finds in Koobi Fora, this book was more about Richard Leakey and the Leakeys in general.

It is clear that there was some tension between Johanson and the Leakeys regarding Lucy and possibly the Turkana Boy but Johanson’s book does a better job of explaining humanity’s time line and the search for the missing link. Willis and by extension the Leakeys seem to have some doubts about the direction of the direction of this search and whether some of the finds in the past have been been a distinct line in humankind’s descent (or ascent, however you prefer to look at it). Willis’ book does a better job of showing the ambiguity in archaeology/anthropology in contrast to Johanson’s more authoritative tone - the lumpers versus splitters debate.

The recent news about Turkana Boy (if I am reading it correctly) seems to have vindicated the Leakeys’ point of view:

Researchers studying fossils from northern Kenya have identified a new species of human that lived two million years ago....

The finds back the view that a skull found in 1972 is of a separate species of human, known as Homo rudolfensis....

For a long time the oldest known human ancestor was thought to be a primitive species, dating back 1.8 million years ago called Homo erectus. They had small heads, prominent brows and stood upright.

But 50 years ago, researchers discovered an even older and more primitive species of human called Homo habilis that may have coexisted with H. erectus. Now it seems H. rudolfensis was around too and raises the distinct possibility that many other species of human also existed at the time.

This find is the latest in a growing body of evidence that challenges the view that our species evolved in a smooth linear progression from our primate ancestors.

Instead, according to Dr Meave Leakey of the Turkana Basin Institute in Nairobi, who led the research the find shows that there was a diversity early on in the evolution of our species.
"Our past was a diverse past," she told BBC News, "our species was evolving in the same way that other species of animals evolved. There was nothing unique about us until we began to make sophisticated stone tools."

The research was published in Nature. Image from BBC.

FTL travel?

The discovery that particles may be traveling faster than the speed of light is still preliminary. But it cannot stop the imagination. So, spin up the FTL drives, folks, we hope to go on a magic carpet ride.

Dark matter theory: RIP?

BBC reports:
Scientists' predictions about the mysterious dark matter purported to make up most of the mass of the Universe may have to be revised.

Research on dwarf galaxies suggests they cannot form in the way they do if dark matter exists in the form that the most common model requires it to.

That may mean that the Large Hadron Collider will not be able to spot it.
…
Scientists' best ideas for the formation and structure of the Universe form what is called the "cosmological standard model", or lambda-CDM - which predicts elementary particles in the form of cold dark matter (CDM).
Prof Carlos Frenk at Durham University, working with … the Virgo Consortium has created computer simulations to visualise how the dwarf galaxies formed, using their assumptions about CDM.
The team found that the final results of these simulations did not at all match what we observe....
Prof Frenk said that after working for 35 years with the predictions of the standard model, he is "losing sleep" over the results of the simulations.
But he believes he has found a solution to the CDM problem. He proposes that instead of "cold" dark matter that formed within the first one millionth of a second after the Big Bang, the Universe may instead be filled with warm dark matter (WDM).

Meanwhile at the other “science”:

One of the biggest issues confronting international macroeconomists is whether or not the large and persistent U.S. current account deficits are sustainable.

[One possible reconciliation is the]... the “dark matter” view of Hausmann and Sturzenegger (2007), henceforth HS. HS propose an alternative method to computing net international positions and current accounts.

… from a relative reliability perspective the dark matter view can be quickly dispensed with. HS suggest that the external position for all asset types should be estimated by capitalizing income at a common discount rate. They then compute the net position from  these capitalized values, and form the current account as the year-to-year change in their constructed net position. This explicitly assumes that investment income, a subcomponent of the current account, is the most reliable portion of the entire set of international accounts, and that it is  appropriate to construct positions in this manner. Given that approximately two-thirds of published investment income data are not measured, but are formed by applying estimates (of yields) to estimates (of positions), from a relative reliability perspective dark matter fails. Moreover, while we have sympathy for some parts of the hypothesis, we find the methodology of capitalizing income streams to be questionable. Even if the investment income numbers are entirely reliable, we doubt this method of constructing the current account or position is an improvement over the published estimates.

Liquid chlorophyll

To drink! I saw a billboard for this in Penang. It's considered an anti-oxidant.

Coincidentally, I came across this article "Wheatgrass Juice and Folk Medicine" in the August 2008 Scientific American by Michael Sherman:

The recent medical controversy over whether vaccinations cause autism reveals a habit of human cognition – thinking anecdotally comes naturally, whereas thinking scientifically does not. ... On the other side are parents who noticed that shortly after having their children vaccinated autistic symptoms begin to appear. These anecdotal associations are so powerful that they cause people to ignore contrary evidence ...

