To strive, to seek, to find...

Japanese food explained

2012-02-09T22:43:00.000-06:00

From the Anthony Bourdain and Eric Ripert show at the Paramount Theatre last night: both chefs sang the praises of Japanese cuisine, citing its increasing influence in restaurants throughout America and both saying it would be the one country's food they would they restrict themselves to if forced to do so.

And why Japanese food? Because of its simplicity, its lightness (try eating rich French or Italian food for more than ten days), and its focus on the ingredients. Which lead to Bourdain providing what I thought was the best comment of the night (approximately quoted):

I think the thing that makes their porn so disturbing is the thing that makes their food so great. That is, their obsessive attention to detail.

And one more letter opposing SOPA/PIPA

2012-01-18T14:55:00.000-06:00

This time, from one of my fellow graduate students:

Hello Senator Hutchison,

My name is Lindsey Wolf. I am a PhD graduate student in molecular genetics and microbiology at UT Austin. I'm also a teacher, textbook editor, and part time tutor for the UT Longhorns football team.

I'm 28 years old and did not grow up with the internet. I learned to use it in high school, but feel as though I'm on the tail end of the generation that needed to wander my college library's basement looking for a biology journal article instead of simply looking it up online.

That said, our tax dollars (I say our because I'm also a homeowner in Austin and know what that means) for science and education that pay my salary are best spent saving me time. The ease and speed of looking something up on the internet or teaching my students to do so is an invaluable skill.

Please encourage congress to appreciate the value inherent in sharing information. The country and the world need scientists and teachers like myself and we would be greatly impeded if SOPA or PIPA pass.

Thank you for your time,

Lindsey N Wolf
PhD candidate
University of Texas at Austin

Second letter in protest of SOPA and PIPA

2012-01-18T13:25:00.000-06:00

In support of the day's protests against SOPA and PIPA, I've sent an updated version of my November letter to my representatives. I strongly urge you to contact your Congressional representatives as well—feel free to use any part or all of my letter below as needed.

Dear [CongressCritter]:

I am writing as a concerned voter in your district to once again ask you to strongly oppose the Stop Online Privacy Act (H.R.3261) and to urge your counterparts in the Senate to oppose the PROTECT IP Act (S.968).

While the Internet continues to raise legitimate questions about intellectual property rights and their enforcement, these pieces of proposed legislation are gross, heavy-handed overreactions to such concerns. In their current form, these bills would provide no meaningful protection for intellectual property rights but still threaten critical features of the Internet. Quoting from a November 18, 2011 article in "The Atlantic":

"[U]nder scrutiny, it's obvious that even a conservative accounting of [the] costs far outweigh even an optimistic assessment of [the] benefits. To sum them up, the certain costs include disrupting the business models of countless technology companies that are not in the business of piracy; handing the federal government substantial and unprecedented powers over the Internet; entrenching a guilty-until-proven-innocent attitude toward copyright infringement; making the Internet less secure for everyone; arguably infringing on the First Amendment; contravening internationally recognized Internet standards; and undermining international press freedoms and human rights."

When the bill was first announced, members of the Business Software Alliance as well as members of the Senate expressed grave concerns that such legislation would seriously harm technical innovation, stifle investment in the new ideas and businesses, and harm technology jobs crucial to future economic growth. Key computer scientists also expressed concerns that these bills would damage core components of the Internet's infrastructure and compromise cyber-security.

On January 18th, some of the web's most popular sites like Wikipedia and Reddit joined thousands of others in protesting these bills by "going dark", replacing normal content with pages asking their users to contact their Congressional representatives to stop these bills. Others like Google, Facebook, and Twitter chose not go dark, but nonetheless, continued to express their strong opposition to this legislation.

Groups across the political spectrum—including the ACLU and Electronic Frontier Foundation on the left and the Heritage Foundation and Americans for Tax Reform on the right—have also expressed their concerns about the detrimental effects these laws would have in a variety of areas.

Most importantly, as The Atlantic article notes, these bills threaten our Constitutional rights to due process and free speech. As written, they would allow sites to be blocked without affording those accused of copyright infringement their rights to answer such charges in a court of law; this sort of "guilty until proven innocent" approach to copyright law would have chilling effects. For example, under such laws, the science outreach and advocacy groups of which I am a member could find their web and social media sites taken offline due to accusations of copyright infringement while leaving them with no meaningful legal recourse to challenge such actions—even if their use of copyrighted material is protected by fair-use provisions.

Over the past few months, numerous organizations and ordinary citizens such as myself have expressed our concerns about the myriad ways that these bills will stifle innovation and our constitutional rights. In the coming days, many more will continue to do so. I hope you will take my concerns to heart and join your colleagues (among them, Representatives Issa, Paul, and Pelosi and Senators Cantwell, Moran, Paul, and Wyden) in opposing such legislation.

Sincerely,
[Name here]

Mozart's Requiem and the public domain

2012-01-16T23:41:00.000-06:00

I had the opportunity this past weekend to see the director's cut of Amadeus at the Alamo Drafthouse, which was being hosted by the Golden Hornet Project (GHP) as a fundraiser for their project finishing Mozart's Requiem. Being an Austin-based organization, GHP is doing this work "in collaboration with composers from the rock, hip-hop, video game and avant garde music scenes" and producing a version far different from what Mozart ever imagined—by, for example, modifying the "Larcimosa" movement to use the musical structure of a modern movie trailer. During the live preview performance of the new "Larcimosa", I started thinking about how different projects like this would be had Mozart's Requiem been protected by modern copyright law.

Commissioned as a work for hire, the Requiem would, under the terms of the Mickey Mouse Protection Act (AKA the "Copyright Term Extension Act" or CTEA), be subject to a 95-year copyright. To get an idea of how long a span of time this is, look at the maps below. When Mozart died in December 1791, the United States had just established itself as a new nation, with a three year old Constitution (still missing the Bill of Rights) and 14 states. By the time a 95-year copyright term would have expired in 1886, the U.S. was a nation of 38 states with what we would recognize as its modern shape. By 1886, the American Civil War had been fought, the Transcontinental Railroad built, and the telephone invented.

The United States in 1791 (left) and in 1886 (right). Pink regions denote states, yellow U.S.-controlled territories, and gray territories controlled by other countries. Images by Golbez via Wikicommons.

In 1791 Europe, Louis XVI of France still had his head, Spain was still a dominant colonial power, and the Holy Roman Empire still existed. By 1886, France and Spain were dramatically weakened, the HRE had crumbled, and imperial power was now wielded by England and the newly unified nations of Germany and Italy.

Put another way, had Mozart's Requiem been a new work covered by the CTEA, it would be in the public domain today and freely available for GHP to compose their movie trailer version of "Larcimosa" only if the original had been written prior to 1917.

So, how exactly does such a long copyright term help "promote the progress of science and useful arts"? Is there really a work of art so wonderful that its creation can be incentivized only by offering a period of protection lasting longer than nearly all human lifetimes?

This is not to say that everything should be public domain should upon creation. Artists, writers, and yes, even scientists deserve compensation and legal protections for the intellectual property that they create. But I genuinely find it hard to believe that those artists, writers, and scientists I know would stop producing if tomorrow their copyrights went from the current 95-years (or lifetime + 70 years) back down to the original 14-year term (renewable once to 28-years).

More importantly, creative endeavors build upon what has come before—art and science thrive when we have a vibrant remix culture. I enjoyed last night's performance precisely because GHP didn't have to ask permission or pay a royalty to remixed eight bars of a requiem mass. I look forward to 2014 when GHP's fully completed work is supposed to be released. But I sincerely hope that the opportunity for someone to take that work and freely create some new vision of Mozart's Requiem comes along in 2028 or 2042—not in 2109 as current law dictates.

CTEA and its follow-on acts (DMCA, Eldred v. Ashcroft, and now SOPA/PIPA) have closed the doors on our public domain and our remix culture. It's time to push back at Congress (and, let's face the truth, its RIAA/MPAA underwriters) to open those doors again.

Another bad science headline

2012-01-11T22:57:00.002-06:00

Bad, usually meaning "not quite accurate", science headlines really bother me. Today's example is this BBC article proclaiming "Exoplanets are around every star, study suggests". Except it's not entirely true, is it?

If you read the Nature letter [1], you'll find that what the authors did was to use a small set of gravitational microlensing events associated with known exoplanets to derive estimates of the number of exoplanets across a range of masses (Figure 2 from the paper). Using this plot and applying a bit more math, the authors estimated the expected number of planets (of all masses) in the galaxy, and by dividing that number by the number of stars, they discovered that "on average every star has [~1.6] planets…in an orbital-distance range of 0.5–10 AU" (emphasis mine).

Note, however, that contrary to what the BBC article suggests, this paper does not actually provide observational evidence that every star has at least one planet. The phrase "on average" is critically important and should not have been omitted from the headline—the authors' claims are no where as definitive as "exoplanet(s) around every star", and I'm entirely confident that if we pointed a telescope in just the right direction, we would find a star in our galaxy with zero planets.

I know all of this sounds overly pedantic, but when reporting about science, accuracy is paramount. I strongly dislike the seemingly pervasive perception in popular science reporting that grand claims, even when not entirely supported by the study being reported on, are necessary to make discoveries sound interesting and/or exciting. Such claims, especially when made in headlines, are a great disservice to science, as they leave the audience with a highly distorted view of what has been accomplished and often put scientists in the awkward position of appearing to abandon great discoveries.

In my personal conversations, I often refer to this as the "'broccoli cures cancer' effect", wherein a single experiment finding that compound A, found only in trace quantities in broccoli, kills tumor cells in vitro generates the headline "Broccoli cures cancer!!"

Rant about bad science headlines aside, this is a really cool study. This, along with a previous study [2] identifying planets not gravitationally bound to a star, leads us to conclude that "planets…in our Galaxy thus seem to be the rule rather than the exception."

References

[1] A. Cassan et al. "One or more bound planets per Milky Way star from microlensing observations". Nature 481: 2012. pp. 167–169.

[2] T Sumi et al. "Unbound or distant planetary mass population detected by gravitational microlensing". Nature 473: 2011. pp. 349–352.

Journal impact factors and the reliability of research results

2011-12-27T11:57:00.000-06:00

Via researchblogging.org: A paper in Molecular Psychiatry (subscription required) finds that impact factor weakly correlated with unreliability of research papers, at least in gene association studies. However, there's no reason to think that this finding is not generally applicable to other areas.

It supports statements I've repeatedly made telling people to be careful about immediately believing stuff that appears in high profile/"sexy" journals like Nature Genetics. The nitty gritty part of science (read "replication studies") are usually published in less well-known and less sexy journals, and lord knows it's extremely difficult, if not impossible, to get negative results (i.e., "see, they were wrong—there's actually no signal there at all") published.

That said, I still want at least one of my papers to eventually appear in Nature Genetics (scientist street cred).

What should computational papers report?

2011-12-20T10:40:00.000-06:00

After spending a part of the weekend helping a co-author figure out how we produced a table for a soon-to-be-published paper, I started thinking about what the minimum reporting requirements for a computational paper are or should be in order to guarantee reproducibility of the results.

Clearly, the minimum standard should be the name and version number of the software package(s) used directly in the analysis (e.g., in my case, DNAcopy 1.22.1). Version numbers are critical, as the algorithms in these packages occasionally change in non-obvious ways, leading to startlingly different results. Unfortunately, in my experience, a large number of papers fail to report version numbers (though this is slowly starting to change), and in the times I've been called upon to review a paper, I've always asked authors to include version numbers of all software they used in their edits prior to publication.

In his 2009 paper on repeatability of microarray analyses [1], John Ioannidis pointed out a major factor limiting reproducibility of results is the lack of enough details in how data were processed. I strongly suspect a key reason why such details aren't provided is that many, perhaps most, researchers don't keep particularly detailed notes about what software they used. Certainly, I've been guilty of this, which is why I had to spend my weekend tracking down this issue.

As far as details go though, it isn't clear to me how far up the tool chain we should go. Details about "parent" software systems (e.g., "Bioconductor 2.6/R 2.12.0") might be especially useful to reproduce results, especially if there have been bug fixes or tweaks in versions released since the original analyses were performed. In my analyses for this paper, I've noticed that the same version of DNAcopy gives slightly different numerical results when used with different releases of R, though not enough to affect the conclusions we drew.

Moreover, in cases where the researcher has built their own software (like I do with R releases), I wonder if details like compiler settings need to be provided or whether those are just minutia that only serve to clutter up the literature. Choices for architecture flags (e.g., "-mfpmath=sse -msse4.1" versus "-mfpmath=387" for gcc) or for aggressive optimizations (e.g., "-ffast-math" [2]) certainly have effects on numerical results, though I would argue that conclusions drawn from results that are especially sensitive to compiler flags are dubious at best.

Similar questions can be asked about whether versions for various linked libraries should be reported. Even "standardized" libraries can lead to different behaviors depending on how they are implemented. For example, R and GraphLab behave badly (i.e., segfault in certain circumstances) when linked to GotoBLAS but run fine when linked to ATLAS or Intel MKL.

A final consideration for reporting has to do with randomized algorithms, such as MCMC simulations. Of course, best practices say that the algorithm should be run several times (at least) to ensure that the results are reasonably stable and consistent. However, should the interests of "full disclosure" and reproducibility require us to report the random seeds used to generate our results? Again, I would be highly skeptical of any results that are that sensitive to the initial seed, and in any case, getting such values might be impossible to get if seeding of the random number generator happens deep in the bowels of code that we don't have access to.

My conclusions after thinking about this? Report the version of any packages you use and the version of the parent software; compiler flags, linked libraries, and random seeds are probably extraneous details that can be left out. Of course, there's also the question of how thoroughly code you've developed needs to be tested for numerical stability and other computational "artifacts", but that's an issue I'll discuss at another time.

[1] J Ioannidis, et al. "Repeatability of published microarray gene expression analyses". Nature Genetics 41(2):2009. 144–155.
[2] Though I would argue that you should never use -ffast-math for numerical software.

A bit of Christmas cheer

2011-12-19T17:02:00.000-06:00

Those who know me personally know that three months of Christmas-themed ads make me more than a little cranky around the holidays. But seeing this "LGBT Welcoming" sign at the church near my house brought a smile to my face; I'm glad to be reminded that not every denomination is as strongly homophobic as the talking heads on TV would have us believe.

Ignorance is not funny anymore

2011-12-18T10:27:00.000-06:00

Over at Motherboard, Joshua Kopstein writes a brilliant piece about the current SOPA ~~mark-up hearings~~ clusterfuck entitled "Dear Congress, It's No Longer OK To Not Know How the Internet Works". In it, he identifies a key problem with the legislative process:

Key members of the House Judiciary Committee still don’t understand how the internet works, and worse yet, it’s not clear whether they even want to.

…

[T]he chilling takeaway of this whole debacle was the irrefutable air of anti-intellectualism; that inescapable absurdity that we have members of Congress voting on a technical bill who do not posses any technical knowledge on the subject and do not find it imperative to recognize those who do.

This used to be funny, but now it’s really just terrifying. We’re dealing with legislation that will completely change the face of the internet and free speech for years to come. Yet here we are, still at the mercy of underachieving Congressional know-nothings that have more in common with the slacker students sitting in the back of math class than elected representatives. The fact that some of the people charged with representing us must be dragged kicking and screaming out of their complacency on such matters is no longer endearing—it’s just pathetic and sad.

Of course, this sort of behavior is not limited to just the current House debate on SOPA. We see it time and time again with science-based policy—creationism, global warming denialism, and anti-vaccination campaigns being some of the more prominent examples.

This is not to say that ignorance, in and of itself, is a bad thing. We're all ignorant about many things, and ignorance can be useful when it leads us to ask the right questions.

