This Thursday…

May 9th, 2006 · 6:22 pm  →  Blog
ZOD. IS. COMING.
May 11, 2006 – the WB

91r

May 9th, 2006 · 6:18 pm  →  Blog
I finally finished my final paper for Biochemistry 91R, wrapping up a tumultuous semester of research in lab with an all-nighter. I can honestly say I’m very proud of it. It wouldn’t have been possible without LaTeX and JabRef handling the layout and bibliography (although I spit at Photoshop for making figure design so difficult — I really must get my hands on Adobe Illustrator). Nor would it have been possible without the postdoc I’m working with (who coincidentally… or maybe it was fate… is named Ben and who’s last name also starts with a T) making things much simpler by creating cute little cartoons and diagrams of the pathways I’ve been working with.

And although I cursed the literature and my computer and my paper for hours, it seemed, I do feel like I’ve learned a great deal from the effort — and I am excited, upon reviewing the data, to further pursue this. Almost makes me feel better about not being home this summer … almost

And then it hits me.. finals are coming up.. and I have a big paper to write which I haven’t started yet on Huang ZongXi’s “Waiting for the Dawn: A Plan for the Prince” (which is actualy quite interesting, as its the first example of a liberal [not left-leaning, but classic liberal] intellectual tradition that I can think of from the Far East).

NextGen Update: Avian Flu

May 5th, 2006 · 3:21 pm  →  Blog
In case anyone’s interested, my article on Avian Flu (which I have to admit is very long) for NextGenMD is up! I got a chance to talk with Dr. Frederick Hayden (professor of clinical virology at the University of Virginia School of Medicine) and Dr. Michael T. Osterholm (director of the Center for Infectious Disease Research and Policy as well as associate director of Homeland Security’s National Center for Food Protection and Defense) about their research and its implications with regards to the spread of bird flu and what we can do if (more likely, when) an epidemic happens. Take a look and tell me what you think!

Applied Math

May 1st, 2006 · 8:45 pm  →  Blog
I loved Applied Math (although I can hate the problem sets). Problem 1 from my problem set for this week:

“Consider a population of bugs. The bugs divide, and they also migrate randomly over the region that they occupy. At the borders of the region, there are terrible bug-eating monsters that eat the bugs.”

(no joke, that is verbatim)

To Torture or Not to Torture

April 28th, 2006 · 6:55 pm  →  Blog
I’m positive someone reading this is going to (at least at first) think that I’m some horribly evil person for even entertaining the notion that torture can be legitimate, so I’ll preface this little rambling by just saying that this is an exploration on the lack of understanding between two sides of an issue.

The other day while I was walking to get some lunch, I noticed a poster which claimed to have evidence of the horrible torture which occurs in Guantanamo Bay and how its an example of Bush’s “barbaric regime” of war or some other equally negative phrasing. Of course, I typically respond to any moral/ethical/political view by taking the exact opposite (I’m somewhat reactionary that way). And, the thought path it led me towards was an assessment of whether or not “torture” is legitimate.

Of course, plenty of people will point out the precedent set in some sort of European convention/treaty of some sort — but that reasoning is really really superficial (for example, the Open Door Policy was a big agreement with a lot of European powers which basically made China Europe’s playground — you’re not going to hear anyone really defend that international treaty).

So when you analyze the “good reasons” you notice that fundamentally, the two sides (those “for torture” [the quotes are b/c I don't think anyone can really be "for torture"] and those against) are arguing completely past each other, making it a big surprise that anyone can really make up their mind or can formulate any reasonable “common ground” policy on it.

Firstly, there seems to be a good deal of disagreement as to what constitutes torture. For instance, there is no real bright line as to what “torture” is, just as there is no bright line to what “cruel and unusual punishment” is. One could imagine people may consider current tactics by the police to intimidate and insult and emotionally rail against those they are interrogating to be a form of torture. One finds that many activists think that torture is some horrible thing, and they are able to describe grusome horrible tortures (ie rape, electrocution, bleeding, etc). On the other hand, “supporters” of torture are talking about food and sleep deprivation (which, I think, are orders of magnitude less worse than firing squad and beating) or a very intense degree of emotional intimidation.

