Armed with a killer acoustic guitar sound, Ani Difranco’s “Both Hands”:

I know that we, computational biologists, are sometimes jealous of ye olde white labcoat that our experimental colleagues wear, and which immediately identifies them as scientists. What can we, who sit in front of a computer all day, wear to truly show that we are master of our cpus in the service of science?

Here’s the solution, from designer Erik De Nijs:

hat tip: Petrice Gaskin

Here’s a thought experiment. What if we think about drugs like any other commercial product? Then a drug company, like any other company, should simply be viewed as a machine geared towards making money. If it doesn’t make money by selling its product for dollars, it has no commercial right to exist.

There are two types of products that make money. A product that moves high volume, or a product with a high margin of return. In terms of drugs, this really means two things – a very common illness, or a life-threatening one. It is either something as common cold or a nasty one like AIDS or cancer. By the fact that the common cold is common, it means that’s it’s incurable, and profit is made by its ubiquitous recurrence. The nasty high-margin one is due to the life-threatening aspect. Death is a wonderful focus to buy a product.

The best products are the ones with a high margin of profit. Low margins of profits won’t bring you a lot of money. That means an expensive drug. What makes a drug expensive? They could be expensive to make, which makes them rare. However, there is another way to push up the price of a product.

Take for example, sneakers. It is a pretty well-known fact that the cost of an expensive pair of sneakers is not due to the manufacturing cost. By marketing a pair of shoes as a luxury item, the price can be marked-up. And if marketed properly, the luxury price of a drug will pay for the marketing and make a tidy profit on top of the cost of marketing. This is the NIKE approach. Take a cheap product and market the shit out of it so that you can sell it as a premium product. Put hot sexy women on billboards, in magazine adds. Make them sing songs. Like NIKE, drug companies spend twice as much on marketing as it does on research. An army of hot young drug reps are needed to push drugs in the corridor of every hospital

Well how do we make a drug into luxury item? Well drugs are not like gold watches, or swedish cars. They are much much easier to make desirable. Basically, the more severe that the drug is aimed to alleviate, the more it is desired. If the disease terminal then you hit pay-dirt. People desire these drugs as much if not more than the latest iPod. This is an excellent marketing leverage point for increasing profit margins.

The opposite is also true. Low margin products are not desirable. If you can’t mark up the profit margin, or market it in such a way that a prestige mark-up can be applied then it won’t be very profitable. For instance, generic drugs earn low margins. Unlike on-patent drugs, which you can market like a luxury item, selling generics is more like a commodity market. Competing in a commodity market is hard work. As advertising doesn’t make much of a dent in commodities, the only way to make money is to manufacture the product cheaper. Potential profits are miniscule and not worth the effort. Best to avoid that market altogether rather than waste precious capital.

Another maxim from business is that it’s the blades that make the money, not the razor. A product that sells once is not nearly as profit as the product that makes you come back again. Therefore vaccines are not profitable. You take it then you are immune from the disease. How are you going to pay more? Vaccines are not very profitable at all. Unless it’s a vaccine that you have take again and again.

And what if you actually have a disease? The drug that actually cures the disease is not very profitable. How can you possibly leverage a revenue stream out of that? No, the best drugs are the ones that alleviate the disease to a certain point, but does not cure it. Then the customer has to come back for more. Like crack. Crack sells itself, and makes the customer come back for more. When it’s addictive to boot, you don’t even have to market the shit. Those smartly dressed men who work out in chrome-finished gyms in Palo Alto, and attend seminars in San Diego, are nothing more than very advanced version of a crack dealer cruising in a Chevrolet on the edge of Oakland. Same ball-park, different stand.

The perfect drug is not a cheap vaccine that saves life threatening disease for very poor people. No the perfect drug is an expensive, patent-controlled, drug for a life-threatening disease that targets rich people that alleviates symptoms periodically but does not cure it. Then you’d throw you marketing department at doctors so that you can lift its street price as high as the market can bear.

But like a drug dealer, the average CEO of a large drug company has image problems in terms of “community outreach”. So you’ll see them toss a bone to the way of the community by funding an occasional cheap drug or a loss-leader. But their hearts and wallets are really not into it. Oh, but you ask, where is the humanity, the compassion in these good doctors of science? Ask yourself this: would the typical CEO of a drug company prefer to make a feature article in National Geographic on the “Third World” issue or make the front cover of Forbes?

If you’re interested in the torturous climb up the academic ladder, then you would be well-advised to head on across to this new blog JUNIORPROF. This is a wonderfully candid blow-by-blow account of the trials-and-tribulations of a newly minted junior professor who studies pain, whether his own or others. Find out how life changes from postdoc to primary investigator:

The number one priority back then was to get the experiments done and everything else was secondary. Not anymore. I’m still in the lab a lot now, but largely to show people how to do things.