But somewhere along the way, our political culture developed to a point where ignorance and a staunch, if not defiantly proud, refusal to do anything about it was not only accepted but celebrated as well. Now, I understand how letting a small group of experts decide "best" policy seems contrary to our collective notion of democracy, and I'll be the first to admit of groups of expert have been wrong before. What I don't understand, though, is why such mistakes in the past means that all expert opinion should be discounted and denigrated. One of the consequences of admitting ignorance should be letting those that should and do know better inform and guide our decision making. Instead, we increasingly seem to reward those who happily stick their finger in their ears and scream "I'm not listening" with (for example) political office, and no good can come from that.

I appreciate the efforts by activists like Lawrence Lessig to reduce to corrupting influence of money on our political processes. But until we find a way to remove the "I reject your facts and substitute my own reality" and "all points of views are equally valid" attitudes that pervade our (political) culture, I don't see any real way to make substantive changes.

Dinner at Hudson's on the Bend

2011-12-09T08:08:00.000-06:00

I went with a friend to Hudson's on the Bend for dinner Wednesday night. Both of us opted for the chef's three course tasting menu with the paired wines, along with an additional appetizer off the regular dinner menu. Our overall impression was very positive: the ambiance and service were great, and the quality of the food was excellent and well worth the price we paid. My tasting notes for each courses are provided below.

Amuse-bouche (courtesy of the chef): apple and goat cheese tart with cranberry sauce. The pastry was well done—properly light and fluffy. The tastes of the goat cheese and apple were well balanced, with the apple providing acidity even if the actual taste of apple was masked somewhat by the stronger tastes of the goat cheese and pastry dough. The cranberry sauce had a nice spice from the chili in it. However, I found it easy to accidentally pick up too much sauce, in which case, the sauce took over and masked the other flavors of the dish, making it taste more like a cranberry tart. The chives seemed a bit unnecessary, adding a not entirely complementary bitterness or grassiness to the dish.

Appetizer (off the regular menu): venison prosciutto wrapped scallops, topped with candied yuzu and American sturgeon caviar, on a cedar plank with a soy yuzu dipping sauce. The scallops were very fresh and perfectly seared to the right soft texture. The venison prosciutto added crispness and saltiness to the dish and fortunately didn't taste very strongly like actual venison (since that would add a potentially off-putting gamey flavor). The candied yuzu and caviar were both wonderful, adding hints of sour and salty, respectively, as well as some textural contrast. The soy yuzu was good and not overly salty.

First course: chipotle lobster bisque with a parmesan puff pastry. Served by placing chunks of butter-poached lobster in the bowl, topping with the puff pastry (the triangle shaped object in the picture), and pouring in the liquid bisque. The lobster was sweet, appropriately buttery, and well textured (not rubbery). I wasn't a huge fan of the pastry, which was a bit chewy, but I was willing to overlook that giving the quality of the rest of the dish. This bisque was a bit thinner than the versions I'm used to, but it was a wonderful mix of the traditional flavors with the smoke and spice from the chipotle. The dish paired well with the Reisling, which had nice acidity and apple flavors, without being overly sweet.

Entrée: espresso-rubbed, smoked elk backstrap with lime chipotle beer blanc. The backstrap was smoked for 12 hours at low temperature to medium-rare with a beautiful smoke ring, then quickly seared on the grill to form a crust. The coffee and smoke mixed well, and the elk had just the right level of gaminess and a soft, almost melt in your mouth consistency. The sprigs of fresh rosemary on the side were a great idea, providing an aromatic complement without the overpowering taste or texture that comes with actually eating rosemary leaves.

The beer blanc tasted great, though given its richness, the amount provided might have been a bit much; as with the amuse-bouche, I found it easy to pick up just a little too much sauce and have that taste overpower the focus of the dish (i.e., the elk). The potatoes and other vegetables were buttery and delicious, though nothing particularly special. The dish was paired with a California pinot noir--earthy, nice oak, not at all tannic, and with the right body to match the elk.

One minor quibble: I'm not entirely sure why the flower was needed in the plating. This is entirely a personal preference, but I find extra items on a plate that don't have a clear purpose mildly annoying.

Dessert #1 (pictured on the right): wild turtle pie (caramel pecan pie dipped in Belgian chocolate). The filling was well textured and tasted very much of pecans. I had minor issues with the consistency of the chocolate coating (which was tough to break through with a fork) and with the crust (which I found to lack the "right" level of richness and flakiness). The fruits were a little lackluster, but that's entirely forgivable since good fresh (non-citrus) fruit is pretty much impossible to find in December. Overall, an enjoyable dessert but nothing spectacular.

Dessert #2 (pictured on the left): pumpkin white chocolate bread pudding with bourbon praline sauce and vanilla ice cream. This was my favorite of the two desserts. The tastes of both the pumpkin and white chocolate were both nicely subtle, enough to provide richness and hints of taste without adding too much sweetness (I don't like very sugary desserts). The bourbon praline sauce was excellent—nutty and not strongly alcoholic. The vanilla ice cream tasted pretty generic (Blue Bell anyone?), but that didn't really from the dish.

Dessert was served with a Spanish grenache, which was a good but not stand out wine. (The lack of more-detailed tasting notes here probably has much to do with me not focusing on the wine during dessert.)

What exactly do we mean by "personalized medicine"?

2011-12-06T22:25:00.001-06:00

Orac wrote a brilliant take down of Stanislaw Burzynski's "personalized gene-targeted cancer therapy" claims yesterday and in it, raised an important reservation about the term "personalized medicine" that I happen to share (emphasis mine):

At the risk of annoying some colleagues I know, I'm going to point out that I never really liked the term "personalized cancer therapy" or its many variants, for the simple reason that it always struck me as more of a marketing term than a scientifically meaningful description of what targeting therapy to the genetic makeup of a patient's tumor will eventually entail. In fact, I think I now prefer another term, which has been used by Cancer Research U.K., namely "stratified medicine." The reason is that what we as clinicians are doing when we "personalize" or "individualize" therapies isn't really "personalizing" the therapy so much as using various measurements and biomarkers to place patients into groups of patients who respond to specific therapies. What the modern version of "personalized" therapy is really doing is producing more and more groups of patients, each of which, is smaller than the last, to be matched to more and more therapies. Whether the groups will eventually reach an N of 1, I don't know, but that is the goal. Only then will we truly have "personalized medicine."

Promises that "personalized medicine"—a therapeutic course tailored exactly to your specific presentation of a disease—is just around the corner seem to follow every announcement of a newly discovered mutation or newly developed technology. We are already largely there when it comes to "personalized genomics". Direct to consumer companies like 23andMe genotype enough markers that each customer's profile is pretty much guaranteed to be unique, and reasonably low-cost whole genome sequencing should be available Any Day Now(TM). Couple these with other technologies (e.g., high-throughput proteomics assays), and I'd venture a fairly confident guess that we'll be able to place each patient into a group of one within a decade.

What I'm much less sure about is how useful being placed in an "N of 1" group will actually be. Suppose the day of the sub-$1000 genome has arrived, and we can easily obtain the full somatic mutation spectrum of a given patient's tumor and even manage to separate driver and passenger mutations. How exactly would the uniqueness of this spectrum help? Any mutation truly private to this patient (e.g., in a gene never before observed to be mutated in cancer) would, with very high probability, be an impossible therapeutic target. The utility of knowing a mutation spectrum comes from our ability to use it to place in the patient in multiple groups, each with N much, much greater than one. In other words, the reason why we know targeted therapies work is because we've seen mutations in the target gene before.

We should also remember that medicine, and biology more generally, are largely a statistics game. Knowing that a breast cancer patient has a mutated HER2 gene is not a 100%-guarantee that Herceptin treatment will be effective—it just makes it far more likely. Similarly, even if we knew all of the risk-conferring or causative variants for a complex trait (height, type-II diabetes, etc.), gene–gene and gene–environment interactions would basically destroy our ability to make definitive statements about an individual's phenotype, regardless of how unique that person's genotype spectrum might be. Like I said before, these sorts of statistics are applicable not because each person is in a group of one but because he/she belongs to a unique combination of groups of many.

All of this then is my long-winded way of saying let's stop (over)using "personalized medicine" and switch to using "stratified medicine" instead. Not only is "stratified medicine" a clearer, much better approximation of our true meaning, it also stops us from making promises that either can't be fulfilled or are much less useful than most people would imagine.

Letter to Congress: Stop PROTECT IP and SOPA

2011-11-21T20:43:00.001-06:00

The Electronic Frontier Foundation and Fight for the Future (among others) have issued calls to action asking us to write our Congressional representatives to have them stop the SOPA and Protect IP from passing. Here's the letter I sent to my representative and senators:

Dear [CongressCritter]:

I am writing to you as a concerned voter in your district. I strongly urge you to oppose the Stop Online Privacy Act (H.R.3261) and to urge your counterparts in the Senate to oppose the PROTECT IP Act (S.968).

While the Internet continues to raise legitimate questions about intellectual property rights and their enforcement, these pieces of legislation are gross, heavy-handed overreactions to such concerns. In their current form, these bills provide no meaningful protection for intellectual property rights but still threaten critical features of the Internet. Quoting from a November 18, 2011 article in "The Atlantic":

"[U]nder scrutiny, it's obvious that even a conservative accounting of [the] costs far outweigh even an optimistic assessment of [the] benefits. To sum them up, the certain costs include disrupting the business models of countless technology companies that are not in the business of piracy; handing the federal government substantial and unprecedented powers over the Internet; entrenching a guilty-until-proven-innocent attitude toward copyright infringement; making the Internet less secure for everyone; arguably infringing on the First Amendment; contravening internationally recognized Internet standards; and undermining international press freedoms and human rights."

A number of a technology companies (including Google, Facebook, Twitter, EBay, and members of the Business Software Alliance), as well as various members of the Senate, have expressed grave concerns that such legislation will seriously harm technical innovation and stifle investment in the new ideas and businesses crucial to future economic growth.

More importantly, as "The Atlantic" article notes, this legislation threatens our fundamental Constitutional rights to due process and free speech. As written, these bills would deny those accused of aiding in copyright infringement the right to answer the charges against them before their sites are blocked from the Internet. The detrimental consequences of such actions cannot be overstated. If this legislation passes, outreach organizations--including those of which I am a member of at my university--could find their web and social media sites blocked due to accusations of infringement arising from use of media normally covered by fair-use provisions, while leaving them with no meaningful legal recourse to challenge such actions.

Over the past few days, numerous businesses, advocacy organizations, and ordinary citizens such as myself have expressed our concerns about the myriad ways that these bills will stifle innovation and our constitutional rights. In the coming days, many more will continue to do so. I hope you will take my concerns under serious consideration and join your colleagues (among them, Representatives Issa, Paul, and Pelosi and Senators Cantwell, Moran, Paul, and Wyden) in opposing such legislation.

Sincerely,
[Name here]

I strongly encourage you to call, write, and carrier pigeon your CongressCritter to stop these ludicrous bills. Feel free to use any or all of my letter (though you might want to change the bit about outreach organizations unless you're so involved), but please, act!

For more information about the potential consequences of the SOPA and the PROTECT IP Act, refer to this CNet FAQ and various articles linked to under the Twitter #protectip and #sopa tags.

Never ending questions in science

2011-11-18T14:28:00.001-06:00

Via RealClimate.org, this great quote by Earl C. Kelley from a 1951 learning workshop:

We have not succeeded in answering all our problems. The answers we have found only serve to raise a whole set of new questions. In some ways we feel we are as confused as ever, but we believe we are confused on a higher level and about more important things.

It's one of the best expressions of "productive ignorance", the notion that no matter how hard we try, we will never truly discover everything there is to know about the universe. This sense of doubt and uncertainty is not a bad thing—it's precisely the thing makes science fun.

Grilled fish with fennel and lemon

2011-10-31T23:51:00.000-05:00

One of the benefits of living in Texas is that the weather in late October is still pleasant enough for evening outdoor activities (unlike, for example, the Northeast which is now under many inches of snow). We made use of this fact and spent this past Sunday grilling at a friend's house, where I experimented with a slightly different approach of grilling fish. Nothing presented here is at all original, so this post is mostly documentation of what worked and what could be improved.

The motivation for this experiment is to find a way to introduce complementary flavors to grilled fish without resorting to wrapping in aluminum foil, which in the presence of ingredients with quite a bit of water in them, tends to steam the fish as much as grill it. The key device that makes it all work is the grill basket, which keeps all the little bits together while cooking with dry heat only. In theory, forgoing the grill basket and directly placing everything on the grill grate is possible, but I don't imagine that would work out well; e.g., plenty of seared fingers while trying to place everything on a hot grill.

Adding complementary flavors to the fish is done by grilling on a bed of other ingredients. For this trial run, I chose a fairly traditional mix of fennel and lemon. Create a base layer of thinly sliced fennel bulb, a second layer of fennel fronds, and a top layer of lemon slices.

One thing I learned from this experiment is that each of these layers should be cut quite thin. For this method to work well, I think each layer of ingredients has to char slightly, so that the resulting smoke can help flavor the fish just that little bit more. So, the slices of fennel bulb and lemon pictured here are far thicker than optimal.

Fish of choice on Sunday was Pacific sockeye salmon, though any firm, fatty fish like sea bass would have worked as well. I would avoid thick cuts of fish (hard to get flavors all the way through without drying out) and things like tuna or swordfish (very strongly flavored to begin with). Prep by removing any pin bones, bringing to room temperature, and seasoning with salt and pepper.

Place the fish meat-side down on the other ingredients and close the grill basket. Grill with the skin-side up until almost done (~90%), then turn over to finish crisping the skin.

Unfortunately, the power went out while we were cooking, so this image of the final product isn't of the best quality. Still, the nice char on the fennel bulb is visible, and all in all, the fish turned out well with the right hints of anise (from the fennel) and lemon. Obviously, some room from improvement (e.g., thinner slices of the fennel and lemon as I mentioned above) but definitely on the right track.

Funny lab quote of the day

2011-10-25T17:13:00.001-05:00

From one of my lab mates, today's funny but cynical truth:

"Heuristic" is basically a nice word for "something you pull out of your ass".

Justified only because "it works", and let's hope to [choice of deity here] that it keeps on working.

Thoughts on "El Bulli: Cooking in Progress"

2011-10-25T14:03:00.001-05:00

Last night, I joined a couple of friends to catch the new documentary on Ferran Adrià's restaurant El Bulli (recently closed to be restructured as a culinary academy). All in all, this is a good film that provides insight into the processes, creativity, and plain ol' hard work that went into creating most highly regarded avant-garde cuisine in the world. Particularly interesting was the manner in which the chefs talked about constructing individual dishes, which strongly reminded me of the way my orchestra conductors (from many years ago) talked about composing music and structuring a performance.

On an entirely different note, the movie also interested me as a scientist in the meticulousness in the chefs displayed in their experiments to find new tastes and methods, even if they engaged in the big no-nos of taking notes on loose leaf paper and in pencil. Also, I was possibly the only person in the theater who laughed at Adrià's question, "Is Nature an important magazine?" Yes, yes, it is, and I would strongly the possibility of sacrificing my grandmother to have a publication in it.

With simple, though well done, shots and with neither narration nor text explanations, this movie clearly targets a very specific audience, and I strongly suspect that people who aren't "foodies" would be easily lost, e.g., in identifying some of the items Adrià's head chefs play around with. Additionally, as my friends noted, this movie is perhaps a bit too long, and several scenes, such as the one showing Adrià tasting and making notes (without subtitles enplaning what exactly he was writing), could have been easily cut without significantly impacting the movie.

A question I walked away with and still haven't found a good answer for is whether I would have actually paid the 250-odd Euros to have eaten at El Bulli; that price was certainly more than reasonable for what one got, even if it contributed to the financial difficulties the restaurant found itself in prior to its closing. As Adrià himself noted in this profile in The Observer, the point of dining at such places is not necessarily "good food" but the emotional experience of witnessing chefs at their creative best:

Ask Adrià and he will agree that a piece of plain fish, freshly caught and grilled to perfection can be as pleasing to taste as the elaborate invention of the cleverest chef. "Eating well is something you can do at home. The point about what we offer is that it is more than eating; it is an experience," says Adrià, who in one of his books has defined eating at El Bulli as a night out at the theatre. "What's radical about us rests not on what we serve, but on how and where."

