An Oxford graduate student by day and a scientific activist by night, Nick Anthis isn't letting his Ph.D. research in protein structure get in the way of defending scientific and social progress.
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In an attempt to save the sinking ship that is his current government, UK Prime Minister Gordon Brown has extensively shuffled his cabinet. As part of this the science (formerly the Department for Innovation, Universities and Skills [DIUS]) has been merged with business (formerly the Department for Business, Enterprise and Regulatory Reform [DBERR]) to form the Department for Business Innovation and Skills (DBIS). Paul Drayson will remain Minister of Science, but--in another twist--he'll now also be moonlighting as Minister of Defence Procurement (a position he has held previously).
Unfortunately, from what I've seen of Drayson previously, both shifts seem to fit very well with his interest in science largely as an applied endeavor. These are worrying developments for a variety of reasons. This gives science a decreased prominence in the current government, both by being combined with another department and now sharing its minister with an only tangentially related area. And, philosophically at least, so closely tying science and defense to one another sends an unsettling message.
I'll admit that I haven't paid a terribly large amount of attention to the upcoming European Parliament elections (taking place in the UK Thursday--i.e. tomorrow) since I can't actually vote in them. However, maybe I should have been paying attention, based on a write-up by Frank Swain (SciencePunk) and Martin Robbins (The Lay Scientist) that appeared earlier this week in The Guardian's Science Blog.
Swain and Robbins' article--about the disconnect between the importance science will play in the issues the European Parliament will face versus the lack of attention science has received in the elections--is a follow-up on a survey they sent to the press offices of five major and minor UK parties on their scientific positions. I'd encourage you to take a look at the survey results yourself, but for me, at least, they solidified my opinion that if I were voting in the UK, I would probably be voting for the Liberal Democrats. Much of my thinking there, though, is influenced by our local situation in Oxford (which isn't related to the European Parliament elections), where we are represented by an excellent Lib Dem MP, Evan Harris, who has been an outspoken pro-science advocate on a variety of issues.
I realize that blogging has been pretty slow here lately. But, I have good reasons, I promise! I spent most of the month of May back in the US for my girlfriend's graduation and then for a cross-country move/Great American Road Trip. Meredith graduated from Texas A&M University College of Veterinary Medicine and Biomedical Sciences on the 14th. Then, after the ensuing festivities, we packed up her truck and headed west to LA, where she's going to be working for the next year as a veterinary intern.
Now that I'm back in Oxford, though, I'm basically in 100% thesis completion mode. The fact that I may have possibly once upon a time told Meredith that I would definitely finish my degree before she finished hers might now be serving as additional motivation. Maybe. Regardless, between my thesis and the various papers I'm working on right now, the blogging will probably continue to be slow for a bit.
Although I've only written a bit about the recent outbreak of influenza A H1N1 (swine flu), I'd encourage you to take a look at this post by Kent Newsome that discusses where to find reliable information on this topic. This post is particularly nice, because it gives concrete examples of some of the useful things this blogger has learned from these various sources. Granted, most of the sources he discusses are affiliated with ScienceBlogs, but that shouldn't really be surprising, given that there has been so much quality blogging here recently on the topic of swine flu (particularly by Effect Measure and Aetiology).
On a mostly unrelated note, I'd also encourage you to check out the ScienceBlogs homepage right now for another example of things that ScienceBloggers do well: taking on pseudoscience. In this case, it's the outrageous ongoing explosion of quackery at The Huffington Post.
Update: Reader Sofia has also pointed me toward Virology Blog, which appears to have a large amount of scientifically-oriented information on the topic as well.
On Wednesday, the CDC reported that influenza A H1N1 viruses from 13 patients with confirmed diagnoses of swine flu had been tested for resistance to a variety of antiviral drugs. The good news was that all of the isolates were susceptible to the antiviral drugs oseltamivir (Tamiflu) and zanamivir (Relenza). However, all 13 were resistant to adamantane-based drugs (amantadine and rimantadine). Resistance to adamantane drugs (which were developed first) has actually become quite widespread among flu viruses in general, so oseltamivir and zanamivir are commonly the drugs of choice.
