The Scientific Activist

Upcoming UCLA Pro-Test Rally: Stand Up for Animal Research on April 8th

Mon, 05 Apr 2010 20:29:48 -0500

The UCLA chapter of the pro-science organization Pro-Test has announced its second major rally to show support for science and to stand up against the ongoing campaign of intimidation being waged by animal rights activists. The organization originated in Oxford in 2006 during a streak of particularly nasty actions by animal extremists, and the UCLA chapter held their first rally about a year ago in response to the escalating threats and destruction of property aimed at animal researchers in the US.

The next rally is scheduled to start at 11:30 am, on Thursday, April 8th. It will convene on the UCLA campus, at the corner of Westwood Blvd and Le Conte Ave. You can read the full text of the Pro-Test press release on the event below:

Supporters of science at the 2009 UCLA Pro-Test rally.

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Here We Go Again....

Tue, 23 Feb 2010 23:51:00 -0500

I don't write much about the antics of animal rights activists these days, because while some of their activities have a very negative impact on the work of some scientists, they're really just a marginal--albeit highly vocal--bloc that thrives on attention. Still, sometimes they need to be called out, and Janet of Adventures in Ethics and Science is doing just that:

Harassment drove UCLA neurobiologist Dario Ringach out of primate research in 2006. This was not just angry phone calls and email messages. We're talking about people in masks banging on the windows of his house in the night, scaring his kids. Without support on this front from other scientists or from UCLA, Dario abandoned research that he believed to be important so that he could keep his family safe.

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The Open Laboratory 2009 Is Out

Tue, 23 Feb 2010 22:23:43 -0500

This year's version of the science blogging anthology, The Open Laboratory 2009, is out and available from Lulu publishing. You can order it in paperback format or as an electronic download. Three cheers to editor Scicurious and series editor Bora Zivkovik for their great work in making this happen!

For more, check out Scicurious' announcement and the earlier unveiling of the posts included in this year's anthology. You can see my contribution here.

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More on the M2 Channel Structure Controversy

Sun, 21 Feb 2010 19:08:28 -0500

Last year, I wrote about a scientific controversy over the structure of the influenza M2 proton channel, particularly over the protein's binding site for adamantane type anti-flu drugs. The Schnell/Chou model, based on solution NMR, had the drug binding to the outside of the channel, within the membrane (at a 4:1 drug:protein ratio). On the other hand, the Stouffer/DeGrado model had the drug binding inside the channel (1:1 ratio), based on X-ray crystallography studies.

A new study was recently published in Nature (the same journal that published the original two competing papers), based this time on solid state NMR. This study, by lead author Sarah Cady in Mei Hong's lab, finds evidence for both binding sites, but argues that the pore (Stouffer/DeGrado model) is the higher affinity site. This subject involves a legitimate scientific controversy, and has clearly been in need of a third party to help resolve it. Unfortunately, the DeGrado group was also involved with this one, so it's not quite the impartial judgment that this subject needed. Regardless, the new study does offer additional evidence to support the Stouffer/DeGrado model, although I don't think it's quite the final word.

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More on Health Care Reform

Tue, 26 Jan 2010 00:14:57 -0500

Clearly, I'm not the only one who thinks that the most obvious solution for health care reform is for the House to pass the Senate bill: The New York Times just published an editorial arguing the same point:

The most promising path forward would be for House Democrats to pass the Senate bill as is and send it to the president for his signature. That would allow the administration and Congress to pivot immediately to job creation and other economic issues. The Senate bill is not perfect, but it would expand coverage to 94 percent of all citizens and legal residents by 2019, reduce the deficit for decades to come, and create pilot programs to move the medical system toward better care at lower costs.

The Times' editorial also notes the hypocrisy in the Massachusetts Senate election:

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We Need to Pass Health Care Reform Now!