My issue then is that while the food that came out of El Bulli looks stunning as works of art (AKA food pron), something about the molecular gastronomy dishes doesn't have the same strong emotional appeal to me as the more traditionally prepared ones from restaurants such as The French Laundry and Le Bernardin. Certainly I would have found Adrià's food delicious and interesting, but somehow, I don't think it would have given me that "I wish I had just one more bite of that" feeling Thomas Keller identifies as key to haute cuisine. And that to me is the whole point of seeking to dine at restaurants such as El Bulli.

Finally, one of my other favorite clips from the movie: shopping Barcelona’s La Boqueria market. It said something about the clout and respect chefs from El Bulli had when they could go and buy exactly seven individual grapes and three beans:

Roasted squash risotto

2011-10-21T00:33:00.001-05:00

Not feeling like discussing technical topics at the moment, I thought I'd try something different and write about a recipe I developed tonight: a roasted squash risotto. The version I present here has pork and dairy in it, but the recipe should work just as well omitting either or both, if you would prefer a vegetarian or vegan version.

Ingredients

Butternut squash
Acorn squash
Mushrooms
Shallots
Arborio rice
Vegetable stock (chicken stock should work as well)
Prosciutto or pancetta (optional)
Parmesan cheese (optional)
Butter (optional)
Olive oil
Salt and pepper
Nutmeg

Procedure

Skin and dice the butternut squash into 1/2" to 3/4" cubes. Slice the acorn squash to ~3/4" rings. Don't worry about skinning the acorn squash at the moment; it's pretty much impossible to do while raw but is trivial once roasted.

Par-cook the squash by roasting in the oven at 350-375ºF for about 20 minutes until just soft. Important: Don't cook the squash all the way through (i.e., to the softness you expect when you eat it) as it will finish cooking when added to the rest of the risotto. Cooking the squash all the way through during the roasting stage will just lead to mush in the final product.

Once the acorn squash has cooled enough, skin and dice into 1/2" to 3/4" cubes.

While the squash is cooking, prepare the rest of your mise en place by slicing the shallots and mushrooms (~1/4" slices), mincing the proscuitto, and shredding the Parmesan cheese.

Sweat the shallots on medium-low to medium heat until slightly translucent. Increase the heat a little, add the mushrooms, and cook until the mushrooms lose most of their water and turn slightly brown.

If using, add the prosciutto (or pancetta), and cook until the fat has been rendered and the edges start to crisp.

Increase the heat a little more. Add the rice, and cook (toast) until the grains start developing translucent edges.

Deglaze the pan using some stock. Then follow "standard risotto procedure" by adding a little bit of stock, stirring until the liquid is absorbed, and repeating.

When using store-bought stock to make risotto, I switch to using plain water about half way through; the taste of such stock tends to be quite strong, and I don't want the stock to overpower the flavor of the rest of the ingredients. With homemade stock (which is what I should really be using), I have a bit more control of how flavorful the stock is, so switching to water may not be necessary.

When the rice is about three quarters of the way done, add the par-cooked butternut squash, and continue with the risotto procedure. Owing to the large number of factors affecting how the rice cooks, the only way to really tell where this three quarters mark is to taste the rice; I find the "right" time to add the butternut squash is when the rice is soft on the outside but still has a raw texture (slightly crunchy and starchy) towards the middle.

When the rice is mostly (say 90%) done, add the acorn squash before finishing the rice. I add the acorn squash towards the end because it's softer than the butternut squash, and adding both at the same time would turn the acorn squash to mush.

When the rice is done cooking and has a nice creamy texture, turn down (or off) the heat, and finish the risotto by stirring in the Parmesan cheese and butter until both are fully melted and integrated.

Plate and serve.

Quote of the day

2011-08-30T14:06:00.000-05:00

This time about language. From a 1990 Usenet post by James Nicoll:

The problem with defending the purity of the English language is that English is about as pure as a cribhouse whore. We don't just borrow words; on occasion, English has pursued other languages down alleyways to beat them unconscious and rifle their pockets for new vocabulary.

On "productive stupidity"

2011-07-11T14:37:00.000-05:00

Martin Schwartz offers some interesting observations about the important role of what he calls "productive stupidity" in scientific research. He begins by explaining the great epiphany that I think all scientists (at least the good ones) eventually have — namely, that no matter how smart or well informed we think we might be, we really don't know all that much:

The crucial lesson was that the scope of things I didn't know wasn't merely vast; it was, for all practical purposes, infinite. That realization, instead of being discouraging, was liberating.

However, such ignorance is far from a bad thing, as it's a key factor in developing research questions (emphasis mine):

Productive stupidity means being ignorant by choice. Focusing on important questions puts us in the awkward position of being ignorant. One of the beautiful things about science is that it allows us to bumble along, getting it wrong time after time, and feel perfectly fine as long as we learn something each time. … The more comfortable we become with being stupid, the deeper we will wade into the unknown and the more likely we are to make big discoveries.

Schwartz notes that the current PhD system fails students by (1) not helping them "understand how hard it is to do research" and (2) not teaching "how to be productively stupid", i.e., that feeling "stupid" is not the same as "not really trying".

One minor quibble I have with this article is Schwartz's choice of words. In the context of driving research, "stupidity" has entirely the wrong connotation. We'd do much better calling this "productive ignorance" instead.

Schwartz's article is a great reminder why it's important, especially for grad students and post-docs starting out in their research careers, to talk to people outside their labs and specific field on interest. PIs and lab members certainly help in identifying the depth of one's ignorance, but going back to the old quip that experts know everything about nothing, discovering the true breadth of your ignorance requires communicating with people in completely unrelated fields.

In my experience at least, "formal" settings such as group meetings or conference talks are strangely not the best places to engage in such communication. Such settings often make us feel constrained about the questions we think about and ask, for reasons ranging from time constraints limiting us to ask precise questions on technical details to not wanting to appear completely ignorant to senior members in our field.

Therefore, I think there's something to be said for meeting as often as possible in more informal settings, e.g., happy hours or meals at conferences with people whose sessions we never really cared to attend. Even better are gatherings with people who don't do research for a living. Deep down, all scientists have more than a little geeky. We like to be asked about and telling stories about our work, and in informal settings, it's far easier to raise those "silly" questions and kick around those "crazy" ideas that ultimately lead to profound research problems and great discoveries.

Rolling Stone on Michelle Bachman

2011-06-27T12:40:00.000-05:00

Matt Taibbi of Rolling Stone offers commentary and a profile of Michelle Bachmann's political career, including her bizarre stances on a number of key issues. Among his more salient points:

In modern American politics, being the right kind of ignorant and entertainingly crazy is like having a big right hand in boxing; you've always got a puncher's chance. And Bachmann is exactly the right kind of completely batshit crazy. Not medically crazy, not talking-to-herself-on-the-subway crazy, but grandiose crazy, late-stage Kim Jong-Il crazy — crazy in the sense that she's living completely inside her own mind, frenetically pacing the hallways of a vast sand castle she's built in there, unable to meaningfully communicate with the human beings on the other side of the moat, who are all presumed to be enemies.

…

Bachmann's entire political career has followed this exact same pattern of God-speaks-directly-to-me fundamentalism mixed with pathological, relentless, conscienceless lying. … She is at once the most entertaining and the most dangerous kind of liar, a turbocharged cross between a born bullshit artist and a religious fanatic, for whom lying to the infidel is a kind of holy duty.

It's terrifying to think she is currently tied with Mitt Romney as the leader in the Republican presidential field. If she does win in the primaries, 2012 will be one interesting election to remember.

Nate Silver compares Cuomo and Obama on gay marriage

2011-06-27T09:46:00.000-05:00

Via Glen Greenwald's Twitter feed, a commentary by Nate Silver (of FiveThirtyEight.com) comparing Governor Andrew Cuomo's leadership on the gay marriage issue compared to President Obama's. The key message (emphasis mine):

It’s also a brand of leadership that many Democrats I speak with feel is lacking in President Obama.

Mr. Obama has some considerable achievements, including his health care bill and the reversal of the military’s ban on openly gay and lesbian soldiers. But he often seems to achieve them by outsourcing much of the work to Democrats in Congress or to his various lieutenants. And his considerable speaking abilities sometimes seem to be directed more toward healing the country in times of crisis than toward persuading it to move in a new direction.

It’s a strategy that Mr. Obama’s critics and admirers have sometimes characterized as “leading from behind.” One could rightly argue that being president of the United States is an order of magnitude more difficult than being governor of New York, and that Mr. Obama’s performance has been fair to good under the circumstances. But his seemingly risk-averse approach roils many Democrats, even as most of them approve of his overall performance.

Quote of the day

2011-06-20T13:05:00.000-05:00

Via Ed Brayton, this quote by Isaac Asimov:

There is a cult of ignorance in the United States, and there always has been. The strain of anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that 'my ignorance is just as good as your knowledge.'

How much is it worth to you?

2011-06-19T09:36:00.000-05:00

Some days, I just have to wonder how much a first authorship is really worth. Due to circumstances I won't describe here, a new graduate student has been added as an author on a paper I've been trying to push out for the last year or so, ostensibly to help finish work on the validation data.

Unfortunately, this has not worked out quite as planned. Instead of expediting the writing process, this new co-author has required me to spend an inordinate amount of time having to explain things like (1) why probes targeting regions of the Y chromosome fail in females and (2) why I'm not going to spend my time re-uploading another 10-GB of data just because said co-author refuses to use sed to replace "NA"s with "Null"s.

Then, there was this recent conversation at 10pm on Saturday (edited for formatting):

Me: Didn't you have all of my old, original data at one point?

Student: Yes I did. And then I generated the [data] file and deleted them for space. But then I found a bug in my calculation so I don't want to use those [generated] files anymore.

Now, I realize that I had more than a few years of lab experience before coming back to graduate school, so I might have some unreasonably high expectations of other grad students. However, I don't think it's that unfair to expect even a first-year student to intuitively realize that deleting your original data files is a Very Bad Idea (TM).

In any case, I don't particularly feel like spending time this weekend writing a script to dig through ~400-GB of compressed tarballs to find the eight files in question, so I think my nice-ish way of saying "You deleted your original data?! Yeah, screw you; you're on your own. I'm going drinking with my friends." will have to do for now. Yet one more thing to add to my "To Do" list on Monday.

PowerPoint Horror

2011-06-16T16:25:00.000-05:00

Via PZ Myers, the InFocus Labs Worst PPT Slide Contest that uncovered this abomination of a PowerPoint slide:

Myer's blog also features this great comment on PowerPoint:

Now I know what you're thinking. 'AJ, software can't be evil. It's like the people with guns kill people thing.'

You are wrong. Dangerously deluded, even. PowerPoint is evil. Worse, it's one of those truly banal evils Arendt warned you about. It's not even an evil you can respect and at least be amused a little by, like a properly flamboyant mad scientist/supervillain/movie baddie...

Nay, PowerPoint and its clones are a beige kind of evil. The kind that eats your brain and doesn't even fucking appreciate the taste. Compare and contrast: Cthulu and the related tentacled horrors from the vasty deeps, at the least, seem to enjoy their work.

That'll do, rover. That'll do.

2011-05-25T10:31:00.002-05:00

Seven years and 4.8 miles later, NASA has decided to abandon Spirit after being unable to communicate with the rover for over a year. This XKCD comic seems poignantly apropos today (even if it is a bit anthropomorphic):

Thanks for Fark (of all places), I've discovered that all 128,222 images taken by Spirit are available online through the mission's webpage.

Quote of the day

2010-05-13T11:49:00.000-05:00

Comes from Scott Cunningham's comment posted at Respectful Insolence:

Science is unpopular for good reason. It caused the extinction of the faeries. It caused magic powers to fail inexplicably on The Amazing Randi's show. It kidnapped every child's imaginary friends and won't tell us where it's hiding them.

So Elvis is dead...

2010-02-23T23:44:00.000-06:00

But at least his passport lives on:

In the name of improved security a hacker showed how a biometric passport issued in the name of long-dead rock 'n' roll king Elvis Presley could be cleared through an automated passport scanning system being tested at an international airport.

Using a doctored passport at a self-serve passport machine, the hacker was cleared for travel after just a few seconds and a picture of the King himself appeared on the monitor's display.

…

Van Beek said: "What we did for that chip is create passport content for Elvis Presley and put it on a chip and sign it with our own key for a non-existent country. And a device that was used to read chips didn't check the country's signatures."

So, the ability to enter a country using an electronic passport is essentially dependent on trusting a certificate authority whose public key we don't have? I feel so much safer now...

How to create TV news

2010-02-22T08:59:00.000-06:00

From Charlie Brooker's Newswipe, the world's most generic TV news report:

Mathematical WTF-ery

2010-02-21T11:17:00.000-06:00

Maybe it was just because it was late, but while reading the comments following Mark Chu-Carroll's post on debating John Gabriel, I found this comment (#432):

[snip]

Reading "axiom of choice" now on Wikipedia...maybe that will help.

followed shortly thereafter by this comment (#433):

Reading "axiom of choice" now on Wikipedia...

And now I wish I hadn't: Whatthefuck?!?!?!?! That's going to bother me for a long time...

[snip]

to be hysterically funny.

The axiom of choice is one of my favorite WTFs in pure mathematics since it's "intuitively obvious" (i.e., "of course I can pick an element from every non-empty set") and yet leads to bizarre results, such as sets of reals having a well ordering and the Banach-Tarski paradox (visit Irregular Webcomic for a decent informal explanation). Now, the follow up comment rightly noted that much of why the Banach-Tarski result seems "wrong" is because our physical intuitions about measures such as "volume" and "surface area" break down when talking about objects like the Menger sponge (which has infinite surface area and zero volume). But that doesn't mean there aren't times when math is just freaking weird.

Yet more evidence to never trust polls

2010-02-12T22:36:00.000-06:00

Posted on today's New York Times Politics and Government Blog:

Seven in 10 respondents said they favor allowing “gay men and lesbians” to serve in the military, including nearly 6 in 10 who said they should be allowed to serve openly. But support was somewhat lower among those who were asked about allowing “homosexuals” to serve, with 59 percent in favor, including 44 percent who support allowing them to serve openly.

Democrats in the poll seemed particularly swayed by the wording. Seventy-nine percent of Democrats said they support permitting gay men and lesbians to serve openly. Fewer Democrats however, just 43 percent, said they were in favor of allowing homosexuals to serve openly. Republicans and independents varied less between the two terms.

As the post notes, "these findings illustrate the influence that simple language can have". That or there is now a new group of "homosexuals" that are neither "gay" nor "lesbian".

Just how anonymous are you?

2010-02-10T13:05:00.000-06:00

The Electronic Frontier Foundation (EFF) posted an interesting tool called Panopticlick that assesses how unique (and consequently trackable) you are online, based solely on your browser configuration. That is, even if you limit or disable cookies, your browser "leaks" information that (potentially) could be used to uniquely identify you.

In my case, the most revealing information came from my plug-in and font listing, which provided 18.22 and 19.22 bits [1] of information, respectively. Translated, my plug-in and system fonts were sufficient to uniquely identify me out of the ~610,000 browsers tested.

Unfortunately, the EFF points out that defending against such tracking is pretty difficult, since completely disabling JavaScript (which provides most of these data) tends to break the functionality of a large number of sites out there these days.

[1] Read the EFF's "A Primer on Information Theory and Privacy" if you're not sure what the term "bits" means.