The reason for the difference is that the adamantane drugs target different viral proteins from oseltamivir and zanamivir. The two major proteins on the surface of the influenza virus are hemagglutinin (the "H" in H1N1) and neuraminidase (the "N"). Due to the evolution of the influenza virus over time, these proteins come in a variety of different forms, and we label strains of flu by the specific class of hemagglutinin and neuraminidase the virus carries (H1N1, H3N2, etc.). These are the largest proteins on the surface of the virus, and they are the ones that our immune system generally reacts to. However, they aren't the only ones.
The surface of the influenza virus also has a much smaller protein called M2, which acts as a channel to let hydrogen ions pass across the virus' outer membrane. M2 plays an important role in viral function (more on that below), and, not surprisingly, so do hemagglutinin and neuraminidase. Specifically, hemagglutinin allows the virus to attach to a cell in order to infect it, and after the virus has replicated within the cell, neuraminidase allows the daughter viruses to detach from that cell and infect other cells. For a more in depth description of these proteins, check out this post at Effect Measure.
Getting back to antiviral drugs, oseltamivir and zanamivir work by inhibiting neuraminidase (for details, once again check out the above post at Effect Measure or this more recent one). The adamantane-based drugs, however, target M2. In January 2008, two research groups independently published atomic-resolution structures of the M2 channel bound to an inhibitor. Using NMR, Jason Schnell (in James Chou's lab at Harvard) solved the structure of rimantadine bound to M2 (shown above with the drug in red). Alternatively, Amanda L. Stouffer (in William DeGrado's lab in Pennsylvania) used x-ray crystallography to solve the structure of amantadine bound to M2.
All academic medical centers, journals, professional societies, and other entities engaged in health research, education, clinical care, and development of practice guidelines should establish or strengthen conflict-of-interest policies, the report says. Disclosure by physicians and researchers not only to their employers but also to other medical organizations of their financial links to pharmaceutical, biotechnology, and medical device firms is an essential first step in identifying and managing conflicts of interest and needs to be improved. The committee noted substantial variations in institutions' conflict-of-interest policies and shortcomings in physicians' and researchers' adherence to policy requirements. The format for disclosure and categories of relationships should be standardized to help institutions judge the risk that a relationship poses and to ease the burden for individuals who must report information to multiple organizations with different policies.
In addition, Congress should require pharmaceutical, biotechnology, and device firms to report through a public Web site the payments they make to doctors, researchers, academic health centers, professional societies, patient advocacy groups, and others involved in medicine. A public record like this could serve as a deterrent to inappropriate relationships and undue industry influence. It also would provide medical institutions with a way to verify the accuracy of information that physicians, researchers, and senior officials have disclosed to them.
The report calls on researchers, medical school faculty, and private-practice doctors to forgo gifts of any amount from medical companies and to decline to publish or present material ghostwritten or otherwise controlled by industry. Consulting arrangements should be limited to legitimate expert services spelled out in formal contracts and paid for at a fair market rate. Physicians should limit their interactions with company sales representatives and use free drug samples only for patients who cannot afford medications. Several professional organizations and industry groups have set new limits on gift giving and other relationships between industry and the medical community, but it is too soon to gauge the effects these changes, the committee noted.
The Republican party today moved another step closer to becoming just the regional party of the South by losing one of its most respected members, Senator Arlen Specter (PA). Citing the Republicans' notable swing to the right in recent years, Specter announced earlier that he would be switching parties to join the Democrats. His switch will give the Democrats a filibuster-proof 60-vote supermajority in the Senate, assuming the courts uphold Al Franken's victory in the Minnesota Senate race.