Or how he snared his first grad student:

it turns out that the website and, to a lesser extent, the talks were a great strategy to attract students to the lab.

All, in all, a great read from a thoughtful writer. You bet I’d be taking some crib notes from this blog.

p.s. JUNIORPROF: if you read this post then please, choose a bigger FONT FOR YOUR WEBSITE!

It’s been a long time coming, but now I am bloody proud of being Australian simply and purely because of the brilliant man who has become the new Austrian prime minister, Kevin Rudd. For many years, I was embarrassed by John Howard, our former neatherdaal of a prime minister. Instead, now I have a prime minister who can connect with everyday people but is also a powerhouse intellectual. In a recent speech (analysis in full) given in Peking University, in fluent Mandarin:

Rudd’s brilliance in the speech involves turning the Chinese term “friend” on its head. Friend (pengyou in Chinese) and frienship (youyi) are two of the most distorted concepts in modern China culture. In modern China, a friend is someone who will do you favors and who expects favors in return. A “foreign friend” is someone the Chinese party-state expects will carry water for them and NEVER criticize them.

Whenever a Chinese official called me “foreign friend” (waiguo pengyou), I knew some type of horrible deal would soon be asked or expected of me.

“To be a friend of China, the Chinese people, the party-state or, in the reform period, even a mainland business partner,” Barme writes, “the foreigner is often expected to stomach unpalatable situations, and keep silent in the face of egregious behaviour. A friend of China might enjoy the privilege of offering the occasional word of caution in private; in the public arena he or she is expected to have the good sense and courtesy to be ‘objective.’ that is to toe the line, whatever that happens to be. The concept of ‘friendship’ thus degenerates into little more than an effective tool for emotional blackmail and enforced complicity.”

So what did Rudd do? He went back — way back — into Chinese history, to the 7th century AD, and used another word for friendship (zhengyou).

“A true friend,” Rudd said, “is one who can be a zhengyou, that is a partner who sees beyond immediate benefit to the broader and firm basis for continuing, profound and sincere friendship.”

For those of you who are citizens of the oldest democracy in the world, I sincerely hope that you elect a former professor of law of the famous University of Chicago, so that you too can experience what it is like to have a brilliant intellectual statesman to steer your nation.

• a library that reads Micro$oft Excel files directly.

• Python replacement for that horrendous but ubiquitously useful program called Make.

• a detailed example in Python on how to create custom plots with rich data manipulations using matplotlib. This is the kind of stuff I do, day-in day-out.

• library to do simple parallel processing.

• a pure Python-based database engine.

• an introduction all the different modules in the Python standard library, using examples.

• library that turns html to pdf.

• library to edit image files.

Why these libraries might be plausibly useful? Perhaps I want to run a bunch of programs on a cluster using data that a colleague sent me in Excel format. I’d store the results in a database and when the calculation is finished, I extract the data to generate different plots of the data. But the plots may not be in the correct size or resolution so I’d have to crop and resize them before combining them into an easy to read html file, with which, I’d convert to pdf, and mail off to my colleague.

With these libraries, I can do all that in one single Python script.

Sometimes something fails so badly that it transcends into another category. This attempted burglary (supposedly) captured on security cameras could have come straight out of a Marx brothers routine:

Saving penalties by a goalkeeper is one of the most heroic individual feat that a soccer player can make. Watch this transcendent own goal that undoes the good work of this goalkeeper seconds after the save:

I occasionally moonlight as an editor and webmaster for a literary journal pax americana and after an interminable childbirth, the new issue is out. Since this is mostly a science blog, let me point you to the story Philadelphia by Mr. Huafeng Xu:

I told her that I had a paper initially submitted to Science but it ended up in American Journal of Physics. She laughed. She thought that I made up the name of the journal. I didn’t.

In a recent coffee break, a discussion broke out about the naming of things in science. For instance, you have the Boltzman constant, Shannon entropy and the Golgi appartus. Then there are the bizarro names given to classic thought experiments such as Maxwell’s demon, the Einstein-Podolsky-Rosen paradox and Schrodinger’s cat.

Someone remarked that people don’t seem to name things anymore. Except that they still do. In my field, I can think of some recent namings such as the Karplus coupling, the Levinthal paradox, the Ramachandran plot and the Connolly surface. Coining new names is easy, and one might be tempted to think that new names just adds to the cess-pool of new jargon, which is very deep indeed. But the use of jargon is not necessarily bad. It’s just that so very names actually pass into useful common usage. This only happens if the new name encapsulates a complicated idea, and the idea is useful, and the new term pops, then communication amongst professionals is enhanced.