Ruining childhood stories

2010-01-19T15:47:00.003-06:00

And in the process, teaching children the cruel realities of life (from the 18th Dec. 2009 edition of "The Now Show"):

It isn't, of course, remotely surprising that we are so sentimental about animals and that we project our own emotions into them. "Oh, I don't like sitting the rain, so seagulls probably don't either." It's not surprising that we think like this because we're conditioned to it right from childhood.

[Cue cutesy music]

Winnie the Pooh looked at Christopher Robin...then ran forward, jumped up, and tore out his throat, biting off great lumps of his flesh.

"Serves him right for not realizing what bears do," said Eeoyre. "Now, where's Owl?"

"Killing mice," said Rabbit. "That's what he does. He's not wise about anything. He's just an anthropomorphic fallacy."

Just then, they heard a terrible squeal, and Piglet was lead into the slaughterhouse to be turned into sausages. "Oh, I knew we shouldn't have sold Hundred Acre Wood to Hugh Fearnley-Whittingstall," said Rabbit.

Amusing things about Frankfurt International

2010-01-08T17:04:00.001-06:00

It's clearly very late because these things are way funnier than they should be:

The security personnel here ride bikes around the airport at very high speeds.
Google AdSense for some reason has decided to offer me a chance to win a U.S. Green Card.

It's finally over

2008-11-04T23:53:00.004-06:00

Almost two years since the long slog we called the 2008 U.S. Presidential Election started, it's finally ended, and Barack Obama is the President Elect. Other blogs can fill in the praise and the analysis, but I'll leave a few comments here.

First, I thought McCain delivered a conciliatory and gracious concession speech; kudos to him. Second, what the hell was wrong with the McCain crowd? Yes, your candidate lost, but come January 20th, there will be a new President. Booing the President Elect (more than once, no less) is not putting "country first".

Kudos to fivethirtyeight.com for being remarkably good at poll aggregation. With Alaska, Indiana, Missouri, Montana, and North Carolina still to be called, the electoral college breakdown is 338-156 for Obama, and the popular vote is 51.3%-47.4% for Obama. This is pretty much in line with fivethirtyeight.com's predictions of 348.6-189.4 for the electoral college and 52.3%-46.2% for the popular vote. Well done indeed.

Finally, to the Democratic Party. You now have control of the Presidency and both houses of Congress. Given the lackluster performance of this party over the last eight years, I ask of you now: please, please, don't screw this up.

Oh Hugo!

2008-10-28T14:07:00.002-05:00

Where would U.S. political humor be without Mr. "Crackers from Caracas" (as The Bugle calls him), Venezuelan president Hugo Chavez. Quoting him:

"I saw the vice presidential candidate, there she was talking about 'the dictator Hugo Chavez.' The poor thing, you just feel sorry for her.…She's a beauty queen that they've pulled out to be a figurehead. We need to say as Christ did: Forgive her, she knows not what she's saying."

Invoking Jesus (Luke 23:34) to take a verbal swing at Sarah Palin — you stay classy, Hugo.

Run for the hills!

2008-10-14T00:01:00.002-05:00

Armageddon is coming! On Fox News Sunday, Bill Kristol said this of John McCain's campaign:

It's a stupid campaign. It's not a horribly mean spirited or racist or disgraceful campaign. But it's...it's really become a pathetic campaign, in the sense that there's no strategy. They're flailing around. They do things that don't work and keep on doing them. They're out of sync with their own candidate now...

To which McCain campaign spokesperson Nancy Pfotenhauer replied on Fox News yesterday (emphasis mine):

Well, you know Bill is entitled to his perspective. And I used to work for Bill. And I can tell you personally sometimes he’s brilliant and sometimes he’s not. And this is one where it’s the latter category. You know, I think unfortunately he has bought into the Obama campaign’s party line.

Yes, Bill Kristol, a co-founder of Project for the New American Century (you know, the geniuses who thought the Iraq War would be a really good idea), is now accused of being "in the tank for Obama" (to borrow Keith Olbermann's words).

To John McCain or whoever it is that's running your campaign: please stop this insanity. Please stop wildly accusing people of "wrongly" supporting Obama. Better yet, please stop driving people with whom I generally have vehement policy disagreements from actually endorsing Obama. Otherwise, I'm going to have to keep on agreeing with Bill Kristol, and that can only lead to horsemen, rains of fire, and the end of days.

Hat tip to Think Progress for the video links.

Did I miss something?

2008-10-02T22:53:00.000-05:00

I'll confess — I didn't actually watch the entire VP debate. I gave up after about 30 minutes and realizing that Biden and Palen weren't actually debating, but were rather just trying to squeeze in sound bites (to put an overly simplistic view on things). Blame it on the silly "debate" format.

What I want to know is this: did I miss something in the candidates' replies when they were asked about whether the United States should or would ever use nuclear weapons in a first strike capacity? Palin seemed have started off saying about Iran and ended up talking about how to fight the war in Afghanistan (and nothing about nuclear first strikes); Biden seems to have taken a circuitous route to end up talking about the non-proliferation and the Comprehensive Test Ban Treaty.

However, neither one of the candidates seems to have answered the damn question. How hard could it possibly be? When asked whether the U.S. would consider a nuclear first strike, just say no!

Addendum: Yes, I'm aware that low-yield tactical nuclear weapons exist. But, I'm also aware of the moral and political stigmas against emploing any sort of nuclear weapon. So, using even one low-yield weapon would lead to opening a can of worms that we simply could not contain.

Oh wow...

2008-10-02T07:48:00.000-05:00

When asked about what happens when democracy (meaning "elections, free or otherwise") leads to results that aren't exactly favorable to the United States (in this context, Hamas winning elections in the Palestinian Territories), Palin gave this response:

She completely ducked the question, but I'll at least give Governor Palin points for pronouncing "Ahmadinejad" correctly. And to be fair, she can't actually see Gaza from her house; come to think of it, she hasn't exactly seen Russia, either. So much for foreign policy "experience".

Not sure whether to laugh or cry

2008-09-30T23:48:00.000-05:00

Ed Brayton writes about the U.S. government losing a FOIA (Freedom of Information Act) case and being required to turn over images of prisoner abuse in Iraq and Afghanistan. Mr. Brayton has the legal analysis, but I want to draw attention to this portion:

When the case was filed, the first argument the government offered - and this is stunning chutzpah even for the Bush administration - was that turning over the photos would violate the privacy of the detainees pictured in the photos.

Say what now?! You claim that these detainees are so bad that they should held in legal limbo and denied the protections of the U.S. Constitution and the Geneva/Hague Conventions, but all of a sudden, you're worried about protecting their privacy? Are you kidding me?

The really galling part is that this isn't the first time this bizarre argument has been tried: while trying Gitmo prisoners, the government denied the media access to parts of a prisoner's testimony (mostly regarding psychotropic drugs he may have been given), claiming, of all things, that doing so would be a violation of HIPAA.

Welcome to Guantanamo Bay. Sure, you'll have no rights to challenge your detention; but dammit, at least your medical records will be safe.

January 20th can't come soon enough. A few more leaps of logic like this, and my head is likely to explode.

Life finds a way

2008-09-29T18:08:00.000-05:00

Ed Yong (Not Exactly Rocket Science) has two interesting posts on tiny life forms with interesting adaptations. The first post deals with the ability of tardigrades (commonly called water bears) to survive the vacuum of space (Current Biology paper here). They do so by replacing water in their bodies with trehalose (a type of sugar) and entering a dormant state; this allows them to survive conditions, including dehydration, vacuum, extremely low temperatures, and in rare cases, large doses of ultraviolet radiation.

The second post deals with the compact genome (~160-kb) of the bacterium Carsonella ruddii, which is found in specialized cells (bacteriocytes) of a group of sap-feeding insects called the psyllids. This bacterium is very organelle-like, both in its role producing nutrients (mostly) absent in the host organism's diet and in its inability to survive outside of the host cell (since Carsonella lack many of the genes required by free living organisms). More importantly, the sequencing of this genome lends further credance to the endosymbiotic theory for the origins of mitochondria and chloroplasts. Take that, all you Creationists — evolution works!

Science funny

2008-09-29T10:32:00.002-05:00

In case you're wondering about the status of the world:

Say what now?!

2008-09-26T17:39:00.003-05:00

Yesterday, I agreed with George Will. Today, I'm agreeing with Wick Allison, a self avowed conservative who was the former publisher of the National Review after being personally recruited by William F. Buckley, Jr. Writing in D magazine, Allison offers his reasons why John McCain isn't really all that conservative (and yes, I'm aware it's bordering on, if not flat out is, the "no true Scotsman" fallacy):

But today it is so-called conservatives who are cemented to political programs when they clearly don’t work. The Bush tax cuts—a solution for which there was no real problem and which he refused to end even when the nation went to war—led to huge deficit spending and a $3 trillion growth in the federal debt. Facing this, John McCain pumps his “conservative” credentials by proposing even bigger tax cuts. Meanwhile, a movement that once fought for limited government has presided over the greatest growth of government in our history. That is not conservatism; it is profligacy using conservatism as a mask. Today it is conservatives, not liberals, who talk with alarming bellicosity about making the world “safe for democracy.” It is John McCain who says America’s job is to “defeat evil,” a theological expansion of the nation’s mission that would make George Washington cough out his wooden teeth. This kind of conservatism, which is not conservative at all, has produced financial mismanagement, the waste of human lives, the loss of moral authority, and the wreckage of our economy that McCain now threatens to make worse.

And in a step that left me confused for a few seconds, Wick Allison goes on to endorse Barack Obama for President:

I disagree with [Obama] on many issues. But those don’t matter as much as what Obama offers, which is a deeply conservative view of the world. Nobody can read Obama’s books (which, it is worth noting, he wrote himself) or listen to him speak without realizing that this is a thoughtful, pragmatic, and prudent man. It gives me comfort just to think that after eight years of George W. Bush we will have a president who has actually read the Federalist Papers.

Most important, Obama will be a realist. I doubt he will taunt Russia, as McCain has, at the very moment when our national interest requires it as an ally. The crucial distinction in my mind is that, unlike John McCain, I am convinced he will not impulsively take us into another war unless American national interests are directly threatened.

So, yes, this may be a WTF moment, but at least it's a moment that offers hope that there still are people out there who are willing to set aside party labels to do what is right for the country. And more importantly, it offers hope that some of those calling themselves "conservatives" aren't the foaming at the mouth, right-wing reactionary caricatures liberals and libertarians imagine them as being.

The 2008 campaign needs to end soon

2008-09-25T00:01:00.001-05:00

Because I'm not entirely sure how much longer I can go on agreeing with people like George Will and not lose my sanity. Quoting Will's op-ed in the Washington Post on Tuesday:

Under the pressure of the financial crisis, one presidential candidate is behaving like a flustered rookie playing in a league too high. It is not Barack Obama.

And that sentiment seems to be borne out by McCain calling for Friday's debate to be delayed (or possibly canceled?), saying:

It's for both parties to come together to solve this problem. We must meet as Americans, not as Democrats or Republicans, and we must meet until this crisis is resolved. I'm directing my campaign to work the Obama campaign and the Commission on Presidential Debates to delay Friday night's debate, until we have taken action to address this crisis.

McCain canceled his appearance on David Letterman's show (which, by the way, Letterman is really not happy about), claiming that he (McCain) had to get back to Washington because the economy is "about to crater".

Really now? Is the economy in that much trouble that John McCain has to stop all aspects of his campaign? Can McCain not, as Obama wryly said, focus on more than one thing at a time, and if not, is that really a characteristic we want in a President?

Now, I will concede that something needs to be done, though (agreeing with George Will and other conservatives once again), I'm not sure offering bailouts without any sort of oversight (as Treasury Secretary Paulson originally proposed) is the best way of achieving that. But is there anything McCain (or Obama, for that matter) can practically do over the next 36 hours other gather a few good photo ops and maybe show up to vote on whatever bill Congress and President Bush manage to work out? As a voter in November's election, I really think my interests are better served by hearing what these two men have to offer come January 2009.

Or at the very least, send in the VP candidates to debate on Friday. They are, after all, supposed to be the surrogates for their respective candidate, ready to take over when necessary. What better for a first test than this?

Getting back to the key point, though, this action by McCain is yet another example of what I think I may start calling his "erratic certainty", the sense McCain seems to convey that what he says at the moment has to be true, regardless of what factual reality may actually be; in effect, what John McCain seems to have done is elevate truthiness to a new, erratic, and somewhat terrifying level. And we've certainly seen some of the evidence of that over the past week or two, as McCain has gone from "the fundamentals of the economy are strong" to "by 'fundamentals' I meant the American workers" (how ever nonsensical that statement may be) to "well, maybe we should do something" to "the economy is about to crater".

And this isn't and shouldn't be worrying only to those who identify themselves as liberals. As George Will points out,

Conservatives who insist that electing McCain is crucial usually start, and increasingly end, by saying he would make excellent judicial selections. But the more one sees of his impulsive, intensely personal reactions to people and events, the less confidence one has that he would select judges by calm reflection and clear principles, having neither patience nor aptitude for either.

It is arguable that, because of his inexperience, Obama is not ready for the presidency. It is arguable that McCain, because of his boiling moralism and bottomless reservoir of certitudes, is not suited to the presidency. Unreadiness can be corrected, although perhaps at great cost, by experience. Can a dismaying temperament be fixed?

The answer to that last question, I'm sad to say, is "probably not". And I'm worried that too few voters will realize or care enough by November 4^th to stop us from discovering the price this country will have to pay for "a dismaying temperament".

Two pieces on politics and the economy

2008-09-23T12:44:00.004-05:00

Frank Rich's NY Times op-ed uses the current meltdown of the financial sector to discuss McCain's adoption of truthiness as a campaign strategy, a strategy which in no small part continues to contribute to my increasing distaste for that candidate (emphasis mine):

McCain has largely pulled it off so far, under the guidance of Steve Schmidt, a Karl Rove protégé. A Rovian political strategy by definition means all slime, all the time. But the more crucial Rove game plan is to envelop the entire presidential race in a thick fog of truthiness. All campaigns, Obama’s included, engage in false attacks. But McCain, Sarah Palin and their surrogates keep repeating the same lies over and over not just to smear their opponents and not just to mask their own record. Their larger aim is to construct a bogus alternative reality so relentless it can overwhelm any haphazard journalistic stabs at puncturing it.

And passed to me by a friend, this Bill Saporito article in Time highlights some of the ways the U.S. has become like the "semi-socialist" states many citizens claim to detest; I'm not sure I agree with all of his points, but these are definitely issues worth thinking about.

This is the state of our great republic: We've nationalized the financial system, taking control from Wall Street bankers we no longer trust. We're about to quasi-nationalize the Detroit auto companies via massive loans because they're a source of American pride, and too many jobs — and votes — are at stake. Our Social Security system is going broke as we head for a future where too many retirees will be supported by too few workers. How long before we have national healthcare? Put it all together, and the America that emerges is a cartoonish version of the country most despised by red-meat red-state patriots: France. Only with worse food.

Admit it, mes amis, the rugged individualism and cutthroat capitalism that made America the land of unlimited opportunity has been shrink-wrapped by a half dozen short sellers in Greenwich, Conn. and FedExed to Washington D.C. to be spoon-fed back to life by Fed Chairman Ben Bernanke and Treasury Secretary Hank Paulson. We're now no different from any of those Western European semi-socialist welfare states that we love to deride.

And yes, science will be returning to this blog. Until then, enjoy.

Help kill HR6845

2008-09-23T12:35:00.000-05:00

This Ars Technica article covers efforts to push through HR-6845 ("Fair Copyright in Research Works Act") would subvert current NIH policy requiring NIH funded work be made open access within 12 months of publication (typically through PubMed Central). Quoting the article:

The House of Representatives has seen the introduction of legislation, HR 6845 that, depending on its final format, may significantly curtail or eliminate the NIH's ability to continue its open access policy. The current bill would prevent any arm of the federal government from making research funding contingent upon "the transfer or license to or for a Federal agency of... any right provided under paragraph (1) or (2) of section 106 in an extrinsic work, to the extent that, solely for purposes of this subsection, such right involves the availability to the public of that work." Those Section 106 rights include the reproduction of the work.