Without a doubt, this is a positive development. Fears that the Democrats will have "too much power" are overblown, as Specter will certainly continue to be an independent voice in the Democratic Party as he was in the Republican Party. More importantly, since Obama's inauguration, the GOP has done little else besides engage in obstructionist tactics, while offering few if any solutions of their own. This move, then, should at the very least help make Congress more productive.
You can read Specter's full remarks here, but here's a taste:
Earlier today, President Barack Obama delivered a major speech on science policy to the National Academy of Sciences. Read more about it in my previous post. Now, though, Andy Revkin of Dot Earth is trying to annotate the speech with relevant background information. Go help him out by providing relevant information in the comments section of his blog post.
I already submitted a comment about Obama's reference to his March 9th memo on political interference in science:
Today, President Barack Obama addressed the annual meeting of the National Academy of Sciences (NAS), making him only the fourth president in modern times to do so (the other three were John F. Kennedy, Jimmy Carter, and George H.W. Bush). He touched on a variety of areas, but the major theme was a renewed commitment to science.
Specifically, Obama pledged that under his leadership, the US will devote more than three percent of GDP to research and development. In his words, this will be the "largest commitment to scientific research and innovation in American History," even exceeding the investment made during the space race.
Obama also reiterated his March 9th pledge to end political interference in science in the federal government, emphasizing that "our values as a nation are rooted in free inquiry.
Overall, it was a reasonably impressive speech that's worth listening to (in addition to there being a lot to like about it from the perspective of a scientist). So, if you missed it this morning, I'd encourage you to give it a listen when you have a chance. There was a live audio feed from NAS and an audio/video feed from The Washington Post during the event, but it looks like those are no longer available. However, I believe that NAS should be posting the video on its site shortly. I'll let you know as soon as I find out it's available (there or elsewhere). In the meantime, you can read the full text of his remarks at Political Intelligence. Update: The National Academies site now has an mp3 audio recording of the speech available, and The National Academies Press site has both audio and video.
Last week, scientists and their supporters at UCLA held the first rally of their new chapter of the pro-research organization Pro-Test. In addition to the various other accounts that have been published, Tom Holder of Speaking of Research has now published his own very comprehensive first-hand account of the event. Check it out. He has included quite a few photos as well, such as this one:
About a week ago, the NIH announced its draft guidelines covering the funding of human embryonic stem cell research. You can read the draft guidelines here and my post on the topic here. As these are draft guidelines, they are open to a month-long period of public comment before the final guidelines are released, and an online system for accepting comments has just been opened up. Comments must be received by 11:00 pm EST on May 26, 2009, and you can enter your comments here.
Earlier I published a post about an interesting article by Andrew Revkin in today's New York Times about industry's willful ignorance of global warming science. There was an interesting quote in there that I didn't mention earlier about how journalistic practices enabled this campaign of misinformation:
George Monbiot, a British environmental activist and writer, said that by promoting doubt, industry had taken advantage of news media norms requiring neutral coverage of issues, just as the tobacco industry once had.
The idea stated in the title of this blog post is not novel--far from it, in fact. We have known for a long time that the auto industry, the oil industry, and others with a vested interest have engaged in a long-running campaign of misinformation to discredit the science behind global warming. Manufacturing doubt is a common strategy employed by those whose agenda falls on the wrong side of scientific fact. This includes creationists, pseudoscientists, global warming denialists, HIV denialists, and, very notably, the tobacco industry's notorious decades-long campaign to deny the link between smoking and cancer, despite the deniers' own undeniable knowledge that such a link existed.
The reason I bring all of this up now, though, is that The New York Times has an article by Andrew Revkin about some particularly interesting documents recently acquired by the Times. The documents, from the Global Climate Coalition (an industry group), shed light on how the group suppressed its own scientists and demonstrate that the group was actively aware it was spreading misinformation:
By all accounts, yesterday's UCLA Pro-Test rally in support of animal research was a great success. Up to 800 people showed up for the Pro-Test rally, but only 30-40 people showed up for a concurrent anti-research rally
These numbers are particularly notable for two reasons. Firstly, the number of supporters of animal researchers greatly dwarfed the number of detractors, an excellent illustration of how large this hitherto silent majority is compared to the fringe but vocal animal rights activists. Secondly, the number of participants at the UCLA rally was similar to the number that showed up at Pro-Test's threeOxfordrallies. This is an auspicious start, given how successful Pro-Test eventually was at making a positive impact in Oxford.