Take wheatgrass juice ... if you can stomach it. The claims for its curative powers are bottomless.

While we're at this here are some other personal examples from my uncle who swears by the following:

1. Fruit wash when used on the skin can eliminate blemishes and acne.
2. The juices from discarded fruits and vegetable (when left to compost) is a very efficient cleaning agent (even for the skin).

The mathematization of medicine

The wisdom of this in the field of economics has been debated and is perhaps also debatable. But what about medicine? I am not in a position to judge how useful nor am I in a position to say how widespread and popular it is but I came across the following

From Cardiovascular Mathematics by Luca Formaggia, Alfio Quarteroni, and Alessandro Veneziani (Eds.). The following is from Chapter 2

Seals as predictors of earthquakes?

This news item in early January caught my eye:

The sea lions of San Francisco are almost as famous as the city's cable cars or even the Golden Gate bridge, says the BBC's Peter Bowes in Los Angeles.

Twenty years ago, for no apparent reason, the smelly, noisy animals took up residence in the docks at Pier 39.

Their numbers grew rapidly to about 1,700 animals, and they became a popular tourist attraction.

But then most of them disappeared.
....
One outlandish suggestion was that they were fleeing the bay because of an imminent earthquake, our correspondent says.

The seals were found off the coast of Oregon. But did they really sense the imminent earthquake on January 9?

Is medicine a science?

Related to an earlier post on what constitutes a science is The Checklist from Atul Gawande:

“The fundamental problem with the quality of American medicine is that we’ve failed to view delivery of health care as a science. The tasks of medical science fall into three buckets. One is understanding disease biology. One is finding effective therapies. And one is insuring those therapies are delivered effectively. That third bucket has been almost totally ignored by research funders, government, and academia. It’s viewed as the art of medicine. That’s a mistake, a huge mistake. And from a taxpayer’s perspective it’s outrageous.”

This third bucket can be made into a science by the introduction of a checklist.

In 2001, though, a critical-care specialist at Johns Hopkins Hospital named Peter Pronovost decided to give it a try. He didn’t attempt to make the checklist cover everything; he designed it to tackle just one problem, the one that nearly killed Anthony DeFilippo: line infections. On a sheet of plain paper, he plotted out the steps to take in order to avoid infections when putting a line in. Doctors are supposed to (1) wash their hands with soap, (2) clean the patient’s skin with chlorhexidine antiseptic, (3) put sterile drapes over the entire patient, (4) wear a sterile mask, hat, gown, and gloves, and (5) put a sterile dressing over the catheter site once the line is in. Check, check, check, check, check. These steps are no-brainers; they have been known and taught for years. So it seemed silly to make a checklist just for them. Still, Pronovost asked the nurses in his I.C.U. to observe the doctors for a month as they put lines into patients, and record how often they completed each step. In more than a third of patients, they skipped at least one.

The next month, he and his team persuaded the hospital administration to authorize nurses to stop doctors if they saw them skipping a step on the checklist; nurses were also to ask them each day whether any lines ought to be removed, so as not to leave them in longer than necessary. This was revolutionary. Nurses have always had their ways of nudging a doctor into doing the right thing, ranging from the gentle reminder (“Um, did you forget to put on your mask, doctor?”) to more forceful methods (I’ve had a nurse bodycheck me when she thought I hadn’t put enough drapes on a patient). But many nurses aren’t sure whether this is their place, or whether a given step is worth a confrontation. (Does it really matter whether a patient’s legs are draped for a line going into the chest?) The new rule made it clear: if doctors didn’t follow every step on the checklist, the nurses would have backup from the administration to intervene.

Pronovost and his colleagues monitored what happened for a year afterward. The results were so dramatic that they weren’t sure whether to believe them: the ten-day line-infection rate went from eleven per cent to zero. So they followed patients for fifteen more months. Only two line infections occurred during the entire period. They calculated that, in this one hospital, the checklist had prevented forty-three infections and eight deaths, and saved two million dollars in costs.