Although that would seem to rule out the existing NIH policy, there is a certain amount of legal wiggle room there. For example, the NIH could fund a private entity to maintain PMC, and thus have the right to reproduction transferred to an independent entity. Nevertheless, the bill would appear to directly target the prior legislation that put the NIH in the business of mandating public access in the first place.

As is seemingly typical of many pieces of legislation, these one seems to have been pushed by "special interests" (in this case, traditional scientific publishing houses) and sponsored by Representatives who really have no idea what the hell is going on. Quoting the article once:

[M]any of the representatives were clearly in need of a primer in academic publishing. Different members of the Subcommittee expressed surprise at various aspects of the current system, such as the fact that peer reviewers perform the function free (although, as noted, the process of arranging for peer review can be expensive). Also eliciting surprise was the revelation that authors are not paid by publishers for the transfer of copyright.

In fact, many publishers charge money for the publication of scientific research, even those that obtain copyright to the work in the process. Dr. Elias Zerhouni, director of the NIH, shocked Berman when he mentioned that the NIH hands out $100 million a year to grant recipients specifically to cover the cost of publishing their results. It would certainly have been possible for those testifying in favor of the open access policy to argue that the public pays part of the cost of nearly every stage of the publishing process, and might expect to have some access to the end product.

Open access is critical in helping scientists disseminate their work, not only to their peers, but to the public as well. It prevents publishers from taking publicly funded scientific work and locking it behind "pay walls" and in some sense, provides accountability for what scientists do with your tax dollars. Coturnix and revere provide more commentary and examples of letters you can send to your Congressperson or Senator.

Because I'm posting this so late, you only have until tomorrow (24 September) to get your letter in. But if you get the time, please do so. We need to stop this bill before it subverts our ability to do research work in the United States.

Thank you Bill Maher and Andrew Sullivan

2008-09-21T23:42:00.000-05:00

Maher can be obnoxious and the occasional loon (e.g., vaccines and germs), and Sullivan may have scary foreign policy positions and maybe a slightly rose-colored version of the British response to The Troubles, but what they're saying here is fundamentally correct:

Middle America as the "real America"

2008-09-21T16:29:00.002-05:00

John Rogers (Kung Fu Monkey) puts into words something that has bothered me for a while now, especially after watching the Republican National Convention: the inanity in thinking of rural ("small town") America as the "real America". Quoting him:

[Rural] life is not holy, it does not bless one with special insight into the intent of the Framers of the goddam Consitution or what America "should" be like. Have I lost some sort of sacred connection with the land? Maybe. But the last time I checked, the land was dirt, same dirt as the rest of the world, and several generations of my family went broke farming other people's dirt, interrupted only when easily annoyed Englishmenwould occassionally show up and burn all their shit down. Pardon me for enjoying my goddam latte.

Hell, I grew up in Massachusetts, and we didn't go around nodding and saying "This is the very birthplace of America both geographically and ideologically, those idiots in Kansas have no idea what being a real American is, like we Commonwealth bastards." One would be considered insane. Whatever connection people in rural America have to the "idea" of America is the exact same as mine -- the Declaration of Independence and the Constitution. They are public documents, accessible by all (well, for now), and last time I checked the versions printed in textbooks in Kansas didn't have special magical ink and secret clauses not included in the versions handed out in the Northeast urban great city of Philadelphia where, if we remember, the damn things were actually written.

Damn straight. Yes, there are good people living in small towns, but this concept of "small town values" is, at best, a vacuous, ill-defined concept (as evidenced by this Daily Show clip) and at its worst, represents the ill-informed, fear driven, reactionary politics that so-called "liberal elites" have been battling for who knows how long. "Small town values" may a favorite social meme, but it's nothing more than a Leave It To Beaver idealization of a history that never existed.

And "small town values" aren't even all that democratic, as the latest census figures show that nearly four times as many Americans live in urban areas than the vaunted rural areas of the country.

So, for those wanting to know what "real Americans" actually belive and want, head down to the local Starbucks. You're more likely to see a "representative citizen" there than in your favorite farm in Kansas.

The phrase "EPIC FAIL"

2008-09-19T17:05:00.002-05:00

Doesn't even begin to describe this:

Seriously, how unobservant were you as a child?! On the other hand, thank you for filling me with hope; you've lowered the bar so much that I now know that no question a student of mine may ask could ever be this monumentally stupid.

Hat tip to Mike (The Mad Biologist)

Fucking batshit insane

2008-09-19T12:22:00.000-05:00

That's pretty much the only way to describe this screed by right-wing nutjob Debbie Schlussel about why China's suppression of human rights may not be a bad thing. Quoting Schlussel:

Why is it that China is fighting islamic fundamentalists the way we should be fighting Islamic fundamentalists especially during Ramadan?

That's a great question. The answer is that China is far more fierce, these days, about protecting its country's borders and national security than we are. And perhaps the Chi-Coms have a stronger will for their nation to survive than ours.…

Oh, and also, the Constitution prohibits us from establishing a national religion or preferring one...unless it's Islam.

Now, I'm not entirely sure which Constitution Schlussel is referring to, but the version I've read says nothing specific about Islam beyond this clause:

Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof…

You know, the same clause that protects every religion (or lack thereof) in the United States.

Schlussel quotes from an International Herald Tribune article describing some of the actions the Chinese government has taken:

They include barring teachers and students from observing Ramadan, prohibiting retired government officials from entering mosques and requiring men to shave off beards and women to take off veils. Mosques may not let people from outside the town stay overnight, and restaurants must maintain normal hours of business. (Many restaurants close during daytime hours over Ramadan because of the fasting, which is supposed to last from sunrise to sunset. Muslims observing Ramadan typically eat substantial meals at night.)

In nearby Xinhe County, the government has decreed that Communist Party members, civil servants and retired officials not observe Ramadan, enter mosques or take part in any religious activities during the month. Worshipers cannot make pilgrimages to tombs, so as to "avoid any group event that might harm social stability," according to the Xinhe government's Web site.

In her world, religious oppression and totalitarianism are bad. Unless, of course, we're talking about Islam; in that case, it's simply a matter of "national survival". Great logic there...

Not to be outdone, one of comments on this article actually calls for a constitutional amendment declaring Islam "an enemy of the United States and [prohibiting] its practice within the United States"; this proposed "amendment" also states that "all Mosques, schools and Muslim places of worship and religious training are to be closed, converted to other uses, or destroyed" and that "[t]he preaching or advocating of Islamic ideals…shall in all cases be punishable by fines, imprisonment, deportation, and death" (emphasis added). I'll leave you to read the Orwellian genius that is Article IV of this proposal.

Just how big a bogeyman do these people imagine Islam to be? We didn't have to append the Constitution to deal with Communism or Nazism, but we need one for radical Islam?! Were it not for the fact that I've actually had conversations with people who seriously think like this, I would simply call Poe's Law and be done with it; instead, I'm left sitting here, wondering how much further our national discourse can sink.

Hat tip to Ed Brayton (Dispatches from the Culture Wars)

The Universe is a dangerous place

2008-09-15T23:43:00.003-05:00

We should all feel very lucky that our local galactic neighborhood doesn't contain anything big enough to produce something along the lines of GRB 080319B, a gamma ray burst so large that even at 7.5 billion light years away, it was "the single most luminous event ever witnessed by humans", visible (for a short time at least) to the naked eye.

Think about this for a second. Something putting out so much energy that even from half way across the known universe, you could have seen it with your naked eye. Fortunately, GRB 080319B was more than far enough away that instead of being instantly lethal to everything on the planet, it's just really freaking cool.

We now return you to waiting for imminent death by LHC, coming to you live on October 21st.

Drilling won't solve anything

2008-09-15T10:45:00.002-05:00

Via Coturnix, one picture that succinctly illustrates why we can't drill our way out of our oil problem (click for the larger version in a new window):

Fifty years ago

2008-09-12T23:23:00.000-05:00

On 12 September 1958, the man on the left developed that blob on the right and launched an engineering revolution.

Parallel computing explained

2008-09-09T09:02:00.000-05:00

Via Phil Plait: one of the best demonstrations of serial versus parallel computing (actually, of CPU versus GPU rendering, but the point is essentially the same), provided by the guys from Mythbusters. I have to say, this demonstration is also one of the coolest ways I've seen someone paint.

YouTube link (in a new window)

Why developing an HIV vaccine is so hard

2008-09-08T17:08:00.000-05:00

In an interview with Scientific American, Anthony Fauci, the director of NIAID (National Institute of Allergy and Infectious Diseases), discussed why developing a vaccine for HIV/AIDS is so challenging. The short version is that unlike other diseases, HIV doesn't seem to illicit a "neutralizing antibody response"; without this response, we have no natural model of infection which can be used as a basis for building a vaccine. This really is an article worth reading, as Fauci goes to great lengths to explain why after nearly three decades of research, an effective vaccine still remains elusive.

Exactly what he said

2008-09-08T08:03:00.001-05:00

Sam Harris in his L.A. Times op-ed, offered here with no further comment:

Americans have an unhealthy desire to see average people promoted to positions of great authority. No one wants an average neurosurgeon or even an average carpenter, but when it comes time to vest a man or woman with more power and responsibility than any person has held in human history, Americans say they want a regular guy, someone just like themselves. President Bush kept his edge on the "Who would you like to have a beer with?" poll question in 2004, and won reelection.

This is one of the many points at which narcissism becomes indistinguishable from masochism. Let me put it plainly: If you want someone just like you to be president of the United States, or even vice president, you deserve whatever dysfunctional society you get. You deserve to be poor, to see the environment despoiled, to watch your children receive a fourth-rate education and to suffer as this country wages -- and loses -- both necessary and unnecessary wars.

Hat tip to James Hrynyshyn (Island of Doubt)

We're going to need a bigger clue bat

2008-09-08T00:47:00.001-05:00

Via Coturnix: last week's Science Friday had an interview with Dr. Paul Offit about the increasing refusal by parents to get their children vaccinated and the corresponding re-emergence of vaccine preventable diseases such as measles and mumps. For those who aren't familiar with this story, the short version is that an appallingly large number of people (including one person I know who went to medical school) have become convinced that vaccines are somehow responsible for the rising number of autism diagnoses in children; for further details, I defer to Orac over at "Respectful Insolence".

Early in the interview, Dr. Offit identifies the root cause for this anti-vaccine insanity, namely the age old problem of bad science communication:

Ira Flatow: Why do you think the science [behind vaccines] is not compelling?

Dr. Offit: I think we're not very good at explaining it. I think that scientific literacy isn't great. I think people tend to see science as just one more opinion in a sea of opinions. I think that the media certainly can be confusing; I think the Internet can be confusing. So I think it's disappointing.

Dr. Offit goes on to properly distribute blame for this situation. He blames anti-vaccine propagandists for constantly moving the goal posts and offering increasingly ludicrous hypothesis about the causative link between vaccines and autism. He blames today's media, who seem obsessed with the notion that stories, especially those involving science, must have at least two equally valid sides — the same notion that gives creationism the same footing as evolution or "alternative medicine", such as homeopathy, the same footing as conventional, evidence-based medicine.

Dr. Offit also notes that today's young parents don't truly know how to assess the risks of not vaccinating, primarily because they haven't had to live with outbreaks of diseases such as smallpox or polio or measles-induced encephalitis.

The last 11 minutes (of this 18 minute piece!) was a pointless argument with a caller named Shantal (sp?), who basically had me banging my head on the desk and lead to the title of this post. Over the course of her call, Shantal managed to run the gamut of anti-vaccine hysteria, starting from too much aluminum in vaccines (ignoring the fact that environmental doses are much higher) to too many vaccines at once (ignoring the fact that a cold presents a much greater immunological challenge) to truly looney tunes conspiracy theory mongering (you know, "no independent studies" since Big Pharma bought the FDA and Dr. Offit off). Her entire stance can be succinctly stated by two of her own words; when asked whether anything Dr. Offit could say would change her mind, Shantal replied, "Absolutely not."

Dr. Offit correctly points out that Shantal and people like her (i.e., the kind who are immune to even the clue bat equivalent of a tactical nuke) are not the type of people that we scientists should be trying reach; they're already too far gone. Instead, scientists need to focus on those parents "who are concerned but are re-assurable with good science."

Unfortunately, I don't entirely share Dr. Offit's optimism that this is entirely doable. Referring back to Robert Krulwich's commencement address, I suspect that the stories anti-vaxers have to tell, no matter how logically and experimentally flawed they may be, are far too alluring and far too easy to believe. In an era where smallpox and polio are dim memories (at least in the developed world), I simply don't see the stories of Jenner and Salk being quite as attractive as those about the big uncaring bogey man (in the form of doctors, the FDA/CDC, or Big Pharma — take your pick) coming to get you. I only hope I'm wrong about this, before we as a society learn the hard way why vaccines are currently required in the first place.

File this under "WTF?!"

2008-09-07T11:49:00.004-05:00

Ed Brayton brings us this story about the Richland County (S.C.) Sheriff's Department's acquisition of an armored personnel carrier, complete with a .50-caliber machine gun, which they've thoughtfully called "The Peacemaker". Seriously, what the hell is going on in South Carolina that requires a police department to have a weapon capable of penetrating an inch of concrete from nearly a mile away?

Pete Guither offers great commentary on the source of the name (Matthew 5:9):

You know, I was raised studying the Bible and had a special interest in the Sermon on the Mount. In all my reading of the beatitudes, I never once imagined Christ astride an Armored Personnel Carrier complete with a turret-mounted .50-caliber belt-fed machine gun, surrounded by apostles in SWAT gear, as he said to the crowd "Blessed are the peacemakers: for they shall be called the children of God."

Fortunately for them, the Richland County Sheriff's Department still doesn't win the contest for "most ironic use of the term 'Peacemaker'"; that dubious honor still belongs to SAC (Strategic Air Command), who used that moniker (or a derivative thereof) for a bomber and an ICBM.

Big bad scientific publishing groups

2008-08-30T20:03:00.000-05:00

Mike Dunford (The Questionable Authority) launched into a tirade against big scientific publishers whose pricing structures have forced many university libraries to cut back on journal subscriptions, thus hampering the ability of many scientists to work effectively. He makes this comparison:

[T]he situation that I've described with journal prices is similar to the gasoline analogy I presented. Both are necessities (at least under certain circumstances). Both have been increasing in price. And the providers of both are making large profits, while their customers suffer.

That's where the analogy ends, though, because scientists are not only the end customers for journals, they're also the people who provide the content. For free. If you want to continue the analogy, you'd have to pretend that during the whole time that gas prices and profits have been rising you were spending five or ten hours a week working on an oil rig, and that you're doing it without pay.

…

The relationship between publishers and the scientific community is not a partnership. It's parasitic.

More on healthcare

2008-08-30T12:16:00.000-05:00

Last week, Jonathan Oberlander was interviewed on NPR's Fresh Air about his article in the 21 August issue of NEJM (New England Journal of Medicine) covering the health care policy positions of the two major Presidential candidates. In both the article and the interview, Oberlander outlines the details of each candidate's plan and offers a balanced view of the pros and cons of each. Definitely worth a read and a listen.

One of those days

2008-08-27T23:09:00.003-05:00

You wake up, skim the headlines delivered to your inbox, and end up reading about Russian skittishness about NATO ships in the Black Sea followed by this interview (emphasis mine):

AMY GOODMAN: Can you talk about significance of this, in terms of nuclear warfare in Russia? Do we have anything to fear along those lines?

COL. SAM GARDINER: Absolutely. Let me just say that if you were to rate how serious the strategic situations have been in the past few years, this would be above Iraq, this would be above Afghanistan, and this would be above Iran.