Secondly, they’re also arguing on completely different levels. The fundamental moral arguments brought up by those against torture are appeals to rights or some Veil of Ignorance logic about how “it could be you in there”. They argue that being tortured goes against our natural rights of liberty and against the fundamental principles of democracy or some equally vague and optimistic (but sadly untrue) assessments about the greatness of Western Enlightenment thinking.

But, those on the other end are argue in terms of the duty of the government to insure the well-being of the people as a whole. We have to torture them, even though its unpleasant, because if we can get some information which can save a hundred people from a meaningless and grusome death, if we can stop the societal destabilization which accompanies terrorism or war, then we have to, because its our duty to do it.

These are fundamentally different arguments and different perspectives with very little being done to find some sort of common ground to which this debate can be handled. I’m not suggesting here that this debate can necessarily be resolved (I find myself going back and forth on the issue many times) or that these people need to necessarily like each other and sit down civilly to have a polite discussion. But, I do think, that there is something to be gained from understanding what the “enemy” is thinking/saying/feeling and attempting to use that to motivate your responses and your tactics. Those against torture need to learn to employ the “rhetoric of duty” to support their agenda, while those “in favor of torture” need to learn to use the “rhetoric of rights” and to use Veil of Ignorance logic to approach their arguments. And those who are trying to make up their mind, need to figure out a way to get both sides to start talking on the same levels so that one can make a better judgement.

FireFox rules

April 24th, 2006 · 3:44 pm  →  Blog
I just thought I’d be a nerd and explain the multitude of actually usable reasons (I don’t care that your browser renders in superHexAscii2.454 if I don’t use it) why I like Firefox (in the hopes that someday I might be able to convince even Andrew Garvin to use it):