... The checklists provided two main benefits, Pronovost observed. First, they helped with memory recall, especially with mundane matters that are easily overlooked in patients undergoing more drastic events. (When you’re worrying about what treatment to give a woman who won’t stop seizing, it’s hard to remember to make sure that the head of her bed is in the right position.) A second effect was to make explicit the minimum, expected steps in complex processes. Pronovost was surprised to discover how often even experienced personnel failed to grasp the importance of certain precautions. In a survey of I.C.U. staff taken before introducing the ventilator checklists, he found that half hadn’t realized that there was evidence strongly supporting giving ventilated patients antacid medication. Checklists established a higher standard of baseline performance.

... In December, 2006, the Keystone Initiative published its findings in a landmark article in The New England Journal of Medicine. Within the first three months of the project, the infection rate in Michigan’s I.C.U.s decreased by sixty-six per cent. The typical I.C.U.—including the ones at Sinai-Grace Hospital—cut its quarterly infection rate to zero. Michigan’s infection rates fell so low that its average I.C.U. outperformed ninety per cent of I.C.U.s nationwide. In the Keystone Initiative’s first eighteen months, the hospitals saved an estimated hundred and seventy-five million dollars in costs and more than fifteen hundred lives. The successes have been sustained for almost four years—all because of a stupid little checklist.

And in the same article, it also establishes why aeronautical engineering is not always science - because of the human element:

On October 30, 1935, at Wright Air Field in Dayton, Ohio, the U.S. Army Air Corps held a flight competition for airplane manufacturers vying to build its next-generation long-range bomber. It wasn’t supposed to be much of a competition. In early evaluations, the Boeing Corporation’s gleaming aluminum-alloy Model 299 had trounced the designs of Martin and Douglas. Boeing’s plane could carry five times as many bombs as the Army had requested; it could fly faster than previous bombers, and almost twice as far. A Seattle newspaperman who had glimpsed the plane called it the “flying fortress,” and the name stuck. The flight “competition,” according to the military historian Phillip Meilinger, was regarded as a mere formality. The Army planned to order at least sixty-five of the aircraft.

A small crowd of Army brass and manufacturing executives watched as the Model 299 test plane taxied onto the runway. It was sleek and impressive, with a hundred-and-three-foot wingspan and four engines jutting out from the wings, rather than the usual two. The plane roared down the tarmac, lifted off smoothly, and climbed sharply to three hundred feet. Then it stalled, turned on one wing, and crashed in a fiery explosion. Two of the five crew members died, including the pilot, Major Ployer P. Hill.

An investigation revealed that nothing mechanical had gone wrong. The crash had been due to “pilot error,” the report said. Substantially more complex than previous aircraft, the new plane required the pilot to attend to the four engines, a retractable landing gear, new wing flaps, electric trim tabs that needed adjustment to maintain control at different airspeeds, and constant-speed propellers whose pitch had to be regulated with hydraulic controls, among other features. While doing all this, Hill had forgotten to release a new locking mechanism on the elevator and rudder controls. The Boeing model was deemed, as a newspaper put it, “too much airplane for one man to fly.” The Army Air Corps declared Douglas’s smaller design the winner. Boeing nearly went bankrupt.

Still, the Army purchased a few aircraft from Boeing as test planes, and some insiders remained convinced that the aircraft was flyable. So a group of test pilots got together and considered what to do.

They could have required Model 299 pilots to undergo more training. But it was hard to imagine having more experience and expertise than Major Hill, who had been the U.S. Army Air Corps’ chief of flight testing. Instead, they came up with an ingeniously simple approach: they created a pilot’s checklist, with step-by-step checks for takeoff, flight, landing, and taxiing. Its mere existence indicated how far aeronautics had advanced. In the early years of flight, getting an aircraft into the air might have been nerve-racking, but it was hardly complex. Using a checklist for takeoff would no more have occurred to a pilot than to a driver backing a car out of the garage. But this new plane was too complicated to be left to the memory of any pilot, however expert.

With the checklist in hand, the pilots went on to fly the Model 299 a total of 1.8 million miles without one accident. The Army ultimately ordered almost thirteen thousand of the aircraft, which it dubbed the B-17. And, because flying the behemoth was now possible, the Army gained a decisive air advantage in the Second World War which enabled its devastating bombing campaign across Nazi Germany.

Medicine today has entered its B-17 phase. Substantial parts of what hospitals do—most notably, intensive care—are now too complex for clinicians to carry them out reliably from memory alone. I.C.U. life support has become too much medicine for one person to fly.

And I've always wondered - could a computer make a better House? There are so many symptoms that correlate with different diseases - would it not be more efficient to use a computer to narrow and eliminate possible candidates? Perhaps it is hero worship that we are after and if something as mundane as a computer could quickly narrow down the possibilities for us we would not be watching the series.