Mon, 25 Jan 2010 22:53:14 -0500

It's been a rocky ride this year, getting heath care bills passed in the House and the Senate. It's been just over a month since the Senate passed its bill in a dramatic Christmas Eve vote (and much longer since the House passed its version), but the fate of health care reform still appears as uncertain as ever. In particular, a surprising political setback in Massachusetts has made the already difficult Senate an almost impossibly hostile environment for reform.

The most obvious solution is for the House to pass the Senate bill without hesitation; however, House Speaker Nancy Pelosi has already said this is unlikely to happen. On the positive side, it looks like Democrats in the House and Senate may be close to brokering a deal allowing reform to pass. But, if this fails--and maybe even instead of pursuing this strategy--the House should do its best to pass the Senate bill.

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The Open Laboratory 2009 Winners Announced

Wed, 13 Jan 2010 08:06:08 -0500

The top 50 science blog posts of the year, as judged by a large panel of bloggers, have been announced and will be included in The Open Laboratory 2009. The fourth annual volume of this blog anthology will be published early this year, but you can go ahead and see the winning posts here and here. The editor, Scicurious, the series editor, Bora Zivkovic, and all of the judges deserve a round of applause for their hard work.

And, I'm happy to announce that my post on H1N1 influenza antiviral drug resistance ("Why Swine Flu Is Resistant to Adamantane Drugs" from 01 May 2009) made the cut and will be included in this year's science blogging anthology. A collection of my posts was included in the first volume (2006), and I'm excited to participate again.

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It's Not Too Late to Get Vaccinated Against H1N1 Flu

Tue, 12 Jan 2010 21:50:31 -0500

Have you gotten your H1N1 flu shot yet? If not, it's still not too late. Due in part to the successes of the public health campaign against H1N1 influenza, people have begun adopting a rather casual attitude toward it. This is problematic, because due to an extent to initial shortages of vaccine, a very large portion of the population remains unvaccinated and susceptible to another wave of flu outbreaks. In fact, I only managed to get my H1N1 flu vaccine about a week ago, when my place of employment began offering it to workers who weren't part of the original target group.

I imagine that many of you had been in a similar situation, so now that the H1N1 vaccine is widely available, I would encourage you to go ahead and get it--to protect yourself and to help protect those around you.

In fact, earlier today I received a press release from the Campaign for Public Health Foundation, announcing an event tomorrow (Wednesday, January 13th) aimed at raising public awareness of the H1N1 vaccine. Here's the press release in full:

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Chad Orzel on Science Blogging

Mon, 11 Jan 2010 09:02:07 -0500

Chad Orzel, of Uncertain Principles, has a nice article today in Inside Higher Ed about the value of science blogging, both in his own career and in the scientific process in general. This is a view that I of course agree with and think is important, and Chad brings a unique perspective on the issue.

Go check out his article, but here's a taste:

As essential as this [communication] step is, it is in many ways the weakest link in the scientific process today. While there are more scientific papers published today than ever before, a combination of technical sophistication and scientific specialization means that as far as the general public is concerned, modern scientific papers might as well be Latin cryptograms.

This is the famous "Two Cultures" problem pointed out by C.P. Snow a half century ago, and in many ways, the problems have only gotten worse since Snow's day. This is especially troubling given that the biggest problems facing human civilization today -- global climate change, pandemic disease, dwindling natural resources -- demand scientific solutions. Public understanding of science remains dangerously low, however, to the point where slick and cynical lobbyists can easily sow doubt about the state of global climate, or the safety of vaccines. When a shameless huckster like Glenn Beck can convince people not to vaccinate themselves or their children, in the face of decades of scientific evidence of the safety and efficacy of vaccines, something is dangerously wrong.

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Check Out Meredith on TV This Sunday!