  1. Tabbed Browsing – This is to me, hands down, the main reason that I chose to use Mozilla products from the get go (yes, I was one of those tech nerds who was using Mozilla back when their icon was a Godzilla breathing fire). One would think that with both Windows and the Mac employing some form of taskbar, that it would actually be very simple to switch between program windows when you’re browsing the web, but for one reason or another, its always a bit awkward. Tabbing, on other hand, allows you to be reading multiple pages at the same time, all in the same window. In Firefox, you can use Ctrl+T to create a new tab, you can also click Ctrl while you click on a link to open it in a new tab, use the context menu when you right click on a link to open a specific link in a new tab, or even use your midde-click button to force things to open in a new tab. It cuts down on clutter in my taskbar (and to my understanding, memory usage by your computer) and is particularly helpful when I’m doing Google or Wikipedia searches to have one tab be my search results and all the other tabs to be links in the search result.
  2. Integrated Search Engine – Firefox comes with several search engines programmed in by default on the upper-right-hand textbar in the browser screen. You don’t have to go to google or yahoo or wikipedia to do your searches, all you have to do is click on the textbar, type, and hit enter.
  3. Download manager – A lot of people already have programs like Gozilla, but Firefox comes built-in with a download manager (hit Ctrl+Shift+D) allowing a quick and easy place to find the information on the names, sizes, and locations of the files you’ve downloaded, and gives you a way to quickly pause, resume, and restart downloads.
  4. Customizability – I may never buy a Mac, but I like the way Safari looks so I’ve happened to pick a Safari/iMac like skin for my Firefox browser (and also for my Thunderbird email program which is also, by the way, made by the Mozilla people). I understand there are mods for Internet Explorer, but the fact that themes are so custom-built into Firefox and so easy to use/deploy is another plus
  5. Bookmarks – I remember trying to use the Internet Explorer bookmark manager … that’s why I never had bookmarks in IE. In Firefox, the Bookmarks manager is a great deal more intuitive (its organized in a similar fashion to Windows Explorer), and a great deal more useful. I’ve set up a lot of my bookmarks so that I can quickly type say “menu” in my location bar and it’ll jump straight to what Harvard Dining Services is offering for the day.
  6. Rendering Engine – As a person who used to have to help manage websites, I can remember the nightmare of trying to get web code to work in both Internet Explorer and Netscape — that was one of the big reasons I kept both browsers on my computer so that I could see the occasional website which did not work. For the most part, I have not seen a website that hasn’t been rendered correctly in Firefox (although I have seen many websites that just aren’t rendered well in IE).
  7. Internal Search – You hit Ctrl+F, type any phrase and Firefox starts searching AS YOU TYPE the window that you’re looking at.
  8. Extensions – I think the number two reason that I choose to use Mozilla are the wealth of extensions and addons that exist (and are, for the most part, located in a central location), making my life a good deal easier, such as:
  1. AdBlock – Lets you block banners and Flash and internal frames with just a click. It also lets you specify RegExpns and URLs of websites which feed advertisements to allow you to craft smarter blocking systems. Better still, an Extension called the Adblock Filterset.G comes built in with a list of websites and RegExpns which have more or less killed almost all the advertisements that I’ve ever encountered. I don’t even see Google Ads anymore :-)
  2. ForecastFox – Puts weather icons in the bottom right of my screen which let me quickly check the weather. It seems kinda stupid, but its very helpful, especially on the damn east coast where the weather changes every two hours.
  3. Google Toolbar for Firefox – I have to say this is a MUCH better toolbar than the one for Internet Explorer. It provides more or less all of the same functionality (except for popup blocking but that’s because Firefox has its own popup blocker) but is more customizable and detects phishing sites (website scams where a website pretends to be your EBay account just to get your account information).
  4. IE Tab – For the occasional website that requires Internet Explorer, this extension allows you to render websites with Internet Explorer in Firefox. You can even set it so that any website which you know looks better or works better in IE (ie Windows Update, Microsoft Sharepoint servers) will by default be rendered in the Internet Explorer engine rather than Firefox’s.
  5. Sage – I used to rely on Google’s Feed Readers and my My.Yahoo start page to aggregate RSS feeds, but now, I just use Sage, which allows me to quickly scan all my RSS feeds and provides a useful SKINNABLE interface such that I can quickly read the stuff that I want to check everyday.
  6. All-In-One Sidebar – A really useful extension which takes advantage and really upgrades the sidebar that comes with Firefox. It lets you customize the Sidebar, and puts all sorts of functionality into it (ie puts your download manager there, your extension manager, etc)
  7. Deepest Sender – I think I’ve mentioned this before, but I use this extension to update my Blogger and LJ.
  8. Scrapbook – Ever wanted to save a website that you’ve really liked but know that you probably won’t get everything (ie the specific text that you’ve typed, the specific graphic that you’ve set it at, etc etc) because Internet Explorer’s save feature only saves the raw HTML and image files? Scrapbook makes it so that it saves EVERYTHING about the page.
  9. Image Toolbar – Something that I actually missed from Internet Explorer was the little icons that pop up when your mouse is over an image that lets you copy or save the image. This extension brings those icons back :-) .

I actually have several more extensions installed (ie an IRC chat extension, a web developer extension, a nice Calculator which lets you type expressions [like on a graphing calculator] which it will then evaluate, and some random aesthetic and web design ones, but I think listing eight reasons and nine extensions is sufficient :-)

Conquering Cancer with Private Medicine

April 20th, 2006 · 6:30 am  →  Blog
suffice to say, I consider this to be very interesting and somewhat close to the truth.

Conquering Cancer with Private Medicine
by Michael D. Tanner

Few things in life are as terrifying as a diagnosis of cancer. But for millions in the United States, the news just got a little bit better. Death rates for those suffering from cancer are actually beginning to drop. In particular, death rates have declined for the four most common forms of cancer: lung, colorectal, prostate and female breast cancers. Overall, fewer U.S. citizens died of cancer than at anytime in the past 70 years.

