The Scientific Activist

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:

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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.

Read the comments on this post...

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:

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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.

Read the rest of this post... | Read the comments on this post...

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).

Read the rest of this post... | Read the comments on this post...

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."

Read the rest of this post... | Read the comments on this post...

Two New Papers on Integrin Activation

Tue, 20 Oct 2009 07:39:20 -0500

Just as I was in the process of finishing my doctorate in August, I found out that my first first-author paper had been accepted for publication by The EMBO Journal. This was good news, because we were reporting some pretty fundamental findings in a relatively saturated field, and one of our competitors had managed to successfully stall the acceptance of this paper since March. Up until that point, witnessing this happen firsthand had been a somewhat frustrating and disillusioning experience for a young scientist, but I think that we were vindicated in the end. Anyway, this paper--and another paper that I contributed to--were published online earlier this month.

These studies both explore the important biological process of integrin activation. The first paper (Anthis et al.) provides some new basic molecular details for how this process is carried out in the cell. Cells in humans and other higher organisms exist in a dynamic environment, alternately grasping and disengaging from the three-dimensional web of their surroundings (i.e. the extracellular matrix). Many of these tasks involve a family of proteins called integrins, which act as the "hands" of the cell. The cell internally controls whether an integrin is adhesive by signals from within the cell, using another protein called talin. By exploring the detailed three-dimensional structure of a talin/integrin complex, we showed how key interactions between talin, the integrin, and the inner surface of the cell membrane can elegantly promote the structural changes outside the cell that modulate adhesion strength.

The following figure (from my thesis) illustrates the process of integrin activation:

Read the rest of this post... | Read the comments on this post...

New Interactive 3D Molecular Images in Scientific Articles

Mon, 19 Oct 2009 23:52:34 -0500

Late last week, I received emails from two journals (The Journal of Biological Chemistry (JBC) and PLoS ONE) indicating that they are now incorporating interactive 3D images of molecular structures in their papers. The atomic coordinates of all published biomolecular structures have been available for some time at the Protein Data Bank. However, making sense of something as complex as a protein structure can require quite a bit of analysis. So, scientists go through great pains to represent important features of their structures in 2D images for publication. Ostensibly, this new functionality will save readers time and enhance their understanding by letting them explore these structures, but starting with the important features already highlighted.

After a quick look at these new interactive 3D images, though, I have to admit that I'm finding the experience slightly cumbersome. Still, this is a good idea, and I imagine that the experience will be improved over time. You can check out the first JBC paper incorporating the interactive images here, and a collection of papers in PLos ONE incorporating the images here. Below is the press release on the subject from PLoS ONE:

Read the rest of this post... | Read the comments on this post...

Health Care Reform: It's a Matter of Convenience

Mon, 12 Oct 2009 22:41:54 -0500

I recently had the pleasure of writing an op-ed piece about health care reform for my hometown newspaper, the Fort Worth Star-Telegram, and it ran in the paper today. You can check it out online here. I grew up reading the Star-Telegram, so this was an exciting opportunity.

My article discusses the need for robust health care reform in the form of a strong public option, comparing and contrasting my health care experiences in the US and the UK to build my case. For regular readers of my blog, you will note that this is a theme I have often explored.

I would have preferred that the Star-Telegram ran this with the title I suggested (given above as the title of this blog post), which I think most precisely conveys the meaning of the rest of the article. (My point is not necessarily that health care reform would cut down wait times, but that it would reduce the time individuals waste dealing with health care administration in general.) But, that is only a minor complaint; overall this was a very enjoyable experience, and I had a good back-and-forth discussion with the opinion editor, J.R. Labbe, in the run-up to publication.

So, go check it out!

Read the comments on this post...

2009 Nobel Prize in Chemistry: The Ribosome

Wed, 07 Oct 2009 12:02:38 -0500

The winners of this year's Nobel Prize in Chemistry have been announced, and the prize will be shared equally between Venkatraman Ramakrishnan, Thomas Steitz, and Ada Yonath "for studies of the structure and function of the ribosome." The information encoded in DNA is decoded to produce functional proteins in two stages: transcription (DNA --> RNA) and translation (RNA --> protein). This prize was awarded for the work that described this second stage in atomic detail, and you can read more about it in the scientific background document released with the prize announcement. This prize complements the 2006 Nobel Prize in Chemistry, which was awarded for atomic-resolution work on transcription (although the transcription prize was specifically for work on eukaryotes, and the work recognized by the translation prize was carried out on prokaryotes).

This prize marks the sixth time in eight years that the Nobel Prize in Chemistry has been awarded for biological work, and most of these have been for atomic-resolution structural biological work (X-ray crystallography in three cases, NMR in one). As I've noted before, crystallography and NMR involve a mix of biology, chemistry, and physics, so it's reasonable that such work is often recognized by the Nobel Prize in Chemistry.

Read the comments on this post...