Fri, 08 Jan 2010 09:07:01 -0500

If you get the Smithsonian Channel on your TV, then tune in at 8 pm this Sunday (January 10th) to watch the program Zoo Vets: Claws, Paws, and Fins. Not only does this look like a pretty neat program (from my admittedly very biased perspective), but it features--among others--my girlfriend, Meredith Clancy, and her long-time mentor, Kathryn Gamble, the head veterinarian at the Lincoln Park Zoo. The program, which follows vets at Chicago's Lincoln Park Zoo, Brookfield Zoo, and Shedd Aquarium, was filmed in fall 2008, when Meredith was completing an external rotation at Lincoln Park as part of her fourth year vet school training.

Here's a sneak peak:

(If this video doesn't work for you, you can also view it on YouTube.

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Multivitamins Don't Work!

Wed, 06 Jan 2010 18:59:52 -0500

This isn't really anything new, but Emily Anthes has a nice summary in Slate today of what we currently know about the effectiveness of nutritional supplements--namely that they don't consistently show any clear benefits except in a few very specific situations:

Vitamins--with their promise to bridge the gap between the nutrients our bodies need and those they get--have always seemed reassuringly simple: Just pop a multivitamin and let your body soak in those extra nutrients. But not any longer. During the past few years, study after study has raised doubts about what, if any, good vitamins actually do a body. They could even pose some real medical risks.

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On Cooking Rice

Mon, 04 Jan 2010 08:20:43 -0500

Go to the bottom of the post to see my recommended methods for cooking rice.

This week, I resolved that for the new year I would start blogging more frequently. Given that I really haven't been blogging at all recently, that shouldn't be too hard. I won't bore you with the various reasons why blogging has been so slow recently, but it seems that starting a new job and a new life in a new city has upended my old routines. One activity that I have been focusing much more effort on in my new life, though, is cooking. Spurred in part by reading Ratio by Michael Ruhlman, I've been trying to elevate my cooking from a practicality to an art and even, in some cases, a science (at the very least I'm trying to be more systematic about it).

The other day, I was thinking quite a bit about one of the first items I learned to cook many years ago: rice. I spent the summer between my sophomore and junior years of college in Australia, and most of that time I lived in a hostel. For the first time in my life I found myself really out on my own (I had lived in the dorms my first two years of college), so I realized that I finally needed to learn how to cook for myself. Hostel cooking was more about practicality than anything else, but I picked up quite a few skills that have served me well since then.

Early on, one of my friends in the hostel showed me a pretty straightforward and effective way to cook rice. She would add her rice to unheated water, then heat both together to a low boil in an uncovered saucepan. Once the excess water had boiled off (about 15 minutes), she would then cover the pan, turn the heat very low, and then let the rice "steam" for another 15 minutes or so. This was a long time ago, so I may not be remembering her method totally correctly, but I believe she used a 2:1 volume ratio of water:rice (i.e. 1 cup rice, 2 cups water; this is also the ratio given on the package of rice I currently have in my cupboard). This technique--which I'll call the "open-pan" method--served me pretty well, but it didn't always work perfectly, for reasons I'll describe shortly. Cooking rice in general isn't too tricky, but you still have to get it right; if it's undercooked it will be hard and slightly crunch, and if it's overcooked it will be mushy and soupy--in either case totally inedible.

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Rhodes Secretary: Wall Street Megabonuses Draining Our Young Talent

Sat, 21 Nov 2009 12:05:10 -0500

In the op-ed pages of The Washington Post today, Elliot Gerson--the American Secretary of the Rhodes Trust--takes a bold stand:

Tonight, 32 young Americans will win Rhodes Scholarships. Their tenures at Oxford are funded by the legacy of the British imperialist Cecil Rhodes, a man whose life would not be honored today were it not for his vision that young people of outstanding intellect, leadership and ambition could make the world a better place.

For more than a century Rhodes scholars have left Oxford with virtually any job available to them. For much of this time, they have overwhelmingly chosen paths in scholarship, teaching, writing, medicine, scientific research, law, the military and public service. They have reached the highest levels in virtually all fields.