Accounts of yesterday's rally abound, but the following are some of the most informative, all from people who, as far as I can tell, were actually at the event. Let's start with a video from CNN:
Reading these memos, it's very clear that there are quite a few CIA employees who are allegedly medical professionals. Those people need to find new professions. I would strongly suggest that you take a few minutes - particularly if you're a doctor or a psychologist - to suggest to your colleagues at the American Medical Association and the American Psychological Association that it might be good to take some formal steps along those lines.
This is related to another topic I've written about in pastposts: the complicity of medical professionals in the death penalty. In either case, people will argue that medical professionals should actually participate in these procedures to make sure they're carried out as humanely as possible. I can understand why people would put forth such an argument, but the fact of the matter is that neither the death penalty nor torture is a humane practice, even with the participation of medical practitioners.
In fact, the presence of these medical professionals does nothing but lend these horrible practices legitimacy. If medical professionals totally abstained from these practices, as the Hippocratic Oath compels them to, these practices would be much more difficult to carry out in the future.
Arguably the biggest news story of the week was the release by the Obama Administration of four Justice Department memos from 2002 and 2005 that were used to justify CIA torture of detainees. An analysis by Jeffrey Smith in today's Washington Post tries to explain the context and the mindset that led to the twisted logic found in these memos:
The four Justice Department memos to the CIA's top lawyer that were released last week reflect an effort by Bush administration appointees to create finely tuned justifications for harsh interrogation techniques, all under a blanket of secrecy covering the agency's prisons and the questioning.
In the wake of the memos' disclosure, it is clear that the lawyers and the CIA got it wrong in measuring the methods against their selected legal test: that they must not "shock the conscience." The brutality of the interrogation measures -- including repeatedly slamming people into walls, simulating their drowning and stuffing them into dark, constricting boxes -- shocked the conscience of at least some.
A month after the Obama Administration lifted Bush era restrictions on federal funding for human embryonic stem cell (hESC) research, the NIH has now announced its new draft guidelines for such research. The new guidelines will greatly expand the scope of federally-funded research by allowing funds to be used for work on stem cell lines derived from excess fertility clinic embryos.
However, federal funds will not be available for work on hESC lines derived from embryos that have been generated specifically for the purpose of stem cell work. This is a pretty severe limitation, actually, and the rules basically ensure that if a cell line was derived from an embryo that was not left over from a fertility clinic, work on that cell line can never be funded by federal dollars. Ever.
The Lay Scientist has a new guest post up from British physician "DeeTee" about measles, a horrible disease that until recently had been virtually eradicated from the developed world. Unfortunately, despite the fact that measles is totally preventable with proper vaccination, the misguided campaigning of anti-vaccination fanatics has caused measles to once again raise its ugly head in our own backyard, as DeeTee explains:
But last year all that changed. Where I work we saw dozens of cases of measles over the summer. It was odd having to dredge my memory banks to remember details of this "lost" disease, but at least with measles once one has seen cases and one knows the symptoms and signs these are not easily forgotten.
And what are these tell tale signs? DeeTee describes some of the dramatic cases (s)he saw when training in Africa:
The LA Times has an article today about the founder of the UCLA chapter of Pro-Test, David Jentsch, a neuroscientist whose car was torched last month by animal rights extremist. This point is particularly relevant:
"People always say: 'Don't respond. If you respond, that will give [the attackers] credibility,' " Jentsch, 37, said in a recent interview in his UCLA office. "But being silent wasn't making us feel safer. And it's a moot point if they are coming to burn your car anyway, whether you give them credibility or not."