While there are many reasons for this welcome trend, one reason is the much-maligned U.S. free-market health care system.

The one common characteristic of all national health care systems, including Canada’s, is that they ration care. Sometimes, they ration it explicitly, denying certain types of treatment altogether. More often, they ration indirectly, imposing global budgets that limit the availability of high-tech medical equipment, or which require long waits for patients seeking treatment.

In the United States, by contrast, there are no such limits, meaning that the most advanced treatment options are far more available. This translates directly into saved lives.

Take prostate cancer, for example. Even though U.S. men are more likely to be diagnosed with prostate cancer than their counterparts in other countries, they are less likely to die from the disease. Less than one out of five American men with prostate cancer will die from it, but 57% of British men and nearly half of French and German men will. Even in Canada, a quarter of men diagnosed with prostate cancer, die from the disease.

That is, in part, because in most countries with national health insurance, the preferred treatment for prostate cancer is … to do nothing. Prostate cancer is a slow disease. Most patients are older and will live for several years after diagnosis. Therefore, it is not cost-effective in a world of socialized medicine to treat the disease aggressively. The approach saves money, but comes at a human cost.

Similar results can be found for other forms of cancer. For instance, just 30% of U.S. citizens diagnosed with colon cancer die from it, compared to 74% in Britain, 62% in New Zealand, 58% in France, 57% in Germany, 53% in Australia, and 36% in Canada.

Even when there is a desire to provide treatment, national health care systems often lack the resources to provide it. In Britain, for example, roughly 40% of cancer patients never get to see an oncology specialist. Delays in receiving treatment under Britain’s national health service are often so long that nearly 20% of colon cancer cases considered treatable when first diagnosed are incurable by the time treatment is finally offered.

Canada has its own problems. For example, the Canadian Society of Surgical Oncology recommends that cancer surgery take place within two weeks of preoperative tests. Yet one study indicates that median waiting time for cancer surgery in Canada ranged from 29 days for colorectal cancer to more than two months for urinary cancers. Radiation treatment and new therapies, such as brachytherapy, are also less available than in the United States. Consider this: Seven out of ten Canadian provinces report sending prostate cancer patients to the United States for radiation treatment

But the advantages of free-market health care go beyond an absence of rationing. With no price controls, free-market U.S. medicine provides the incentives that lead to innovation breakthroughs in new drugs and other medical technologies. U.S. companies have developed half of all the major new medicines introduced worldwide over the past 20 years. In fact, Americans played a key role in 80% of the most important medical advances of the past 30 years. Eighteen of the last 25 winners of the Nobel Prize in Medicine either are U.S. citizens or work here.

Obviously, there are problems with the U.S health care system. Too many Americans lack health insurance, or are unable to afford the type of care they want. But it is important to understand that, for all its faults and all the criticism that it has received, the United States’ free market health care system has made it the place you want to be if you have a serious illness. Millions of cancer patients have discovered that. And much of the rest of the world might be able to learn something from it as well.

This article appeared in the National Post on March 16, 2006.

Bird Flu

March 27th, 2006 · 4:16 pm  →  Blog

In January, Jane posted this great informational bit on bird flu. If you haven’t looked at it and you’re still under the mistaken assumption that eating chicken will give you bird flu, take a look. She lays it out very plain and simple, although she shows a bit of optimism that I’m not too sure I agree with.

While I share her assessment that the species jump from birds to humans is a very difficult and unlikely one, and the jump from bird-human transmissability to human-human transmissability is a tough leap to make, I do think that its more or less inevitable for two reasons:

  1. Flu viruses mutate RAPIDLY. That’s why you have to (“have to”, the government ought to do a better job of subsidizing this given its almost purely externality, but that’s a different story) get a new flu shot every couple of years. This is something I intend to touch on in a bit, but suffice to say, the virus’s capacity to mutate rapidly will make it more likely to jump species especially since…
  2. Human population density is high, and a large chunk of the world (even though us sheltered Westerners oftentimes forget it) lives in reasonably close contact with animals. Yes, the recent onslaught of bird flu news on the media is more due to people actually paying attention and the media liking to blow things out of proportion, but the fact that we have such dense, mobile populations of humans, especially in close proximity to animals which are oftentimes killed in unsanitary and unclean fashions (remember SARS? not a big deal of a disease, really, but we got it b/c of improper animal killing and preparation). Moreover, research into corpses and medical information from the huge 1918 flu epidemic which probably is a reason the World War I period had such a high death toll suggests that it was a flu virus which jumped from bird to human, so this isn’t without historical precedent.