In the 1980s, however, the pattern of career choices began to change. Until then, even though business ambitions and management degrees have not been disfavored in our competition, business careers attracted relatively few Rhodes scholars. No one suggested this was an unfit domain; it was simply the rare scholar who went to Wall Street, finance and general business management. Only three American Rhodes scholars in the 1970s (out of 320) went directly into business from Oxford; by the late 1980s the number grew to that many in a year. Recently, more than twice as many went into business in just one year than did in the entire 1970s.

This break in an almost century-old pattern coincided with great increases in occupational earnings differentials, which have continued to grow, seemingly exponentially. It seems quaint, if not unfathomable, that just three decades ago the differentials in earnings -- generally two- to fivefold between business leaders and doctors or lawyers, or five- to tenfold with professors, scientists and public servants -- were often rationalized by Rhodes scholars as reasonable additional compensation to balance the lower standing of business jobs among their peers.

When differentials could become a hundredfold or far more -- and as investment banking and similar firms started to recruit young Rhodes scholars who had degrees in math, physics or even history, English and theology -- the yawning prospective wealth chasm understandably became impossible for many to ignore. Even for a few of those most deeply committed to other, more public-spirited pursuits, the lure of such rewards, especially as they are reasonably attainable for people of such high abilities, became much harder to resist.

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On Mimicking Phosphotyrosine

Thu, 12 Nov 2009 07:39:49 -0500

When doing science, there's generally one totally optimal way of performing an experiment. But, there may also be several other less optimal means of gathering similar data, and one of those may be much more feasible than the totally optimal method. As a scientist, you have to determine whether this other method is sufficient, or whether it's necessary to expend the extra effort and/or resources on the more difficult method. Sometimes it's totally fine to take the simpler approach (and this will spare some of your precious time and your lab's precious funding), but this post is about a case where it's not.

My colleagues and I have a new paper in JBC (the Journal of Biological Chemistry) that went online late last month. Although I think that the science is pretty interesting, I'm not going to write at length about it here. Instead, you should check out my post about an earlier paper on this subject (integrin phosphorylation) here. Superficially, the two are reasonably similar (at least on the level that I would discuss things on the blog). In fact, much of the newly published work was was actually conducted around the same time as the earlier work (a few years ago), but for a variety of reasons we didn't publish it then. The new paper marks a major advancement of that work, and the new biological data from Jake Haling (in Mark Ginsberg's lab at UCSD) also increases its depth considerably.

However, what I want to write about here is how one goes about studying tyrosine phosphorylation. Tyrosine is one of the 20 amino acids that form the building blocks of the proteins in our bodies. Proteins are often modified after they are produced in the body, and one type of modification is phosphorylation (the addition of a phosphate group to the -OH group of serine, threonine, or tyrosine, i.e. changing -OH to -PO₄^2-). This modification is catalyzed by a type of enzyme called a kinase, and phosphorylation is a type of "posttranslational modification" because it occurs after the mRNA has been translated into a chain of amino acids (i.e. a protein).

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AMA Advocates Change in Marijuana Classification

Wed, 11 Nov 2009 12:37:28 -0500

Yesterday, the influential AMA (American Medical Association) announced that it would cease its opposition to the concept of medical marijuana and instead advocate for a change in federal classification of the drug. From the LA Times:

The American Medical Assn. on Tuesday urged the federal government to reconsider its classification of marijuana as a dangerous drug with no accepted medical use, a significant shift that puts the prestigious group behind calls for more research.

The nation's largest physicians organization, with about 250,000 member doctors, the AMA has maintained since 1997 that marijuana should remain a Schedule I controlled substance, the most restrictive category, which also includes heroin and LSD.

In changing its policy, the group said its goal was to clear the way to conduct clinical research, develop cannabis-based medicines and devise alternative ways to deliver the drug.

"Despite more than 30 years of clinical research, only a small number of randomized, controlled trials have been conducted on smoked cannabis," said Dr. Edward Langston, an AMA board member, noting that the limited number of studies was "insufficient to satisfy the current standards for a prescription drug product."

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