On little notice to Americans, the Russians learned at the end of the first Gulf War that they couldn’t—they didn’t think they could deal with the United States, given the value and the quality of American precision conventional weapons. The Russians put into their doctrine a statement, and have broadcast it very loudly, that if the United States were to use precision conventional weapons against Russian troops, the Russians would be forced to respond with tactical nuclear weapons. They continue to state this. They practice this in their exercise. They’ve even had exercises that very closely paralleled what went on in Ossetia, where there was an independence movement, they intervene conventionally to put down the independence movement, the United States and NATO responds with conventional air strikes, they then respond with tactical nuclear weapons.

I feel so much safer, now that the Cold War has ended.

Tell me a story

2008-08-27T12:22:00.002-05:00

Via Alex Palazzo (The Daily Transcript), one of the best commencement addresses I have ever heard, delivered by Robert Krulwich at Caltech earlier this summer. In it, he issues a challenge to those working in science and engineering:

When you are asked "What you are working on?", should you think, "There's no I way I can talk about my science with this guy, because I don't have the talent, I don't have the words, I don't have the patience to do it. It's too hard. And anyways, what's the point?"

…

[In writing his Principia,] Issac Newton didn't care to be understood by average folks. But here's the argument I want to make to you guys this morning. You're not going to hear this advice often; I suggest you may never here it again. When asked about your work, do not do what Isaac Newton did. No, no, no!

When a cousin or an uncle or a buddy comes up and asks you "So, what are you working on?", even if it's hard to explain, even if you know they don't really want to hear it (not really), I urge you to give it a try. Because, talking about science, telling stories to regular folks, is not a trivial thing. Scientists need to tell stories to non-scientists because science stories, and you know this, have to compete with other stories about how the universe works and how the universe came to be. And some of those other stories -- Bible stories, movie stories, myths -- can be very beautiful and very compelling. But to protect science and scientists (this is not a gentle competition), you've to get in there and tell yours, your version of how things are and why things came to be.

…

[T]here is a tension here among scientists between two kinds of truth: math and narrative. But the job that we face, and I should come clean with you and tell you what's really on my mind here, is to put more stories out there about nature that are true and complex -- not dumbed down -- but still have the power to enthrall, to excite, to remind people there's a deep beauty, a many-level beauty, in the world. And what scientists say is not their off-hand opinion; it's hard won information. It's carefully hewn from the world. It's not the bunch of ideas from a tribe of privileged intellectuals who look down on everybody…But it's my sense that if more scientists wanted to, they could learn how to tell their stories with words and pictures and metaphor, and people will hear and remember those stories and not be as willing to accept the other folks' stories. Or at least, there will be a tug of war. And I think the science stories will, surprisingly, win.

Basics: Groups, Rings, and Fields

2008-08-26T08:48:00.006-05:00

In talking about Keith Devlin's call to stop teaching multiplication as repeated addition, I mentioned that multiplication is one of two basic operations defined for a type of algebraic structure called a ring. However, I realized I never explained what that statement means, and in this article, I hope to remedy that by explaining what rings and their related structures (groups and fields) are and why we care about them.

Background concepts

Before getting into groups, rings, and fields, we have to first understand the concepts of sets and binary operations. Mark Chu-Carroll has written a great introduction to set and set operations, but I'll provide a condensed version here.

Intuitively, a set is a well-defined collection of mathematical objects (e.g., numbers, matrices, or functions). We use the term "well-defined" so we can tell whether some arbitrary object is a member or element of a set; the notation "a ∈ S" simply says that object a is an element of set S. A set is non-empty if it contains at least one element.

I should point out that a formalism called axiomatic set theory provides a stricter definition for the term "set" that helps avoid certain paradoxes that would otherwise occur when working with sets. However, for purposes of this article, the simple and intuitive definition of "set" provided above will do.

A binary operation or binary relation on S (represented by a symbol like ◊) is a rule for taking two elements from a set S (call them a and b) and combining them to get a third object (call it c); we write this as "c = a ◊ b". Notice that there is no intrinsic requirement for c to be an element of S. However, if combining any pair of elements of S using the operation ◊ always results in an object that is also an element of S, then we say that "S is closed under ◊". Mathematically, we say "S is closed under ◊ if and only if for all a ∈ S and b ∈ S, a ◊ b ∈ S."

A algebraic structure consists of one or more sets closed under one or more binary operations that satisfy certain conditions.

Defining groups, rings, and fields

One of the simplest algebraic structures is a group, which consists of a non-empty set S and a binary relation on S (written as ◊) that satisfies the following conditions:

Closure under ◊: For all a, b ∈ S, a ◊ b ∈ S.
Associativity of ◊: For all a, b, c ∈ S, (a ◊ b) ◊ c = a ◊ (b ◊ c); i.e., the order in which we apply ◊ doesn't matter.
Existence of an identity element: There is some element e ∈ S such that for all a ∈ S, a ◊ e = e ◊ a = a.
Existence of inverse elements: For every element a ∈ S, there is some element a^-1 ∈ S such that a ◊ a^-1 = a^-1 ◊ a = e. The element a^-1 is called the inverse of a.

A group defined in this way is written using the notation (S, ◊).

There are two things to notice. First, the definition of a group requires us to provide or define the operation ◊; in other words, saying "Set S is a group" without saying anything about some binary relation on S is a meaningless statement. Second, the definition of a group does not require ◊ to be commutative; that is, we don't require that a ◊ b = b ◊ a for all a, b ∈ S. If ◊ does commute, then the group (S, ◊) is called a commutative, or Abelian, group.

A familiar example of a group is the set of integers Z = {…, -2, -1, 0, 1, 2, …} under ordinary addition (i.e., the addition taught in elementary school). For this group, the identity element is 0, and the inverse element of a given integer, a, is the negative of that integer, −a.

Like a group, a ring is a type of algebraic structure, but defined using two binary operations. The ring (S, ⊕, ⊗) consists of a non-empty set S, a "ring addition" relation ⊕, and a "ring multiplication" relation ⊗ and satisfies the following conditions:

Closure under ⊕: For all a, b ∈ S, a ⊕ b ∈ S.
Closure under ⊗: For all a, b ∈ S, a ⊗ b ∈ S.
Commutativity of ⊕: For all a, b ∈ S, a ⊕ b = b ⊕ a.
Associativity of ⊕: For all a, b, c ∈ S, (a ⊕ b) ⊕ c = a ⊕ (b ⊕ c).
Existence of an identity element for ⊕: There is some element z ∈ S such that for all a ∈ S, a ⊕ z = z ⊕ a = a. The element z is called the additive identity or the zero element of the ring.
Existence of inverse elements for ⊕: For every element a ∈ S, there is some element x ∈ S such that a ⊕ x = x ⊕ a = z. The element x is called the additive inverse of a.
Associativity of ⊗: For all a, b, c ∈ S, (a ⊗ b) ⊗ c = a ⊗ (b ⊗ c).
Distributive law of ⊗ over ⊕: For all a, b, c ∈ S, a ⊗ (b ⊕ c) = (a ⊗ b) ⊕ (a ⊗ c) and (b ⊕ c) ⊗ a = (b ⊗ a) ⊕ (c ⊗ a).

As noted above with the definition of a group, saying "S is a ring" without defining both the ⊕ and ⊗ relations is a meaningless statement. Also, notice that the ring multiplication relation ⊗ need not be commutative; because of this, the order in which we write the terms in the distributive law (#8) above matters. If ⊗ is commutative, then the ring is called a commutative ring.

A field is a ring that satisfies two additional conditions:

Existence of an identity element for ⊗: There is some element u ∈ S, u ≠ z, such that for all a ∈ S, a ⊗ u = u ⊗ a = a. The element u is called the multiplicative identity or the unity element of the ring. Note that the multiplicative identity and the additive identity cannot be the same element of S.
Existence of inverse elements for ⊗: For every element a ∈ S, a ≠ z, there is some element a^-1 ∈ S such that a ⊗ a^-1 = a^-1 ⊗ a = u. The element a^-1 is called the multiplicative inverse of a.

The set of integers Z under ordinary addition and ordinary multiplication, written (Z, +, ×), form a ring. In this ring, the integers a and −a are additive inverses of each other, 0 is the additive identity, and 1 is the multiplicative identity. However, (Z, +, ×) is not a field because, except for the case a = 1, the multiplicative inverse of a ∈ Z is not a member of Z; e.g., the multiplicative inverse of 2 is 1/2, which is not an integer.

The set of real numbers R under ordinary addition and ordinary multiplication is a field (and thus a ring as well). The additive inverses, additive identity, and multiplicative identity are the "same" as those for integers. However, unlike the integers, the multiplicative inverse r^-1 of every non-zero real number r ∈ R is itself a member of R.

What Devlin was talking about

Looking at the definition of a ring above, you can see (fairly easily, I hope) what Devlin meant when he said that multiplication is not repeated addition, but is instead another "basic operation" you can perform on numbers. Nothing in the definition of a ring requires us to assert that ring multiplication is repeated ring addition; in fact, the definition of a ring requires no relation between multiplication to addition, except through the distributive law.

Devlin's arguments boil down to this: Because rings are typically the structures through which mathematicians understand the numbers we commonly deal with (e.g., the integers, rationals, reals, and complex numbers) and because of the way a ring is defined, teachers should not introduce a concept (multiplication = repeated addition) that really isn't there.

Why care about groups, rings, and fields?

From a pure math perspective, proving statements using only the definitions above automatically tells us the properties of a large range of mathematical objects of interest. For example, using only the definition of a field, we can show that the additive and multiplicative identities must be unique, as must the pairs of additive and multiplicative inverses (i.e., each element of a field has a unique additive and a unique multiplicative inverse). Thus, even though the rules for adding and multiplying numbers, matrices, and functions differ, we know that so long as these sets and their operations form a field, the uniqueness properties of identities and inverses must hold. Without such broad theories, every time a new field is defined, we would have to go back and prove these uniqueness criteria using a different set of rules.

Moreover, the theory underlying these structures has played a key role in the mathematical development of modern science, ranging from physics and chemistry (which rely on group theory to understand the symmetries found in nature) to computer science and electrical engineering (which rely on group theory to develop the coding systems used in encryption and digital communication systems). Without these algebraic structures, many of the results that present day scientists and engineers depend on would have been difficult, if not impossible, to derive and understand.

What the heck is multiplication anyways?

2008-08-25T08:12:00.000-05:00

Speaking of misusing words, Keith Devlin issued a call to teachers to stop teaching multiplication as repeated addition, and instead, to teach multiplication simply as one of the basic operations we can apply to numbers. The crux of Devlin's argument is the following:

Multiplication simply is not repeated addition, and telling young pupils it is inevitably leads to problems when they subsequently learn that it is not. Multiplication of natural numbers certainly gives the same result as repeated addition, but that does not make it the same. Riding my bicycle gets me to my office in about the same time as taking my car, but the two processes are very different. Telling students falsehoods on the assumption that they can be corrected later is rarely a good idea. And telling them that multiplication is repeated addition definitely requires undoing later.

Of course, Devlin is right in that what multiplication really is is one of two operations defined for a algebraic structure called a ring. He is also correct in asserting the need to undo the perception of multiplication as repeated addition, especially when it comes times to multiply things like complex numbers, matricies, or functions.

However, Mark Chu-Carroll and Jason Rosenhouse both highlight a key problem: Devlin really doesn't really provide any real answers as to what to teach elementary school students when they first encounter multiplication. They correctly point out that taking an approach other than "multiplication is repeated addition" would likely fail to build students' intuitions about what multiplication is and how to carry out the mechanics of the process.

To a certain extent, I disagree with Devlin that continually "redefining" the rules of multiplication leads to frustration and "thinking mathematics is just a bunch of arbitrary, illogical rules that cannot be figured out but simply have to be learned"; like Jason Rosenhouse, I think most of the frustration comes from the fact that mathematics forces us to think using specific abstractions we aren't entirely comfortable with. Moreover, I (and I suspect many others) do eventually stop considering multiplication to be repeated addition without really thinking about it. For me, this unconscious transition happened when I started working with formulae that involved units, such as those from physics. By that point, it was no longer clear how repeatedly adding two kinds of units (e.g., mass and acceleration) gave a third kind of unit (e.g., force), and multiplication became a basic operation performed on two numbers to get a third number.

On the other hand, like Devlin, I'm not a fan of the lie to the children approach to teaching, primarily because doing so leaves "brain bugs" that are notoriously hard to get rid of. Going back to Devlin's argument, defining multiplication as repeated addition implies that the inverse operations are related as well, i.e., that division is repeated subtraction; as we discovered one day at work, this leads to enormous complications when trying to explain certain things, like why dividing by zero is undefined. Another good example Devlin points to is the teaching of exponentiation as repeated multiplication; because this "definition" has been beaten into my head, I have tremendous difficulty understanding what matrix exponentiation (i.e., e^A where A is some matrix) really means.

I'm not entirely sure as to what to make of all this. Devlin wrote a follow up article, saying essentially "however you teach it…, don't do anything that is counter to the way the mathematicians do it." While I agree in principle, I'm still not sure how to translate this to the classroom. So far, the only good solution I can think of is simply to attach and repeat a caveat like this when teaching multiplication:

Aside from addition, the other thing we can do with numbers is to multiply them. When working with the counting (natural) numbers, multiplying works like adding over and over again. But multiplying and adding over and over again are not always the same thing, as you will see in higher grade math.

Not the way to recruit new engineers

2008-08-24T23:14:00.002-05:00

Via Chad Orzel, this laughably silly billboard:

Matthew Yglesias provides the only comment necessary: "If anything, characterizing the sex-engineering link in this manner seems overwhelmingly more likely to reduce interest in engineering than to reduce interest in sex."

Articles on teaching evolution

2008-08-24T13:22:00.000-05:00

The New York Times recently ran two good articles on the teaching of evolution. First, Olivia Judson's op-ed makes arguments for teaching evolution. Two of the arguments Judson made I especially like. The first is the scientific argument that evolution is one of, if not the, organizing principle of modern biology:

[Evolution] provides a powerful framework for investigating the world we live in. Without evolution, biology is merely a collection of disconnected facts, a set of descriptions. … Add evolution — and it becomes possible to make inferences and predictions and (sometimes) to do experiments to test those predictions. All of a sudden, patterns emerge everywhere, and apparently trivial details become interesting.

The second is a more philosophical argument as to why we should bother doing science in the first place:

It’s that the endeavor [of studying evolution] contains a profound optimism. It means that when we encounter something in nature that is complicated or mysterious, such as the flagellum of a bacteria or the light made by a firefly, we don’t have to shrug our shoulders in bewilderment.

Instead, we can ask how it got to be that way. And if at first it seems so complicated that the evolutionary steps are hard to work out, we have an invitation to imagine, to play, to experiment and explore. To my mind, this only enhances the wonder.

This sense of wonder, this sense that if we imagine and play and experiment and explore enough, we can really figure out how this universe is put together, is the main reason why I, and many like me, became a scientist in the first place. And it's also one reason why I react so strongly against Creationism: because saying "God did it, and that's all there is to it." is vacuous and intellectually unsatisfying, and ultimately robs us of this sense of wonder.

The second NY Times article is more depressing, covering the efforts of David Campbell, a Florida high school teacher trying to teach evolution to a group of skeptical kids. It really quite impressive to see how Campbell walks that fine line of teaching the science while trying to avoid alienating kids entirely by "[forcing] them to look at themselves in the evolutionary mirror".

I had the unfortunate experience of having a high school biology teacher who was a Creationist. While picking apart his arguments in class was good fun (especially when it came to that asinine second law of thermodynamics "argument"), it really was disturbing to have a science teacher publicly deny and denigrate to core principles of the science he was purportedly "teaching".