Jentsch is right. The lesson of Pro-Test Oxford was that silence only encourages the extremists, and scientists have to stand up for their work in order for any real change to occur.
Just to put all of this in perspective, though, this is what the animal rights extremists have to say about the attack:
The gold standard for measuring the impact of a scientific paper is counting the number of other papers that cite that paper. However, due to the drawn-out nature of the scientific publication process, there is a lag of at least a year or so after a paper is published before citations to it even begin to appear in the literature, and at least a few years are generally needed to get an accurate measure of how heavily cited an article will actually be. It's reasonable to ask, then, if there exists a mechanism to judge the impact of a paper much earlier in its lifetime.
Several analyses now indicate that how frequently a paper is downloaded soon after publication predicts--to an extent--how highly it will be cited later on. The most recent analysis (Watson, 2009) compared download counts with citations for the Journal of Vision. There is a lot of extraneous, or at least uninteresting, information in this paper (i.e. that total number of citations correlate with total paper downloads over the lifetime of a paper and that both numbers increase year after year), but the key data is in Figure 6. This figure shows that the number of downloads per day over the first 1,000 days after publication correlates well with the number of citations per year five years down the line (r = 0.62).
As mentioned here previously, the stimulus package passed in February includes funds to encourage evidence-based medicine. Some uninformed critics will claim that this is some big government conspiracy to exert socialized control over private medicine. But, truly, encouraging a firmer empirical basis in all aspects of medicine--through more studies, government guidelines, and just improved common practice--is a very desirable outcome.
A post by David Newman at The New York Time's Well blog lays out a variety of examples of why this is so (with links to original studies!). Also, Hugh Pickens has a nice summary of this post at Slashdot. Newman lists a variety of clinical interventions that are commonly used, despite ample evidence indicating they're ineffective, or even harmful: early administration of beta-blockers, general use cough remedies, various applications of antibiotics, and certain surgeries. Check out his post for more.
Although people who know me can attest that I made countless assurances that I would never do such a thing, I have once again succumbed to the relentless force of progress, and I'm now on Twitter. Check me out. I'm actually finding it quite useful, and I'm currently using my feed to provide updates on new blog posts, to pass along interesting links I won't get around to blogging, to give other random thoughts, and to interact with my online network in general. I've put a widget on the sidebar of my blog, but if you're interested you can also follow my Twitter feed to stay up to date on all of these Scientific Activist-related happenings.
You see, this is why you want to fill your administration with smart, qualified, thoughtful, and innovative people--especially in the sciences. From The Times
A major investment in fighting tropical infections and chronic conditions like heart disease and diabetes in poor countries would transform international perceptions of the US, according to Harold Varmus, who co-chairs the President's Council of Advisers on Science and Technology.
In an exclusive interview with The Times, Dr Varmus said that American diplomacy had undervalued the role of medicine and science in fostering friendly relations with developing nations.
He is asking President Obama to endorse a plan from the US Institute of Medicine that would almost double annual US support for global health to $15 billion by 2012.
Dr Varmus is also advocating a "Global Science Corps" of scientists willing to spend at least a year working in a poor country, and a network of science attachÊs for every US embassy.
Today, George Will is back on the subject of global warming. The occassion for his column is the alleged uselessness of energy-efficient light bulbs. The column is basically a cut-and-paste job on a recent New York Times article on the bulbs-the same newspaper that Will claimed in an earlier column is "a trumpet that never sounds retreat in today's war against warming." Somehow, a paper Will knows is nothing but a climate propaganda machine can publish an article related to global warming that he relies on as absolute authority.
Through the results of widespread experimentation of the... well... let's say "non-scientific" variety, it's pretty well known that marijuana has the side effect of making the user very hungry. This is one of the many physiological effects of the active ingredient THC (Δ9-tetrahydrocannabinol). More relevantly, however, THC and other cannabinoids are actively being investigated for various useful clinical purposes, including the treatment of cancer through the inhibition of tumor growth.