The big issue, though, isn’t whether or not the virus jumps species. The issue is whether or not we can control such an outbreak. The problem is, simply, we can’t. Today’s world is heavily globalized and inter-connected (which is most of the time a good thing), except that people (and animals) are highly mobile, and impossible to contain. Its simply not possible to quarantine bird flu away. Most areas and countries don’t even have pandemic control plans in place, so even if we wanted to try, there would be little organization (anyone remember the FEMA debacle with Katrina?). Moreover, since the species jump will probably happen in the poor countries where little effort is being undertaken to monitor infected birds and educate farmers and butchers in how to properly kill and dispose of animals, little money is available to implement pandemic controls, it seems highly unlikely that US domestic policy (or the ineffectual WHO) would be able to do anything of significance.

Moreover, and this is really the only real part of where I disagree with Jane, the drug situation is ABYSMAL. For starters, the pharmaceutical industry has no real incentive to produce flu drugs, for two reasons:

  1. Kleenex is cheap. It sounds silly, but it was the reason Vicki Sato (former president of Vertex pharmaceuticals) gave as to why flu drugs aren’t made. For the most part, the accessibility of the vaccine, the high probability of survival with minimal complications (other than feeling really sick for a couple of days), makes people not really want to spend lots of money on flu drugs, making it not a very smart business bet for the pharmaceutical industry
  2. Recent eminent domain acquisitions and the threat of activists around the world to seize flu drugs (ie Taiwan’s ignoring Roche’s patent on Tamiflu) makes it doubly unlikely that pharmaceuticals are going to create a drug which they know they won’t be able to sell for political reasons.

So, that leads us to the drugs and vaccines that we have now. In terms of a vaccine, we are so far away from that its not even funny. We first need a clinical isolate of the virus, then we need to be able to grow it (which is no small task), then we need to be able to know which strains are going to infect people, and then we need to do LOOONG ass clinical trials even if the FDA is on your side and is trying to rush things along. Moreover, our current methodology of mass-producing vaccines relies on ENORMOUS quantities of eggs and specialized equipment — a break in the supply chain (aka like the one recently which prevented Chiron from getting enough flu shots to the US) would completely screw the effort.

With regards to the drugs that we do have, there are two classes. The amantadines and the neuraminidase inhibitors. Frankly, they suck. The amantadines have been in use since the 60s/70s I think, and it has been shown that not only are they highly toxic (they’re teratogenic and they cause Central nervous system problems), but resistance emerges rapidly. Recent studies have also shown that, whether a product of genetic drift or by uneducated Chinese farmers throwing amantadine into their chicken feed (I’m not even joking), many of the viruses out today are resistant to amantadines.

The neuraminidase inhibitors are slightly better in that they are not as prone to resistance because most of the resistant viral strains show a compromised ability to reproduce and spread. But, sadly, there are only two drugs, Tamiflu and Relenza. Both drugs have only been shown to be effective if given prophylactically (ie BEFORE one gets the flu) or within 48 hours of infection, and they only manage to reduce duration of symptoms between 1 to 2 days and ONLY if given during that critical time (so, if you start feeling really sick, its already too late). The drugs themselves are very expensive, and in the case of Tamiflu is synthesized from a naturally derived compound which is in limited supply (Shikimic acid). This is no joke, as apparently Roche has literally bought up the entire world supply, which really comes from apparently four provinces in China which harvest the plant that produce it, the star anise. As for the other drug, Relenza, GSK has stopped making it due to production and formulation problems, as well as very low demand given its price and limited effect.