I can somewhat understand why people are scared (if that is the right word to use) of evolution, and of science in general. Science tells us certain uncomfortable facts about the reality in which we live, that perhaps we aren't as unique as we imagine ourselves to be, being fairly ordinary animals living on a fairly ordinary planet orbiting a fairly ordinary star in the corner of some fairly ordinary galaxy.

But science does not say that we cannot make ourselves special. And it certainly does not say, contrary to what Creationists seem to believe, that we should abandon all moral and ethical precepts. Science merely is a tool by which we can understand how the universe works.

Hat tip to Jason Rosenhouse (EvolutionBlog) for pointing out the Judson op-ed.

The color of stars

2008-08-21T17:21:00.000-05:00

Phil Plait (Bad Astronomy) explains why there are no green stars. The short version:

[T]he only way to see a star as being green is for it to be only emitting green light. But as you can see from the graph above [showing the broad spectrum of emitted light], that’s pretty much impossible. Any star emitting mostly green will be putting out lots of red and blue as well, making the star look white. Changing the star’s temperature will make it look orange, or yellow, or red, or blue, but you just can’t get green. Our eyes simply won’t see it that way.

That’s why there are no green stars. The colors emitted by stars together with how our eyes [and brains] see those colors pretty much guarantees it.

For those who are really interested, Matt Springer (Built on Facts) explains the Stefan-Boltzmann distribution, which provides a reasonable approximation for the intensity of a given wavelength of light given a star's temperature.

Dealing with sexual harassment

2008-08-21T11:05:00.002-05:00

Instead of suing, try the female guppy's approach:

...the [female guppies] are segregating the sexes by choosing to spend time in areas where there are high numbers of predators. The brightly-coloured males are far more likely to attract the predators than the dull brown females, so they keep their distance.

Science link dump

2008-08-19T19:51:00.000-05:00

In no particular order, five pieces of interesting science:

Overly well fed oysters compromise their immune systems in pursuit of sex.
Stopping beams of protons energetic enough to melt half ton blocks of copper at the Large Hadron Collider.
Calculating the bite force of two species of sharks (the great white shark and the now extinct megalodon) using finite element methods.
Increasing endurance without exercise by using drugs to alter muscle metabolic processes.
Studying Drosophila to understand one purpose of sleep: the integration of sensory data and experiences into memory

Energy policy explained

2008-08-19T09:21:00.003-05:00

Via CR McClain (Deep Sea News), Stephen Colbert explains off shore drillling and other aspects of energy policy:

Choice quote (towards the end): "Hey, it's your choice. [You can either play] the game that doesn't exist yet [alternative energy] or the one that destroys your furniture [offshore drilling]."

Why even bother

2008-08-18T16:57:00.004-05:00

Ed Brayton (Dispatches from the Culture Wars) writes about how the Pentagon may ignore tribunal verdicts and continue hold Salim Hamdan even after his prescribed sentence has been served. I have seriously wonder sometimes whether our government is run by a bunch of six year olds: "Oh no, I don't like the way this game is going, so let's change the rules."

One quote from the Washington Post article succinctly summarizes my feelings about the situation:

"We had a court. We had a jury. It was a military jury. They heard the evidence. They gave him five months," Hollander said. "That ought to be his sentence. Either we believe in American justice or we don't."

Enabling the Georgian War

2008-08-18T08:31:00.000-05:00

Juan Cole writes in Salon about how the Bush administration's cavalier attitude towards international law is coming back to haunt the U.S.:

An emboldened Russian Prime Minister Vladimir Putin sarcastically likened Russia's actions [in Georgia] to Bush's foreign policy.

…

In the run-up to the Iraq war, Bush officials repeated ad nauseam the mantra that Saddam Hussein had killed his own people. Thus, they helped create a case for unilateral "humanitarian intervention" of the sort Putin says Russia is now pursuing.

…

Indeed, Putin's invoking Bush's Iraq adventure points directly to the way in which Bush has enabled other world powers to act impulsively. With his doctrine of preemptive warfare, Bush single-handedly tore down the architecture of post-World War II international law erected by the founders of the United Nations to ensure that rogue states did not go about launching wars of aggression the way Hitler had. While safeguarding minorities at risk is a praiseworthy goal, the U.N. Charter states that the Security Council must approve a war launched for this purpose or any other, excepting self-defense. No individual nation is authorized to wage aggressive war on a vigilante basis, as Bush did in Iraq or Russia is now doing in the Caucasus.

This, of course, is the same "moral high ground" argument used against allowing torture. Once that U.S. cedes that ground, it is only a matter of time before another state attempts to use that argument in a manner we don't entirely approve of.

Just in time for the start of school

2008-08-15T12:10:00.004-05:00

A new hobby:

"You keep using that word."

2008-08-14T09:14:00.001-05:00

"I do not think it means what you think it means." Meghan Daum writes in the Chicago Tribune about misuse of the word "nonplussed", which in the common parlance, has come to mean "unfazed, unperturbed or unconcerned", even though its proper definition (as provided by the Oxford English Dictionary) is "surprised and confused". Similarly, the word "peruse" is commonly used in the sense of "to skim or to read over quickly" even though its proper definition is "to read thoroughly or carefully."

This phenomena, of course, is simply the evolution of language through what linguist Mark Liberman calls "change by mistake", though embarrassingly, I have to admit to misusing both these words.

I bring this up because (1) it's amusing and (2) it serves as a reminder as to how difficult processing language can be, especially from a computational (read "natural language processing") standpoint. In a world where words can acquire meanings quite contrary to what appears in a dictionary, how are humans, let alone computers, expected to truly understand the semantics of an ambiguous statement such as "He was nonplussed by the situation."? In a world where we are allowed to take a Humpty Dumpty-esque approach to language ("When I use a word, it means just what I choose it to mean -- neither more nor less."), I'm not entirely convinced that we will ever reach a point where NLP has anything but domain specific applications.

The biology of the very small

2008-08-13T08:08:00.000-05:00

Moselio Schaechter (Small Things Considered) describes some of the smallest eukaryotes in the world, the picoeukaryotes. These organisms are so small that they contain only one each of the major organelles (chloroplast, mitochondrion, Golgi body, etc.); however, they play major ecological roles by producing a large fraction of the photosynthetic output at the bottom of oceanic food chains.

Elsewhere on the web, Ed Yong reviews a Nature letter describing a virophage named Sputnik, which acts as a parasite on a larger mimivirus, hijacking the host virus' machinery to make copies of itself.

Finally, Mo (Neurophilosophy) describes kuru, a prion induced neurodegenerative disease characterized by loss of motor coordination and spread, in large part, by "ritualistic mortuary cannibalism". The article provides a great introduction to prion diseases (and other diseases caused by protein misfolding such as Alzheimer's). It also raises the question of whether we may see a sudden outbreak of Creutzfeldt-Jakob disease (the human manifestation of BSE or "mad cow disease"), given the discovery of the long incubation period (up to 50 years) of kuru and related diseases.

Now, go read.

Is anyone really surprised?

2008-08-12T18:35:00.000-05:00

On Sunday's All Things Considered, host Andrea Seabrook interviewed Masha Lippman, a columnist and political analyst. The last part of the interview has this very telling Q&A:

Andrea Seabrook: Does the way this conflict has unfolded reveal anything about the power relationship between Prime Minister Vladimir Putin and President Dmitry Medvedev?

Masha Lippman: Indeed. During this conflict, Prime Minister Putin, from the statements that he's made, he sounded like he was the higher authority compared to the President of the country. And even though, formally, he's acting on orders of the President, [Putin] certainly looked as if the decisions were his. He was the first to appear on the Russian television. He certainly has looked through this conflict so far as the person who's taking decisions.

Really now? Is anyone all that suprised that Medvedev is pretty much Putin's puppet? As John Oliver once quipped on The Bugle shortly after Medvedev's election: "Meet Russia's new president -- Vladimir Putin."

Wikipedia for gene annotations

2008-08-12T15:15:00.000-05:00

The people over at 23andme describe a proposed project to develop a gene wiki, built on top of Wikipedia. The idea is to provide a gene annotation resource similar to the Entrez Gene that exploits the collective knowledge of "the community", instead of relying on only a few curators. Of course, such a project will be plagued by questions of accuracy, though a 2005 Nature study suggests Wikipedia comes close to the accuracy of Encyclopedia Britannica (not that the NCBI curated databases are entirely accurate in the first place). It will be very interesting to see how this project develops.

For reference, here's the link to the PLoS Biology paper proposing this project.

[Via Coturnix]

Interesting biology

2008-08-12T08:04:00.000-05:00

PZ Myers reviews a Nature paper on snake fang development and evolution, while Ed Yong reviews a PNAS paper on binge drinking tree shrews that somehow manage to stay sober.

And in news that illustrates the dynamic and self-correcting nature of science, the 2005 publication of the recovery T. rex soft tissue (see PZ Myers' review) may have been wrong. A recent PLoS ONE paper suggests that the observed structures, originally believed to be blood vessels and red blood cells, may in fact be a bacterial biofilm; Grrlscientist and Tara Smith offer reviews, while the Panda's Thumb post offers discussion, including comments from the first author on the PLoS paper.

On glass

2008-08-11T23:53:00.000-05:00

Chad Orzel (Uncertain Principles) points to a New York Times article on the nature of glass and the glass transition. Understanding the structure of glass and how the glass transition occurs is one of the large remaining problems in condensed matter and solid state physics.

Glass, of course, is a solid, insofar as it holds it shape without a container; yet, it exhibits the properties of a liquid in that it lacks any long range molecular structure. To quote the article:

When a liquid solidifies into a glass, [the] organized stacking [of a crystal] is nowhere to be found. Instead, the molecules just move slower and slower and slower, until they are effectively not moving at all, trapped in a strange state between liquid and solid.

Further complicating the issue is the fact that the transition temperature and final structure of a glass is dependent on the rate at which the liquid is cooled. The complexity of the problem has led one physicist working on the problem to joke, "There are more theories of the glass transition than there are theorists who propose them."

In any case, the article provides a great summary of the questions involved in glass and glass transitions and the current theories proposed to address them. Definitely worth a read.

Interesting fact about π

2008-08-11T11:46:00.007-05:00

Matt Springer (Built on Facts), in responding to a post on "Good Math, Bad Math", highlights an interesting property of π, namely, that it is (widely believed to be) a normal number.

Roughly speaking, a number x is said to be normal in base-b if its digits exhibit a uniform distribution, such that the asymptotic probability of every length k string occurring within the representation of x in base-b is 1/b^k. For example, for a number normal in base-10, the probability of observing a given digit '0' through '9' is 1/10, while the probability of observing a string of length 3 ('000' through '999') is 1/1000.

We can observe this using the first 1.25 million digits of π from Project Gutenberg and a simple Perl script. If π is a normal number, then the observed frequency of each digit '0' through '9' should be around 10%, which is precisely what we see:

Digit	0	1	2	3	4	5	6	7	8	9
% observed	10.01	9.97	10.01	10.03	9.99	10.03	9.95	10.00	10.00	10.02

Using this same script, we can also observe that within the first 1.25 million digits of π, length 3 strings occur at a frequency of about 1/1,000 and length 4 strings at a frequency of about 1/10,000; this is in line with our expectations that π is a normal number.

Of course, this exercise doesn't actually prove that π is a normal number. To date, no one has proven that π and other "interesting" numbers like e, which we strongly suspect are normal numbers, actually are.

One final comment: While the digits and finite length strings in π appear in a uniform distribution, π and the digits within it aren't actually "random" or "randomly distributed", at least not in the algorithmic sense. This is because fairly simple formulas that will generate the digits of π, though those are the topic for another discussion. I mention this only to highlight the fact that being pedantic about vocabulary does matter when talking about math.

The liberal media

2008-08-10T22:52:00.002-05:00

The 13 June 2008 episode of On The Media has an interview with Frank Scandale, who, as editor of The Record of Bergen County, New Jersey, launched a six month "self-examination" after the paper was accused by its readers of being too liberal. The interview itself is interesting, but this quote in particular caught my attention, as it provides a great explanation as to why people tend to think of the media as being "liberal":

BROOKE GLADSTONE: You know, it's been argued that the values of journalism naturally line up with the values of liberalism, in that journalists question authority – at least they're supposed to do that when they're doing their job – that they challenge institutions, that they dig deep into places where they're not supposed to go, that this is sort of part and parcel of the craft.

FRANK SCANDALE: I totally agree. Two points to make is I've written a column basically espousing what you just said, that we tend to be those kinds of people.

I have a letter here from a fellow who said he used to be a newspaper reporter, editor and columnist, and he said, yep, you guys have a liberal paper, albeit one I have never read. How can I know this? Well, and I say this with tongue in cheek, it would never occur to a conservative paper to engage in such introspection.

The short version of this, of course, is Stephen Colbert's quip at the White House Correspondents' Dinner, "Reality has a well-known liberal bias."

Meta funny

2008-08-09T23:33:00.004-05:00

To Billy, Steve, and all others sending me LOLcats pictures, I give you this:

[Via Greg Laden's blog]

What does "universal health care" mean anyway?

2008-08-02T15:28:00.000-05:00

On the 18 July 2008 broadcast of On The Media, Trudy Lieberman discusses how the press has done a poor job covering the politics and language of healthcare. In particular, she addresses one of the key misconceptions I've heard quite a bit; namely, that when Barack Obama speaks about "national" or "universal" healthcare, he really isn't talking about creating a system like the National Health Service in the UK. Instead,

TRUDY LIEBERMAN: Essentially, what Obama would like to do is craft a plan that builds on private insurance coverage from Aetna, Cigna, Blue Cross and the like, and add to that a public program, a national insurance exchange people might be able to go to and buy coverage. If this entity, this health insurance exchange works, then people will have another option.

Let me say what the lead of an AP story was that I think came very close to describing what Obama is doing; that Obama was proposing universal access to coverage. Access is the key word, as opposed to automatic coverage as a matter of right.

Indeed, in her posting "One Step Forward, One Step Back" on the Columbia Journalism Review blog, Lieberman notes that Obama's position "leaves unanswered the knotty question of whether people will actually be compelled to buy a policy. If they will not, it’s hard to figure where the universality comes in."

Not that McCain's plan is much better:

TRUDY LIEBERMAN: Basically, McCain wants you to pay taxes on the employer provided insurance that you get. And when that happens, he’s going to give tax credits to people, 5,000 dollars for families, 2,500 dollars for individuals, to go into the individual market to buy their own coverage.

It’s likely young, healthy people will leave the employer plan and go into this individual market, leaving only the sick people left in the boss’ insurance, and that will send the premiums through the roof.

What this will do eventually is force a large crack in the employer provided insurance market, and ultimately, people will have to go to the individual market to buy their coverage.

Both the CJR post and the On The Media segment are worth reading/listening to.

Today's useless facts

2008-07-23T09:25:00.003-05:00

Picked up while driving to work this morning:

On the floor of the British House of Commons are two red lines, 2.5 meters apart¹, which separate the two front benches. According to tradition, these lines are just over two sword lengths apart and were meant to keep MPs from resorting to duels to settle debates. Protocol forbids crossing this line while speaking and may be the origin of the expression "toe the line".

The two oldest parliaments in continuous existence are the Tynwald, the Parliament of the Isle of Man, and the Althing, the Parliament of Iceland.

[1] Appendix A of "The Palace of Westminster" factsheet.

Argentina...

2008-07-21T23:56:00.002-05:00

Possible winner of the Greatest Orwellian Euphemism Ever Conceived: The series of military dictatorships of that country between 1976 and 1983 was called (by its leaders)...

The "National Reorganization Process".

Wait, so you're telling me....

2008-07-16T22:11:00.001-05:00

...that roaches aren't going to survive a nuclear war? From this Slate.com article:

The cockroach survival myth seems to have originated with the development of the atom bomb. In The Cockroach Papers: A Compendium of History and Lore, journalist Richard Schweid notes that roaches were reported to have survived the blasts at Hiroshima and Nagasaki, leading some to believe that they would inherit the Earth after a nuclear war.