Still the coining of names brings up an interesting question: why do we decide that a person shall be forever conjoined with an idea? Naming a idea after a person is perhaps the highest honor we can give to a fellow scientist for discovering that idea in the first place. It suggests not only that the scientist did in fact discover it, but the discovery is one of consequence.

Still the debate over who discovered what, may seem like an armchair debate, but there are often major consequences. Like any kind of competition, there are no prizes for coming second. Publication of a new experiment often prevents the publication of similar experiments coming after. And grants and research money flow through the doorway of a good publication record.

Life-long shit fights have been fought over the originality of scientific ideas. The classic example is Isaac Newton and Gottfried Leibniz fighting over the mantle of the inventor of calculus. Newton was known to have made up pseudonyms to pen articles attacking Leibniz in various scientific journals. In that particular butting of heads, the entire scientific communities of Germany and England were enlisted to fling shit at the other side over a period of decades.

The problem with the attribution of originality is that discovery can be plausibly broken into 4 different persons. There is 1) the person who brainstormed the initial idea, 2) the person who got a working prototype of the idea, and 3) the person who got the prototype to do something useful and 4) the person who polished the idea into a useful tool that everybody can and would want to use. Or for lack of better words: brainstorm, prototype, utility, ubiquity. Until an idea or method reaches ubiquity, it’s not really considered significant enough to warrant a special name. The have many cases of the history of science of interesting but useless discoveries. Don’t believe me? Just peruse the number of articles in the literature with 1 citation or less.

Now, when one person takes an idea from brainstorming all the way to ubiquity, there’s no question about who discovered the idea. The problem is when different people partake in the process.

Take brainstorming. The classic example of the brainstorm is the idea of parity violation for the weak interaction, the interaction that was postulated to hold a electron to a positron in order to make a neutron. This was needed to explain the commonplace disintegration of neutrons to protons that is observed in many radioactive materials. The parity violation of the weak interaction was traditionally attributed to the theorists Lee and Yang. However, the story of the discovery of the parity violation of the weak interaction goes that in a particular conference in the 60’s, which Lee and Yang attended, there was a lively discussion the nature of the weak interaction. During the first night, Richard Feynman and his room-mate Martin Block continued the discussion when Block blurted out, “maybe parity is not conserved”. Feynman pooh-poohed this idea, but suddenly stopped and realized that this could be one of those ideas that seem so stupid it just be right. The next day, Feynman brought this up. Lee and Yang who had been working on the weak interaction, slowly came to the conclusion that there was merit to the idea and after careful study of the literature, realized that no one had actually tested parity violation in the weak force, even though it had been done many times for electro-magnetism and the strong force. So they wrote up a famous analysis of the parity violation, with a proposed experiment. Their friend, Wu, one of a handful of influential female physicists broke off her honeymoon to run the experiment. And thus, the physics community found that one of their fundamental symmetries of nature was violated.

Who then discovered parity violation? Block clearly had the original idea, Feynman conveyed it, and Lee and Yang developed a prototype of the idea. It was then Wu who actually got it working as an experiment. Only after it was experimentally proved, was this hailed as one of the great moments of physics. Block, Feynman, Lee, Yang and Wu all partook in the childbirth of the idea. But due to the stature that Lee and Yang already had in beta-decay studies, their part in the drama propelled them to a Nobel Prize.

A more interesting case is the discovery of the positron. When Paul Adrien Dirac first discovered the relativistic equation of the electron, he realized that it entailed the possibility of a particle just like an electron but with a positive charge. Since no one had observed anything like that before, Dirac conjectured that this was really a shrouded description of a proton, even though a proton was many times heavier than an electron. Indeed the belief in the non-existence of a positron was so strong, Dirac explained the positive particle as a “hole” in an unseen sea of virtual electrons.

Many years later, Carl Anderson was credited with the actual discovery of the positron when he photographed in his bubble chamber the tracks of a particle that had a positive charge but the mass of an electron, as deduced by the curvature of the track in a known magnetic field. However, before Anderson, similar particles had also been observed in cloud chambers that measure tracks from cosmic rays except no one knew exactly what they were. Nevertheless, without Dirac’s equation, no-one would have the framework to understand how positrons fit in to the scheme of things. Dirac was allegedly quite upset to find out that an actual positron was discovered because he had hoped his equation also described protons, the other important constituent of a normal atom. This was a case where Dirac had discovered everything about the positron except believing that it exists.

