The Scientific Activist

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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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:

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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:

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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!

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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.

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Bad Math at The Weather Channel

Tue, 06 Oct 2009 18:50:23 -0500

I have a bone to pick with The Weather Channel, and it has to do with misuse of statistics. This is something I noticed a long time ago, so it's about time I said something about it. The problem here is fairly obvious, so I'm sure many others have noticed this before. Also, this may not be specific to The Weather Channel, but I'm just using it as an example because that is where I have observed this problem.

To the left, you can see tomorrow's forecast for Austin, Texas, from The Weather Channel. The key piece of information here (for this post) is that there is a 40% chance of precipitation. There is a little bit of ambiguity as to what exactly this means, but I interpret this as saying that there is a 40% chance that at some point tomorrow it will rain. Since The Weather Channel gives forecasts for both the day and the night, I'm going to assume that this forecast only pertains to daylight hours.

That's all well and good, but below I have pasted the hourly forecast for tomorrow. Can you spot the problem?

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2009 Nobel Prize in Medicine: Telomeres and Telomerase

Mon, 05 Oct 2009 11:21:58 -0500

Today, the Nobel Committee announced the winners of the 2009 Nobel Prize in Physiology or Medicine, equally shared between Elizabeth Blackburn of UCSF, Carol Greider of Johns Hopkins, and Jack Szostak of Harvard Medical School--all three American. This year's prize was awarded for the discovery of telomeres, the repeated sequences of DNA at the ends of chromosomes that protect the integrity of the chromosomal DNA, and for the discovery of telomerase, the enzyme that builds the telomeres.

This prize recognizes seminal work in molecular genetics and biology that unlocked some of the basic secrets of how our cells function. These studies were also relevant to cancer biology. Most cells in the adult exhibit only limited telomerase activity, meaning that as cells divide and replicate their DNA, the chromosomes' telomeres become shorter. This limits the number of times a cell can divide and contributes to aging. Cancer cells, however, can exhibit overactive telomerase, allowing them to divide uncontrollably.

Another interesting dimension of this prize is that Elizabeth Blackburn in particular has been highly engaged in the national dialogue on science policy in recent years. In 2004, Blackburn was instrumental in revealing how politically-charged and dysfunctional George W. Bush's President's Council on Bioethics was. From 2001 to 2004 she served as one of only three full-time biomedical researchers on the 17-to-18-member council. In 2004, she was fired from the council, along with another member who disagreed with the administration's position on some of the relevant issues.

Blackburn spoke out about the Council of Bioethics, demonstrating that despite its written mission to be a body that monitors research developments and recommends appropriate guidelines, it was really just a tool for parroting the Bush Administration's positions on certain hot-button issues--particularly embryonic stem cell research. Thus, Blackburn played a central and important role in revealing the extent of the political interference in science that pervaded the Bush Administration.

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Scientific Diplomacy and the Universality of Science

Thu, 17 Sep 2009 08:30:00 -0500

Members of the Obama Administration have mentioned using science for diplomatic purposes on various occasions, most notably when President Barack Obama himself included this idea in his address at Cairo University in June. Today, SEEDMAGAZINE.COM published an article by Harvard's Sheila Jasanoff on this subject, which you can read here. Seed has asked me to provide commentary on her article as this week's Featured Blogger, which you can read here.

The Jasanoff article focuses specifically on the appointment of science envoys, a central component of the Obama Administration's scientific diplomacy plan. Mine, on the other hand, is more about scientific diplomacy in general. I generally agree with the Jasanoff article, although I think that her "five common misconceptions" should be taken with a grain of salt, since they're more related to the application of science rather than using a common interest in science to bridge a cultural gap.

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An Update from The Scientific Activist

Tue, 15 Sep 2009 14:52:27 -0500

As I indicated earlier this summer, the blogging would continue to be a bit slow as I entered the home stretch of grad school. Since then, I'm happy to report that I have submitted my thesis, successfully defended it, resubmitted a corrected version, and had my final thesis accepted. Within the next few weeks, I should receive a letter from Oxford officially conferring my D.Phil. (Oxford's equivalent of the Ph.D.) in biochemistry, and I'll head back to Oxford with my family in late October for graduation. Then, in November, I'll start a postdoc at the NIH.

So, I anticipate that the blogging will remain slow for the next couple of months, as I won't be settled in to my new job and new apartment until sometime in November. In the meantime, I'll be bouncing around from place to place; I'm currently visiting my girlfriend in LA, but later this week I'll head back to Texas before flying to DC to try to secure housing for myself. I appreciate your patience during this transition, and I'm looking forward to getting back in the swing of things before too long.