So… the virus is inevitably going to jump to humans. We have no vaccine and even if we did no system to distribute it or manufacture it to the levels we need. Our drugs suck and are expensive and in limited supply. Not a pretty picture…

Ben 1 – Kitchen 0

March 25th, 2006 · 7:38 pm  →  Blog
My first (pitiful) experience with cooking ended with a reasonable success!

To be frank, I didn’t make an epicurean delight, and I didn’t try to be bold with anything as this was a test run to see whether or not I COULD cook and not poison myself or burn the kitchen down. All I made was rice (which I’ve been making for years already), some pork chops (new for me), and some cabbage/lettuce mix which I stir-fried. Rather pathetically, I had to ask Sophia about how to stir fry vegetables, and about the location of almost all of her utensils and kitchen implements (she was kind enough to give me her room key so I could use their kitchen).

And, much to my delight, the vegetables tasted good! (although a little strange because I cooked them with olive oil, which my family typically doesn’t use since we use corn oil) The meat, too, tasted good (although somewhat bland until I seasoned it some more — its surprising how much you can do with just salt and pepper :-D ). And, of course, I added my zo song (uhh.. dried meat product — seriously, it tastes better than it sounds) to the rice and voila! A meal which made me happy at my first culinary experience (although “culinary” is probably me embellishing my experience with words to make me feel better).

And, on the subject of food, ever wonder why Wasabi burns? For the same reason (or one of them) as to why mustard gas stings :-)

I Toil/I Hate

March 24th, 2006 · 4:58 pm  →  Blog
  • Fourier Series/Transform – Last night (well technically this morning) was the fourth time I had to stay up for a prolonged time toiling over evaluating Fourier Transforms and finding Fourier series. Don’t get me wrong. The concept of Fourier series is very interesting insofar that one can express any function … well, if you factor in Gibbs phenomena distortions … as the sum of sines and cosines, but in practice, they’re just tedious — tests of whether or not I can evaluate long sums of integrals. At least, however, they’re easily checkable … well, again, “easy” in principle in the sense that I spent an hour and a half debugging my MATLAB program (which I must say is the most poorly written computer programming system EVER) to figure out why I wasn’t getting what I was supposed to. On the other hand, the concept of the transform, however, while basic in nature (converting the functional form of one function into another basis) — is very difficult to be able to verify (a problem I had last semester), because I have no idea what the Fourier Transform of anything is SUPPOSED to be, let alone the questions they throw at me for problem sets.
  • Western Blot – This past week, I’ve been working on a large Immunoprecipitation (IP) experiment which is the culmination of all my work in lab since November. 15 plasmids, 30 samples, 3 gels — a week in work for this specific experiment… more or less 5 months of work to get to this stage.. and what happens? I REVERSED THE ORDER OF THE MEMBRANE AND THE GEL (translation to people who don’t know what I’m talking about: the proteins on the gel became lost to the liquid that the experiment was taking place in, rather than move onto the blotting paper which I would then probe to get data). One week of work … gone :-( . At least I’m on Spring Break now … which means I can run the experiment… AGAIN
  • Procrastination – I have been allowing procrastination to screw me over a few too many times. First, I drop the ball on applying to the PRISE program to get free housing for my summer research work. Second, Eric and I (so its not ENTIRELY my fault) don’t figure out who to enter the DeWolfe Lottery (a lottery to get housing from one of the college buildings) until the night before. Third, most of my problem set and academic stresses stem from the fact that at some point in the semester I stopped staying on top of things — leading to my long nights of prepping for presentations and working on problem sets. Fourth, I almost miss out on the chance to go to the Leverett Student-Faculty Dinner by not inviting Vicki Sato early enough (although luckily I did, and we had a very nice and enlightening talk). Fifth, I make the decision to go home for Spring Break too late — causing the plane tickets I can find to be too expensive.