An example close to home is the concept of the funnel in the energy landscape of a protein. The idea of a funnel energy landscape is that there are many conformations of a protein at high energy but at progressively lower energies, there are fewer conformations. Thus an unfolded protein naturally falls into the lowest conformations. The idea of the energy funnel solves the infamous Levinthal paradox that had plagued protein theorists for 2 decades. Although the actual term “funnel” was coined by Peter Wolynes, my former boss, Ken Dill, wrote an earlier paper that demonstrated this very idea using 2 dimensional lattice models but he did not use the term ‘funnel’ in the paper. History shows that the term ‘funnel’ stuck. Still, Ken always cites his paper for the definition of ‘funnel’ whereas Peter cites his paper for the first coinage of the term. Depending on who you to talk, someone different discovered the energy “funnel” concept of protein folding.

The thing is, in research, good ideas are a dime a dozen. I learnt this the hard way. In gradschool and the various postdocs I’ve had, when I’d have a idea for a new idea and tried to pitch to my boss, more often than not, they’d try to shoot it down. They’d look for flaws or sometimes veto it with their hard-earned intuition. They were pathologically opposed to shiny new ideas. I used to think that it was because they were old fuddy-duddies, grown foggy and conservative by the grinding process of tenure. But I now realize they were resistant for a very good reason. This was because in reality, new ideas are cheap. In the course of supervising generations of students and postdocs, they must have been pitched thousands of seemingly clever ideas that came to naught. It was thus experience that taught them to be skeptical of novel ideas.

What I’ve found that presenting new ideas to the boss is a multi-stage process. The first step is to propose the idea and watch it get shot down. Then, in my spare time, I’d actually develop a prototype. A prototype is kind of messy and poorly articulated of the original idea. I’d plead for the potential of the idea but chances are the boss would be a little more intrigued with the prototype but overall dismissive. But with a prototype, I could then finally apply it to a real system. I’ve learnt best to keep my mouth shut until I could bring the boss some actual results applied to a real system. Then we’d talk about it and reach some kind of wall and I’d disappear again. Wash, rinse, recycle.

The tipping point would come when my boss would burst into my office and tell me how he’d figure out something crucial that had been missing in my explanation. Of course, that would be the very thing I’d tried to say at the very beginning, but it would be boorish of me to mention it now. The trouble has always been that communicating a mal-formed idea is not a very effective process. But you can’t really clarify an idea without actually building a prototype. What is really happening is that in the to-and-fro between me and my boss, we had developed a mini-language to talk about the original spark of an idea. Only when we had a shared language through building a prototype is the idea actually communicated. Indeed, what had happened here is but a mini recapitulation of the stages of discovery – brainstorm, prototype, application and ubiquity – writ small in the interaction between two people. Application is generating results from which one can think about the idea. Ubiquity is when we both get it.

In the end though, ubiquity is the real test of a scientific discovery. Only discoveries that are useful to a large number of people are significant discoveries. I have no shame in using the word useful in the selling of the science I make. The test of a good article is how many people want to collaborate with you after finding out about it. A little advice that was floated my way from a previous supervisor was that to earn your stripes from postdoc to professor, you’ve got to find a niche that you, and only you, can do. As a young investigator, it would be suicide to dive straight into an area where you’re competing with the big boys, at least at the beginning of your career.

Indeed selling the science well can also make reputations. The physicist Freeman Dyson made his career by carving the rosetta stone between the competing formulations of quantum electro-dynamics of those two giants of postwar physics Richard Feynman, Julian Schwinger and Sin-itiro Tomonaga. These formulations were remarkably different. On the one hand, you have the famously child-like strokes of Feynman diagrams, on the other hand, you have the crushing weight of equations in Schwinger’s papers, one of which had the reputation of containing the most number of equations in a Physical Review article for many years. Although Dyson himself admitted that he was not the driving force behind quantum electro-dynamics, he produced a cogent description of electro-dynamics that normal physicists could could use, and his efforts were both appreciated and honored.

Making new discoveries is not simply a matter of serendipidity. Luck falls on the prepared mind. A salty piece of advice comes from the great computer scientist Richard Hamming who noted that the really great scientists were lucky many times over. If you want to be great and receive the blessings of chance when they fall, you have to be ready to receive it. How you ask? Simple, says Hamming, you must always been thinking about the great problems, regardless of whether you can solve them right now or not (Quick: what are the top ten problems in your field?). If you cultivate brilliant collaborators, and learn to listen, then it is inevitable that you will bump into someone who has the idea to crack the insoluble, much as Wu did when she came upon Lee and Yang’s paper about the parity violation in the weak interaction. At that moment, you must rush to the quick, drop everything else, and chase that insight to the bitter end. You may even have to cut your honeymoon short.

Animal psychologists and evolutionary biologists have a lot of ‘splaining to do. Mesmerising.