Speculations of the future

1. What Battling Spacecraft will look like (HT: MR)
2. Disappearance of currency
All transactions would be made with POS or cell phones, backed by interest-bearing assets, in one form or another. You might think that's unlikely today but it's at least possible in the future. In any case, it's a thought experiment.

In this world there would no longer be a trade-off between currency and interest-bearing assets, as we find in traditional Keynesian models. There would be no substitution out of one and into the other and there would be no swapping of currency for interest-bearing assets.

What would the macroeconomics of this world be like? Would the AD curve slope upwards? Would increases in employment be contractionary? No and no. It would only be slightly different from our current world, a point Kroszner and I made in our book Explorations in the New Monetary Economics. It just doesn't matter that much if you pay for your retail transactions by leaving a five on the counter or by using a credit or debit card backed by interest-bearing assets.

3. Krugman - Stross interview - This was an interesting pairing - perhaps because in his younger days Paul Krugman contemplated about The Theory of Interstellar Trade? Sci-fi author Stross had some interesting insights:

CS: I think things have changed a lot in the last 30 years, but not in the direction that somebody 30 years ago would have expected. The 20th Century, and going back to the 19th Century, the real visible vector of change technologically was transportation speeds. ....

PK: ... What you came out believing if you went to the New York’s World Fair in 1964 was that we were going to have this enormously enhanced mastery of the physical universe. That we were going to have undersea cities and supersonic transports everywhere. And there hasn’t been that kind of dramatic change. ... My favorite test, which shows something about me, is the kitchen. If you walked into a kitchen from the 1950’s it would look a little pokey, but you’d know what to do. It wouldn’t be that difficult. If someone from the 1950’s walked into a kitchen from 1909 they’d be pretty unhappy – they might just be able to manage. If someone from 1909 went to one from 1859, you would actually be hopeless. The big change was really between 1840 and the 1920’s, in terms of what the physical nature of modern life is like. There’s been nothing like that since. So we can do fancy information searches in a way that no one envisioned 30 years ago – as one of my colleagues at the Times, Gail Collins, likes to say all the time where are the flying cars?

CS: Yeah, where is my food pill, where are my jetpacks. .... I think that what has been happening rather than progress continuing and accelerating in a visible direction that everybody’s expected from 1960, we’ve seen immense progress in other directions and the effects are not immediately obvious because they take time to sink in. ... It’s not a great cognitive leap from aeroplanes capable of carrying loads to bombers. It’s a hell of a leap from idea of getting a cheap camera chip and adding it to a mobile phone and coming up with a phenomenon of “Happy Slapping”. I don’t know if everyone knows what Happy Slapping is, it isn’t Slapping, and it isn’t Happy, but its where kids basically find some random stranger beat them up while one of their friends videos it with their camera and then upload it to YouTube. As social phenomenon go, that’s not one you can predict from the input technology. That’s a second order effect. ...

CS: Actually, if I had to make a guess at one of the major things that’s going to affect us in the next 20 years … periodically, I keep hearing about peak oil and the long emergency that’s going to come … and it’s going to be very, very grim … and how our food travels an average of a couple of thousand miles between where its produced and where we consume it. I have a slightly different way of looking at this. We’re going to come to the end of cheap energy not because energy is going to be innately expensive because we’ve used all the oil up, but because we can’t afford to keep pumping more carbon into the air. Now we’ll be able to actually maintain an oil-based economy indefinitely. My betting is on Craig Venter, the guy who founded Celera Genomics tried to bootstrap a private enterprise genome program. His current venture with Shell is to try and crack the problem of producing diesel oil using genetically produced algae. And they’re throwing large amounts of money at this problem. I would reckon in 50, 60 years time Shell will still be selling you oil. It won’t be oil they’ve pumped out of the ground, though, it will be oil they’ve synthesized using atmospheric carbon, so it will be carbon neutral. That’s a whole lot cheaper than switching to a hydrogen economy because you don’t have to scrap all of your plant and tankage, just keep using the same stuff. But going a step further, there’s a huge inefficiency in these hub and spoke models of distribution and shipping stuff long distances. If you can produce stuff locally, and distribute it locally, that gives you a huge advantage. I think one of the things logistics is going to … well, computers are going to give us, is much tauter supply chains between production and consumption.

PK: That’s by the way one of the mysteries … we don’t quite know why there’s so much stuff being shipped long distances, …

Measuring BMI

The optimal BMI seems to be 22 according to Wii Fit. It seems to be based on this on women and coronary heart diseases.