...

But studies over the last half-decade, such as those conducted by the United Nations Scientific Committee on the Effects of Atomic Radiation, have found that these "other insects" are more likely to reign in the age after humans; the cockroach might, in fact, be one of the first bugs to go.

Not the most science heavy article, but definitely a great short read.

The Day of Days

2008-06-06T10:03:00.007-05:00

Sixty four years ago...

Soldiers, Sailors and Airmen of the Allied Expeditionary Force! You are about to embark upon a great crusade, toward which we have striven these many months. The eyes of the world are upon you. The hopes and prayers of liberty loving people everywhere march with you. In company with our brave Allies and brothers in arms on other fronts, you will bring about the destruction of the German war machine, the elimination of Nazi tyranny over the oppressed peoples of Europe, and security for ourselves in a free world.

Your task will not be an easy one. Your enemy is well trained, well equipped and battle hardened, he will fight savagely.

…

I have full confidence in your courage, devotion to duty and skill in battle. We will accept nothing less than full victory!

Good Luck! And let us all beseech the blessings of Almighty God upon this great and noble undertaking.

— Gen. Dwight D. Eisenhower

Off with his head!

2008-05-28T23:43:00.008-05:00

John Oliver is bound for the Tower of London to have his head cut off. From this week's edition of The Bugle:

John: As we know, this queen's got back, Andy...I'm not ashamed to say that: Queen Elizabeth has got back. She's got a big butt, and I cannot lie. All the other royals can't deny; when Her Majesty walks in with an itty-bitty waist and a round thing in my face, I get sprung.

Andy: Do you, John?

John: I do. It's a compliment, Andy. My anaconda don't want none, unless my monarch has bum, son. She can do side bends or sit-ups, but don't lose that healthy butt.

Combining Sir Mix-a-lot ("now Lord Mix-a-lot since the tragic death of his father") and Her Majesty in the same paragraph: truly disturbing and yet completely hysterical.

People who work with Drosophila...

2008-05-20T00:04:00.002-05:00

Should not be allowed to name genes any more. As if "sonic hedgehog" weren't silly enough, the naming of the Fringe genes in the Drosophila Notch signaling pathway leads to ludicrous names such as "manic fringe", "radical fringe", and "lunatic fringe" for the vertebrate homologs. You know it's bad when you can tell what organism a gene was first discovered in based on the silliness of its name.

Oh, and it turns out that these critters aren't really fruit flies, anyways.

Commenting code

2008-05-15T22:55:00.006-05:00

It pays to reread your code and its comments from time to time; while reviewing an analysis script I wrote this morning, I noticed this particularly politically insensitive comment:

# Purge people of "other" ethnicities

Needless to say, I removed this comment so as not to leave the impression that I am in favor of genocide.

For those who are curious, this comment was attached to a line of code that removes data from subjects whose ethnic backgrounds we are uncertain about. Without doing so, it becomes difficult to correct for the effects of population admixture in genetic analyses.

Quote of the day

2008-05-09T21:20:00.002-05:00

From this cracked.com article:

[A] few years ago, in an act of insensitive fuckery so colossal it could blot out the sun, Siemens tried to trademark the name "Zyklon" with the intent of marketing a series of products under the name. Including gas ovens.

To which someone posted in the comments:

I want to meet the guy working at Seimens who proposed the "Zyklon" trademark idea: either he's a liberal prankster with balls the size of tanks, or he's got the most rocking gestapo accent ever.

Quotes of the day

2008-05-06T21:58:00.003-05:00

The first quote comes from this week's edition of The Bugle:

John Oliver: Is not the biggest story of [the recent British elections] that yet again, the landslide winner was the concept of people not giving a shit about things?

Andy Zaltzman: That's always going to be the way, John, though. That's what we fought the wars for. We fought wars so that we have the right not to give a shit about stuff.

The other quote comes from the comments on an old post by PZ Myers, dealing with suggested research topics for a creationist science fair:

97. Why did God make birds to fly?

Because otherwise that sappy John Ashcroft song would have been "Let the Eagle Plummet," and that just wouldn't have been the same!

One more thing...

2008-05-05T22:04:00.008-05:00

To check off my "things to do in life" list: Go to a Pink Floyd concert. Or at least get close enough by attending last Friday's Roger Waters concert in Dallas.

The first set opened with "In the Flesh" (from The Wall) and featured (listed here in no particular order):

"Mother" - featuring the audience responding "Hell, no!" to "Mother, should I trust the government?"
"Set the Controls for the Heart of the Sun"
"Shine on You Crazy Diamond"
"Wish You Were Here"
"The Fletcher Memorial Home" - visuals updated to include photographs of bin Laden.
"Southampton Dock"
"Sheep" - featuring the appearance and escape of a giant inflatable pig (see photos)

This set also featured a new song from Waters called "Leaving Beirut", which is based on his experience hitchhiking through Lebanon as a young adult. Definitely a song worth listening to, especially if you can the visuals (pencil drawings) to go along with it.

The second set featured a complete performance of The Dark Side of the Moon, with an encore performance of some of the most recognizable songs from The Wall ("The Happiest Days of Our Lives", "Another Brick in the Wall (Part 2)", "Vera", "Bring the Boys Back Home", and ending with "Comfortably Numb").

All in all, an excellent concert, worth much more than the $30 ticket price. Photos from the concert are available through my Flickr page.

Edit [7 May 2008]: In response to a Facebook comment, neither David Gilmour nor Clare Torry were there, but Roger Waters did have other band members (whose names I don't remember) in their places. You really had to listen very closely to notice the difference.

Fear and paranoia

2008-04-28T14:06:00.004-05:00

A great statement on the state of paranoia and fear we currently live in:

More (semi-)useless knowledge

2008-04-24T23:06:00.003-05:00

Only non-royal eight Britons have been given state funerals. Among them are Winston Churchill (the Prime Minister during World War II); Arthur Wellesley, 1st Duke of Wellington (commanding general at the Battle of Waterloo); and Horatio Nelson, 1st Viscount Nelson (commanding admiral at the Battle of Trafalgar). The strange things you learn reading late at night...

The value of a good compiler

2008-04-16T16:30:00.001-05:00

In the process of installing a new compute cluster at work, I evaluated several compilers and was surprised at how well Intel's compiler (icc) performs. This was made apparent by some of the results I obtained from the Scimark2 benchmark, as shown below.

The graph shows the MFLOPS measured by each of the Scimark2 computational kernels on three different machines:

A Dell PowerEdge 6650 with 4 Intel Xeon MPs (32-bit, hyperthreaded, 2.0-GHz);
A Sun X200 M2 with 2 AMD Opteron 2200s (64-bit, dual core, 2.8-GHz); and
A Dell PowerEdge 2950 with 2 Intel Xeon 5130s (64-bit, dual core, 2.0-GHz)

The 32-bit version of Scimark2 was compiled using version 10.0 of the Intel C++ compiler, while the 64-bit version was compiled using gcc 3.4.6 (the default compiler with the Rocks 4.3/CentOS 4.5).

Not surprisingly, the 64-bit machines perform better on the whole, as evidenced by the scores for the "Composite", "FFT" (fast Fourier transform), "SOR" (Jacobi successive over-relaxation), and "LU" (dense matrix LU factorization) computational kernels. What is surprising, however, is that the five year old PowerEdge 6650 using icc actually managed to outperform the shiny new 64-bit machines using gcc. I haven't looked in detail as to why this happens. However, based on the descriptions of the benchmark kernels, I suspect much of the performance gain comes from the Intel compiler being much better at managing certain types of memory operations.

RIP: John Wheeler (1911 - 2008)

2008-04-16T16:07:00.002-05:00

The New York Times has an article on the life and death of John A. Wheeler. Over at Cosmic Variance, Daniel Holz offers an excellent personal tribute to one of the great physicists of the last century. Dave Bacon (The Quantum Pontiff) offers another remembrance of Wheeler and the impact he had in the world of physics.

For my part, Misner, Thorne, and Wheeler's book Gravitation remains close to the top of my list of books I should get around to reading.

Quote of the day

2008-04-03T21:18:00.004-05:00

Seen on the Rocks clusters mailing list: "A supercomputer is a device for turning compute-bound problems into I/O-bound problems."¹ So true.

¹ Credited to either Seymour Cray or Ken Batcher, depending on who you ask.

Our intuition about probability (part 2)

2008-01-31T23:32:00.000-06:00

In a previous post, I described how our intuition about probability can lead us astray, using an example dealing with the average number of tosses needed of a fair coin to generate specific sequences of heads and tails. I provided an informal argument as to why the pattern 'HTH' took more tosses, on average, to generate than 'HTT', and I also provided the results of a simulation demonstrating this. In this post, I'll discuss the mathematical proof of this, as described in a paper by V. C. Hombas, though in a manner that is (hopefully) more suitable for a lay audience.

First, some definitions and notations. Let X be the number of tosses until the pattern of interest (either 'HTH' or 'HTT') appears; the average number of tosses for this pattern to appear (or more formally, the "expectation value of X") is then written as 'E[X]'. The concept of conditional probability is also important; written 'P(A|B)', it asks what the probability of event A is given the fact that event B has already occurred. In this discussion, then, the notation 'E[X|H]' asks what the average number of tosses for generating pattern X is, given the fact that the first toss was a head. Similarly, the notation 'E[X|HT]' asks what the average number of tosses for generating pattern X is, given the fact the first two tosses were a head and a tail, and so on.

With that, let's calculate what the E[X] is for the pattern X = 'HTH'. With a fair coin, we are equally likely to get a head as a tail on any toss (i.e., P(H) = P(T)), giving us an equation for the first toss of our search:

E[X] = 0.5 E[X|H] + 0.5 E[X|T]

If we is toss a tail, then we count a one toss "penalty" and restart our search for the 'HTH' pattern; mathematically speaking, E[X|T] = 1 + E[X]. Substituting this expression into the last one, we get our first numbered equation:

(1) E[X] = 0.5 E[X|H] + 0.5 (1 + E[X])

The next step is to evaluate E[X|H], which is the expectation value of X once we have the first head in the 'HTH' pattern. Again, because P(H) = P(T),

E[X|H] = 0.5 E[X|HT] + 0.5 E[X|HH]

If we toss 'HH', we must start the search over again; however, we can use the second head we tossed as the beginning of the 'HTH' pattern and only have to pay a one toss "penalty". Thus, E[X|HH] = (1 + E[X|H]), and we get our second numbered equation:

(2) E[X|H] = 0.5 E[X|HT] + 0.5 (1 + E[X|H])

Again using the fact that P(H) = P(T), we expand E[X|HT] as

E[X|HT] = 0.5 E[X|HTH] + 0.5 E[X|HTT]

Since 'HTH' is what we're looking for, we count the number of tosses since we started searching and say E[X|HTH] = 3. If we toss 'HTT', we have to start searching for the pattern from the beginning, paying a three toss "penalty" in the process; so, E[X|HTT] = 3 + E[X], and

(3) E[X|HT] = 1.5 + 0.5 (3 + E[X])

Substituting equation (3) into equation (2) into equation (1) and working through the algebra, we find E[X] = E[HTH] = 10, which matches the result we got from the simulation performed in the previous post.

Finding E[X] for X = 'HTT' is the same up to the last step of expanding E[X|HT]. Here, E[X|HTT] = 3 since we are looking for 'HTT'. E[X|HTH] forces a restart of the search from the last head along with a two toss "penalty" for the initial 'HT'; so, E[X|HTH] = 2 + E[X|H], and

E[X|HT] = 1.5 + 0.5 (2 + E[X|H])

Making the substitutions into equations (1) and (2) and crunching the algebra, we find E[X] = E[HTT] = 8, again matching the results from the simulation.

Since E[HTT] < E[HTH], we have proved that on average, the pattern 'HTT' should appear before 'HTH' when tossing a fair coin.

Multiple Inspector windows

2008-01-28T10:44:00.000-06:00

From the unofficial Apple blog, a great tip on how to open multiple Inspector windows in applications like Keynote and Pages. Inspector is the little toolbox that allows you to tweak things like object size and alignment; producing multiple Inspector windows is ridiculously simple: hold down the Option key and click on the tab you want.

Our intuition about probability (part 1)

2008-01-23T02:25:00.001-06:00

Peter Donnelly's TED talk highlights some common mistakes made in interpreting probabilities and statistics as well as the consequences of such mistakes.

One of the interesting questions he poses is this: Suppose we toss a fair coin repeatedly, counting the number of tosses made before getting the pattern 'HTT' (head, tail, tail); for example, if we toss 'HHTHHTTH', the count would be 7. We perform a large number of trials, resetting the count of tosses between trials, to get the average number of tosses required to produce 'HTT'. We then repeat this experiment (counting number of tosses requried to produce a pattern across a large number of trials), but instead of looking for 'HTT', we look for 'HTH'. We then ask which, if either, is larger: the average number of tosses needed to produce 'HTT' or the average number of tosses needed to produce 'HTH'?

If you are like most people (including me), your reasoning goes something like this: For a fair coin, the probability of a head P(H) = 1/2, and each toss is independent of the one before it. Thus, P(HTT) = P(HTH) = (1/2)(1/2)(1/2) = 1/8, and the average number of tosses required to produce 'HTT' is equal to the average number of tosses required to produce 'HTH'.

However, when you actually perform this experiment, you discover that the average number of tosses required to produce 'HTH' is larger than the average number of tosses required to produce 'HTT'. We can demonstrate this using the following R code:

# Number of tosses per trial; this should be fairly large to ensure (so
# far as we can) that the 'HTH' and 'HTT' patterns occur in each trial
n.tosses <- 50;

# Number of trials to run; this should be large so we get a good
# estimate for the average number of tosses required to generate each
# pattern ('HTH' or 'HTT')
n.trials <- 10000;

# Perform n.trials of coin tosses; the value of each toss is either
# '1' (head) or '0' (tail), as drawn from a binomial distribution with
# one trial and a probability of success of 0.5
generate.string <- function(x)
    { paste(rbinom(n.tosses, 1, 0.5), collapse=''); }
data <- sapply(1:n.trials, generate.string);

# Number of tosses for the patterns of interest in the data.
# We need the '+ 2' correction factor since the number of tosses is
# counted at the end of the pattern, but regexpr returns the index of
# where the pattern starts.
hth <- regexpr('101', data) + 2;
htt <- regexpr('100', data) + 2;

# Print the average number of tosses required to produce each pattern
cat('HTH:', mean(hth), 'tosses\n');
cat('HTT:', mean(htt), 'tosses\n');

Running this simulation, we see that 'HTH' takes an average of ~10 tosses to produce while 'HTT' only takes an average of ~8 tosses. The explanation for this lies in the fact that the 'HTT' pattern allows for some overlap in our search while the 'HTH' pattern does not.

Borrowing from Donnelly's talk, suppose we have already tossed the 'HT' pattern, and the next toss is a 'H'. If we are looking for 'HTH', we are done. If we are looking for 'HTT', we have to continue looking, but we can use the 'H' that was just produced as the possible start of the 'HTT' pattern we are looking for.

On the other hand, suppose we have already tossed the 'HT' pattern, and the next toss is a 'T'. If we are looking for 'HTT', we are done. If we are looking for 'HTH', we have to continue looking; unfortunately, unlike the case in the last paragraph, we cannot use our most recent toss (a 'T') as the possible start of the 'HTT' pattern we are looking for. We are forced to wait for the next 'H' to show up, and thus, are now behind by at least one toss. This explains why the 'HTH' pattern takes more tosses, on average, to generate than the 'HTT' pattern.

Obviously, a formal, mathematical proof of this exists, but that is a topic for another post.

EDIT [31 Jan. 2008]: I have now added another post with the mathematical proof of the situation.