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A Tale of Two Health Care Systems

Thu, 06 Aug 2009 16:22:26 -0500

Mike Dunford tells a compelling story today at The Questionable Authority:

Yesterday, I took the kids to the doctor for their school physicals. I wouldn't normally subject you to an account of the day-to-day minutia of my personal life, but given the current debate about how we should handle health care in the United States, the details might be of interest.

We arrived - without an appointment - at a medical facility that we had not been to before. We did not have medical records with us, and the only paperwork of any kind that we had brought were the forms that needed to be filled out to enroll the kids in sports programs. When we checked in, the only thing I had to do was hand the clerk a government-issued photo ID. I did not have to fill out any insurance forms, I did not have to hand over any payment of any kind, and I didn't touch a clipboard. Within two hours, both the children had been seen by a doctor, received physical exams, had their shot records checked and brought up to date where necessary, and I'd been given the completed school and sports forms.

That's not fiction, and it's not a prediction of what could happen in the future. That happened yesterday, it happened in the United States, and it happened in a health care system that's owned and operated by the Federal Government.

That's right. I got to use the dreaded socialized medicine yesterday, because I've got access to the Department of Defense's medical system.

We didn't have to fill out forms yesterday because all the paperwork that needed to be done to switch our primary care doctor from one in Florida to one in Alabama was done when my wife checked in to her new assignment. We didn't need to bring records, because both facilities have access to the same electronic system. All that the clinic needed to access the records was my wife's information.

I mention this because it reminded me so much of something I wrote about previously on my blog:

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The Most Recent Counterfactual Attack Against the Obama Administration

Thu, 16 Jul 2009 18:23:25 -0500

This is kind of silly, but it's always interesting to see what the right-wing attack machine comes up with when it gets desperate. Now it appears that they're going after President Obama's rather innocuous science advisor, John Holdren. Specifically, a recent article in The Washington Times--that bastion of rational commentary--claimed that Holdren "has toyed with extreme measures of population control, even suggesting in one book how to make it more publicly acceptable for the government to spike drinking water in order to sterilize people."

Does that sound just a bit too absurd to be true? That's because it is. Chris Mooney explains just how misinformed this claim is in a post at Science Progress:

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AMP Announces 2009 Michael D. Hayre Fellows in Public Outreach

Thu, 16 Jul 2009 16:50:40 -0500

Yesterday, Americans for Medical Progress revealed the three recipients of its 2009 Hayre Fellowship in Public Outreach. Applicants submitted proposals for programs aimed at spreading awareness about the role of animal research in medicine, and the three fellows will receive a $5,000 stipend each, plus an addition $2,000 to fund their proposals. This year's fellows are Gillian Braden-Weiss and Breanna Caltagarone, who are veterinary students at the University of Pennsylvania, and Megan Wyeth, a graduate student at UCLA. Here's a summary of the projects they are going to be working on:

As veterinary students at the University of Pennsylvania and active members of the Laboratory Animal Medicine Club, Gillian Braden-Weiss and Breanna Caltagarone will create a "Thank a Mouse" animal research outreach program for private practice veterinarians and their clients. Through the development of a website and other interactions, they will raise awareness for existing and future contributions of animal research to veterinary care.

Megan Wyeth, a graduate student who conducts epilepsy research at UCLA, was a student leader of the UCLA Pro-Test campus rally this April in support of scientists' work in animal research. Now, as a Hayre Fellow, Megan will help to expand the student-based group Pro-Test for Science on the UCLA campus and foster similar student organizations nationwide.

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NIH Releases Final Embryonic Stem Cell Research Guidelines

Mon, 06 Jul 2009 13:47:14 -0500

When the NIH released its draft guidelines on human embryonic stem cell (hESC) research in late April, they were open to a 30-day period of public comment before the formulation of the final rules. Today, the NIH has released its final guidelines (pdf).

Not much has changed, so there's not really much to say that I haven't already. The bad news is that the fairly restrictive nature of the rules was maintained (i.e. no federal funds for hESC lines derived from embryos generated specifically for research), but the good news is that the government didn't cave into some fairly outlandish requests (clearly from anti-abortion activists) to insert some loaded language into the rules.

Check out the full document (pdf) for the text of the final rules and a point-by-point reply to the major comments.

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