This result is based on the assumption that BMI can be accurately measured when it facts it varies over the course of the day. What if my BMI ranges between 21.7 and 22.5 over the day? P.S. It doesn't - my BMI is over the 22 cutoff which makes me wonder who made the 22 cutoff seem so great.

Why cost benefit analysis will always be unacceptable

A rotavirus vaccine is developed and the vaccine goes to clinical trials. (Full details here - preview only.)

In 1991 the Food and Drug Administration granted the pharmaceutical company Wyeth Ayest (later Wyeth Pharmaceuticals) permission to make and test this vaccine, which they named RotaShield. Over the next five years it launched large-scale clinical trials in the U.S., Finland and Venezuela, verifying RotaShield's safety, ability to induce a protective immune response and lasting efficacy. ... Over the next nine months months more than 600,000 children received an estimated 1.2 million does of RotaShield. ...

The disaster struck. In 1999 several infants suffered a serious complication within two weeks of receiving the vaccine: a segment of the intestine folded into a nearby region (like part of a telescope collapses into another), creating a blockage called intussusception. The condition can be excruciatingly painful and must be quickly reversed with either an air or fluid enema or fixed surgically. In rare cases, the intestine perforates and the infant dies. The CDC, which was monitoring experience with RotaShield, called for an immediate halt to the immunization program, thereby sinking a vaccine that had taken 15 years and several hundred million dollars to launch.

The agency initially estimated the risk to be one intussusception in 2,500 vaccine recipients, which was considered unacceptable. Later studies pegged the probability at only one in 11,000. Then Lone Simonsen of the NIH correlated risk with age: infants younger than three months were in less danger than older ones. If the vaccine were given only to young babies, the likelihood of intussusception could drop 10-fold to perhaps one in 30,000.

The new data raised new questions. Was this risk acceptable in the U.S., where children are often hospitalized but rarely die of rotavirus? Were the odds more palatable in the developing world, where one child in 200 dies of rotavirus? If 150 lives could be saved for each complication from intussusception, might the risk be justified? Given these statistics, was it unethical, in fact, to withhold a vaccine that might save half a million lives a year? Or no matter what the risk-benefit analysis showed, was it unethical to market a vaccine in the developing world that had been withdrawn from use in the U.S.?

The CDC and the WHO called a meeting of policymakers from developing countries. After heated discussion, science bowed to politics. As a high-ranking Indian official said, "I know this vaccine would save 100,000 children in my country. But when the first case of intestinal blockage occurred, I would not be forgiven for allowing a vaccine that had been withdrawn in the United States to be used in my country."

Intelligent design or efficient evolution

Gary Stix's article An Antibiotic Resistance Fighter (preview only) has a graphic on how a bacteria can undermine the effectiveness of antibiotics. I only reproduce the text here:

Rapid-fire mutations in Escherichia coli bacteria can undermine the effectiveness of ciprofloxacin (cipro), an antibiotic that is increasingly being prescribed by physicians.

1. Cipro's Action: Cipro usually harms bacteria by binding to an enzyme called gyrase and preventing it from functioning properly.

2. How Resistance Arises: Resistance is initiated when E. coli responds by generating single-stranded DNA. Individual molecules of another protein, RecA, the line up in a chain and attach to the single-stranded DNA. RecA facilitates cleavage of a regulatory protein, LexA. This change frees a set of formerly repressed genes to induce mutations elsewhere. The mutations end up blocking cipro's binding to gyrase, thereby preventing the drug from working.

3. A Possible Solution: Drugs that bound to LexA and prevented its cleavage - such as the hypothetical compound X detected here - would stall that sequence and thus could overcome resistance and restore effectiveness to the antibiotic.

The above mechanism was hypothesised and experiments were run to confirm this hypothesis by Romesberg, Cirz, Chin and others and the results were published on PLoS Biology.

An unexpected - and undesired - aside to the publication of the PLoS Biology paper emerged when the intelligent-design community embraced the results as confirmation of its unorthodox worldview. The frenzied mutations in Romesberg's experiments were not random, its members contend, but were set off under deliberate direction of the bacterium: "Life takes control of its fate. Living things are not passive participants of the interplay between stochastic events and envrionmental pressures," writes the pseudonymous Mike Gene on the website idthink.net, while adding, "That evolution may be under some form of intrinsic control is only a piece of the telelogical [design in nature] puzzle. But it is a significant piece, in that the ability to adapt, at least to these two antibiotics, is under control."