A new study by Salazar et al. in The Journal of Clinical Investigation demonstrates that THC causes tumor cells to begin to degrade themselves from the inside (a process called autophagy, i.e. "self-eating"). Although autophagy has been shown to promote cell survival in some cases and cell death in others, the authors show that in this case it causes cancer cells to undergo programmed cell death (apoptosis). Thus, THC activates a series of events within cancer cells, inhibiting tumor growth.
In discussions lamenting modern day political interference in science and the less-than-prominent role science plays in formulating policy, bringing back the Congressional Office of Technology Assessment (OTA) is commonly offered as a key facet of any comprehensive solution. And, this is for good reason, as Gerald L. Epstein explains in a new article at Science Progress:
Over its history, OTA informed members of Congress and their staffs and helped shape legislation. But its reports played a far wider role. Since they explained complicated technical concepts to a non-technical audience, they were widely circulated, attracting considerable public attention. "The Office of Technology Assessment does some of the best writing on security-related technical issues in the United States," said the journal Foreign Affairs. OTA has "produced hundreds of policy-related reports, and has developed a reputation for objective, non-partisan, and comprehensive assessments of public policy issues with highly technical aspects," according to the American Association for the Advancement of Science. Critical review of OTA reports from both public and expert audiences amplified their message and validated their value and quality.
Following in the footsteps of the Pro-Test group in Oxford, UK, students and scientists at UCLA have pledged to stand up against the lies and misinformation of animal rights groups, and the violence of extremist organizations. They have formed the new group UCLA Pro-Test, which stands for science, reasoned debate and the belief that life-saving medical research must continue without violence and harassment from misguided activists.
On Wednesday, 22nd April 2009, at 11:30 we call for all students, scientists and members of the public to make their way to the UCLA campus and meet at the junction of Westwood Blvd and Le Conte Ave. Stand up for Science, Research and the Medicines of Tomorrow - Stand up and have your voice heard at the UCLA Pro-Test rally!!
This rally will coincide with an anti-research demonstration at UCLA planned during the World Week for Animals in Laboratories (Week of Mon April 20th).
UCLA Pro-Test was founded by David Jentsch, and he has been joined by a number of other scientists who have also been the victims of animal rights extremism in California. With the support of Speaking of Research, and Pro-Test UK, they aim to challenge this climate of fear that has descended upon researchers in California and beyond!
Will you play your part? Not only are we looking for the silent majority to find their voice and march with us, but also for a few motivated individuals to get involved and help us get the word out. Anyone interested should contact us at contact@speakingofresearch.com. We especially need students and scientists on campus to join us in advertising, publicizing and organizing the demonstration! Get involved in this once-in-a-lifetime movement.
Compact fluorescent lamps (CFLs), or "energy saving light bulbs", are much more energy efficient than conventional light bulbs, and they have a significantly longer lifetime. On top of that, replacing your conventional bulbs with CFLs won't just save energy, but will also save you money. Most importantly, this is one small action that we can all contribute to the fight against global warming.
However, yesterday's New York Times included an article by Leora Broydo Vestel entitled "Do New Bulbs Save Energy if They Don't Work", which hypes up concerns about compact fluorescent lamps (CFLs) not working properly:
An Oxford graduate student by day and a scientific activist by night, Nick Anthis isn't letting his Ph.D. research in protein structure get in the way of defending scientific and social progress.
The reason for the difference is that the adamantane drugs target different viral proteins from oseltamivir and zanamivir. The two major proteins on the surface of the influenza virus are hemagglutinin (the "H" in H1N1) and neuraminidase (the "N"). Due to the evolution of the influenza virus over time, these proteins come in a variety of different forms, and we label strains of flu by the specific class of hemagglutinin and neuraminidase the virus carries (H1N1, H3N2, etc.). These are the largest proteins on the surface of the virus, and they are the ones that our immune system generally reacts to. However, they aren't the only ones.
